diff --git a/.github/workflows/generate-schema.yml b/.github/workflows/generate-schema.yml index f1484db9..dac9ad03 100644 --- a/.github/workflows/generate-schema.yml +++ b/.github/workflows/generate-schema.yml @@ -1,13 +1,52 @@ -name: Java CI with Gradle +name: Build specifications, schemas and comparisions on: push: workflow_dispatch: jobs: + check: + runs-on: ubuntu-latest + outputs: + skip_job: ${{ steps.skip.outputs.skip_job }} + skip_commit: ${{ steps.check-tag.outputs.skip_commit }} + steps: + - name: Checkout code + uses: actions/checkout@v4 + - name: Check last commit message + id: commit-message + run: | + echo "COMMIT_MESSAGE=$(git log -1 --pretty=format:'%s')" >> "$GITHUB_ENV" + - id: skip + name: Skip if automated push + if: contains(env.COMMIT_MESSAGE, 'Apply automatic changes') + run: | + echo "Automated commit detected - skipping job" + echo "skip_job=true" >> "$GITHUB_OUTPUT" + - name: Check Branch with Regex + id: check-tag + run: | + regex="^refs/heads/brapi-V[0-9]+\.[0-9]+$" + if [[ "${{ github.ref }}" =~ $regex ]]; then + echo "skip_commit=false" >> "$GITHUB_OUTPUT" + echo "Release branch - WILL commit of generated files" + else + echo "skip_commit=true" >> "$GITHUB_OUTPUT" + echo "Normal branch - Will NOT commit of generated files" + fi generate: runs-on: ubuntu-latest + needs: check + if: needs.check.outputs.skip_job != 'true' steps: - - uses: actions/checkout@v4 + - name: debug + run: | + echo ${{ needs.check.outputs.skip_job }} + echo ${{ needs.check.outputs.skip_commit }} + - name: Checkout code + uses: actions/checkout@v4 + with: + fetch-depth: 0 + ssh-key: ${{ secrets.DEPLOY_KEY }} - name: Set up Docker Compose uses: docker/setup-compose-action@v1 - name: Build and run the Docker image @@ -36,4 +75,5 @@ jobs: - name: Compare OpenAPI working-directory: ./generator run: ./gradlew compareAll - - uses: stefanzweifel/git-auto-commit-action@v5 + - if: needs.check.outputs.skip_commit == 'false' + uses: stefanzweifel/git-auto-commit-action@v5 diff --git a/Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json b/Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json index ba5e5430..b4bab73e 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json @@ -2,11 +2,18 @@ "$defs": { "AdditionalInfo": { "additionalProperties": { - "type": "string" + "description": "A free space containing any additional information related to a particular object.", + "type": [ + "null", + "string" + ] }, "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "title": "AdditionalInfo", - "type": "object" + "type": [ + "null", + "object" + ] } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/AdditionalInfo.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json b/Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json index 124a69e9..428d6d5b 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json @@ -30,6 +30,7 @@ } }, "title": "OntologyTerm", + "description": "A pointer to an ontology used by a genomic reference", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json index 98a8264e..efa77ec3 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json @@ -12,7 +12,8 @@ "type": [ "null", "string" - ] + ], + "example": "Maize" }, "contextOfUse": { "description": "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])", @@ -22,14 +23,16 @@ "type": [ "null", "array" - ] + ], + "examples": ["Trial evaluation", "Nursery evaluation"] }, "defaultValue": { "description": "Variable default value. (examples: \"red\", \"2.3\", etc.)", "type": [ "null", "string" - ] + ], + "example": "2.0" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -37,7 +40,8 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org/documentation.html" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -57,21 +61,24 @@ "type": [ "null", "string" - ] + ], + "example": "flowering" }, "institution": { "description": "Name of institution submitting the variable", "type": [ "null", "string" - ] + ], + "example": "The BrAPI Institute" }, "language": { "description": "2 letter ISO 639-1 code for the language of submission of the variable.", "type": [ "null", "string" - ] + ], + "example": "en" }, "method": { "description": "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". ", @@ -93,14 +100,16 @@ "type": [ "null", "string" - ] + ], + "example": "Dr. Bob Robertson" }, "status": { "description": "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", "type": [ "null", "string" - ] + ], + "example": "recommended" }, "submissionTimestamp": { "description": "Timestamp when the Variable was added (ISO 8601)", @@ -118,7 +127,8 @@ "type": [ "null", "array" - ] + ], + "examples": ["Maize Height", "Stalk Height", "Corn Height"] }, "trait": { "description": "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". ", @@ -132,6 +142,7 @@ "scale" ], "title": "Variable", + "description": "A unique combination of Trait, Method, and Scale to define a clear context for an Observation.", "type": "object", "brapi-metadata": { "interface": true diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Contact.json b/Specification/BrAPI-Schema/BrAPI-Core/Contact.json index e72571cd..1b3e3f0d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Contact.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Contact.json @@ -47,6 +47,7 @@ ], "type": "object", "title": "Contact", + "description": "A persons contact information", "brapi-metadata": { "primaryModel": false } diff --git a/Specification/BrAPI-Schema/BrAPI-Core/DataLink.json b/Specification/BrAPI-Schema/BrAPI-Core/DataLink.json index d00aa686..f1cc349e 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/DataLink.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/DataLink.json @@ -1,6 +1,7 @@ { "$defs": { "DataLink": { + "description": "A link to a data file associated with a study. Extra data could include notes, images, and reference data. Based on the MIAPPE V1.1 (DM-38) Data file description.", "properties": { "dataFormat": { "description": "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", @@ -61,6 +62,7 @@ } }, "title": "DataLink", + "description": "A link to extra data files associated with this study. Extra data could include notes, images, and reference data.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Core/List.json b/Specification/BrAPI-Schema/BrAPI-Core/List.json index c37cc22d..fd4fda23 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/List.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/List.json @@ -16,7 +16,8 @@ "type": [ "null", "array" - ] + ], + "examples": ["758a78c0", "2c78f9ee"] }, "dateCreated": { "description": "Timestamp when the entity was first created", @@ -56,18 +57,21 @@ "type": [ "null", "string" - ] + ], + "example": "This is a list of germplasm I would like to investigate next season" }, "listName": { "description": "Human readable name of a List", - "type": "string" + "type": "string", + "example": "MyGermplasm_Sept_2020" }, "listOwnerName": { "description": "Human readable name of a List Owner. (usually a user or person)", "type": [ "null", "string" - ] + ], + "example": "Bob Robertson" }, "listOwnerPerson": { "$ref": "Person.json#/$defs/Person", @@ -80,14 +84,16 @@ "type": [ "null", "integer" - ] + ], + "example": 53 }, "listSource": { "description": "The description of where a List originated from", "type": [ "null", "string" - ] + ], + "example": "GeneBank Repository 1.3" }, "listType": { "description": "A flag to indicate the type of objects that are referenced in a List", @@ -101,8 +107,12 @@ ], "title": "List", "type": "object", + "description": "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study.", "brapi-metadata": { - "primaryModel": true + "primaryModel": true, + "subQuery": [ + "data" + ] } } }, diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Location.json b/Specification/BrAPI-Schema/BrAPI-Core/Location.json index bde16ec1..fcf03673 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Location.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Location.json @@ -7,7 +7,8 @@ "type": [ "null", "string" - ] + ], + "example": "L1" }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", @@ -19,14 +20,16 @@ "type": [ "null", "string" - ] + ], + "example": "North East corner of greenhouse" }, "coordinateUncertainty": { "description": "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", "type": [ "null", "string" - ] + ], + "example": "20" }, "coordinates": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", @@ -38,14 +41,16 @@ "type": [ "null", "string" - ] + ], + "example": "PER" }, "countryName": { "description": "The full name of the country where a Location is located\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.", "type": [ "null", "string" - ] + ], + "example": "Peru" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -53,21 +58,24 @@ "type": [ "null", "string" - ] + ], + "example": "https://brapi.org" }, "environmentType": { "description": "Describes the general type of environment of a Location. (ex. forest, field, nursery, etc)", "type": [ "null", "string" - ] + ], + "example": "Nursery" }, "exposure": { "description": "Describes the level of protection/exposure for things like sun light and wind at a particular Location", "type": [ "null", "string" - ] + ], + "example": "Structure, no exposure" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -87,29 +95,34 @@ "type": [ "null", "string" - ] + ], + "example": "71 Pilgrim Avenue Chevy Chase MD 20815" }, "instituteName": { "description": "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.", "type": [ "null", "string" - ] + ], + "example": "Plant Science Institute" }, "locationDbId": { "description": "The unique identifier for a Location", - "type": "string" + "type": "string", + "example": "3cfdd67d" }, "locationName": { "description": "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place.", - "type": "string" + "type": "string", + "example": "Location 1" }, "locationType": { "description": "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)", "type": [ "null", "string" - ] + ], + "example": "Field Station" }, "parentLocation": { "$ref": "Location.json#/$defs/Location", @@ -150,21 +163,24 @@ "type": [ "null", "string" - ] + ], + "example": "Private" }, "slope": { "description": "Describes the approximate slope (height/distance) of a Location.", "type": [ "null", "string" - ] + ], + "example": "0" }, "topography": { "description": "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)", "type": [ "null", "string" - ] + ], + "example": "Valley" }, "seedLots": { "title": "SeedLots", @@ -200,6 +216,7 @@ "locationName" ], "title": "Location", + "description": "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Person.json b/Specification/BrAPI-Schema/BrAPI-Core/Person.json index cbd8569d..f96aa03c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Person.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Person.json @@ -12,14 +12,16 @@ "type": [ "null", "string" - ] + ], + "example": "Bob likes pina coladas and getting caught in the rain." }, "emailAddress": { "description": "email address for this person", "type": [ "null", "string" - ] + ], + "example": "bob@bob.com" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -39,46 +41,53 @@ "type": [ "null", "string" - ] + ], + "example": "Bob" }, "lastName": { "description": "Persons last name", "type": [ "null", "string" - ] + ], + "example": "Robertson" }, "mailingAddress": { "description": "physical address of this person", "type": [ "null", "string" - ] + ], + "example": "123 Street Ave, City, State, Country" }, "middleName": { "description": "Persons middle name", "type": [ "null", "string" - ] + ], + "example": "Danger" }, "personDbId": { "description": "Unique ID for a person", - "type": "string" + "type": "string", + "example": "14340a54" }, "phoneNumber": { "description": "phone number of this person", "type": [ "null", "string" - ] + ], + "example": "+1-555-555-5555" }, "userID": { "description": "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", "type": [ "null", "string" - ] + ], + "example": "bob-23" }, "lists": { "title": "Lists", @@ -113,6 +122,7 @@ "personDbId" ], "title": "Person", + "description": "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Program.json b/Specification/BrAPI-Schema/BrAPI-Core/Program.json index de38f391..ab710c6c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Program.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Program.json @@ -7,7 +7,8 @@ "type": [ "null", "string" - ] + ], + "example": "P1" }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", @@ -19,7 +20,8 @@ "type": [ "null", "string" - ] + ], + "example": "Tomatillo" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -27,7 +29,8 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -47,7 +50,8 @@ "type": [ "null", "string" - ] + ], + "example": "EU: FP7-244374" }, "leadPerson": { "$ref": "Person.json#/$defs/Person", @@ -60,15 +64,18 @@ "type": [ "null", "string" - ] + ], + "example": "Make a better tomatillo" }, "programDbId": { "description": "The ID which uniquely identifies the program", - "type": "string" + "type": "string", + "example": "f60f15b2" }, "programName": { "description": "Human readable name of the program", - "type": "string" + "type": "string", + "example": "Tomatillo_Breeding_Program" }, "programType": { "description": "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", @@ -80,7 +87,8 @@ "type": [ "null", "string" - ] + ], + "example": "STANDARD" }, "trials": { "title": "Trials", @@ -172,6 +180,7 @@ "programName" ], "title": "Program", + "description": "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Season.json b/Specification/BrAPI-Schema/BrAPI-Core/Season.json index 6b2a7652..ecaf3959 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Season.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Season.json @@ -25,6 +25,7 @@ "seasonDbId" ], "title": "Season", + "description": "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\".", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index 68c83b51..00b6a664 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -7,7 +7,8 @@ "type": [ "null", "boolean" - ] + ], + "example": true }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", @@ -19,7 +20,8 @@ "type": [ "null", "string" - ] + ], + "example": "Grape" }, "contacts": { "description": "List of contact entities associated with this study", @@ -37,7 +39,8 @@ "type": [ "null", "string" - ] + ], + "example": "Irrigation was applied according needs during summer to prevent water stress." }, "dataLinks": { "description": "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data.", @@ -55,7 +58,8 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org" }, "endDate": { "description": "The date the study ends\n\nMIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended", @@ -68,10 +72,8 @@ "environmentParameters": { "description": "Environmental parameters that were kept constant throughout the study and did not change between observation units.\n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).", "relationshipType": "one-to-many", - "referencedAttribute": "study", "items": { - "$ref": "../BrAPI-Core/Study.json#/$defs/EnvironmentParameters", - "description": "EnvironmentParameters" + "$ref": "../BrAPI-Core/Study.json#/$defs/EnvironmentParameter" }, "title": "EnvironmentParameters", "type": [ @@ -115,7 +117,8 @@ "type": [ "null", "string" - ] + ], + "example": "MIT License" }, "location": { "$ref": "Location.json#/$defs/Location", @@ -134,6 +137,11 @@ "type": [ "null", "array" + ], + "examples": [ + {"levelName": "field", "levelOrder": 0}, + {"levelName": "block", "levelOrder": 1}, + {"levelName": "plot", "levelOrder": 2} ] }, "observationUnitsDescription": { @@ -141,7 +149,8 @@ "type": [ "null", "string" - ] + ], + "example": "Observation units consisted in individual plots themselves consisting of a row of 15 plants at a density of approximately six plants per square meter." }, "observationVariables": { "description": "The list of Observation Variables being used in this study. \n\nThis list is intended to be the wishlist of variables to collect in this study. It may or may not match the set of variables used in the collected observation records. ", @@ -160,7 +169,8 @@ "type": [ "null", "array" - ] + ], + "examples": ["Spring_2018"] }, "startDate": { "description": "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started", @@ -175,36 +185,42 @@ "type": [ "null", "string" - ] + ], + "example": "Grape_Yield_Spring_2018" }, "studyDbId": { "description": "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution.", - "type": "string" + "type": "string", + "example": "175ac75a" }, "studyDescription": { "description": "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study", "type": [ "null", "string" - ] + ], + "example": "This is a yield study for Spring 2018" }, "studyName": { "description": "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study", - "type": "string" + "type": "string", + "example": "INRA's Walnut Genetic Resources Observation at Kenya" }, "studyPUI": { "description": "A permanent unique identifier associated with this study data. For example, a URI or DOI", "type": [ "null", "string" - ] + ], + "example": "doi:10.155454/12349537312" }, "studyType": { "description": "The type of study being performed. ex. \"Yield Trial\", etc", "type": [ "null", "string" - ] + ], + "example": "Phenotyping" }, "trial": { "$ref": "Trial.json#/$defs/Trial", @@ -316,12 +332,17 @@ "studyDbId" ], "title": "Study", + "description": "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies.", "type": "object", "brapi-metadata": { - "primaryModel": true + "primaryModel": true, + "controlledVocabularyProperties": [ + "studyType" + ] } }, - "EnvironmentParameters": { + "EnvironmentParameter": { + "description": "An environmental parameter that was kept constant throughout the study and did not change between observation units.\n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables.", "properties": { "description": { "description": "Human-readable value of the environment parameter (defined above) constant within the experiment", @@ -382,7 +403,8 @@ "parameterName", "description" ], - "title": "EnvironmentParameters", + "title": "EnvironmentParameter", + "description": "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).", "type": "object", "brapi-metadata": { "primaryModel": false @@ -395,14 +417,16 @@ "type": [ "null", "string" - ] + ], + "example": "CO_715:0000145" }, "description": { "description": "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.", "type": [ "null", "string" - ] + ], + "example": "Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information." }, "study": { "description": "Experimental design associated with a study", @@ -412,6 +436,7 @@ } }, "title": "ExperimentalDesign", + "description": "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology", "type": "object", "brapi-metadata": { "primaryModel": false @@ -424,14 +449,16 @@ "type": [ "null", "string" - ] + ], + "example": "CO_715:0000162" }, "description": { "description": "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.", "type": [ "null", "string" - ] + ], + "example": "field environment condition, greenhouse" }, "study": { "description": "Growth facility associated with a study", @@ -441,6 +468,7 @@ } }, "title": "GrowthFacility", + "description": "Short description of the facility in which the study was carried out.", "type": "object", "brapi-metadata": { "primaryModel": false @@ -453,6 +481,7 @@ "type": "string" }, "timestamp": { + "description": "The timestamp of the update.", "format": "date-time", "type": [ "null", @@ -460,10 +489,12 @@ ] }, "version": { + "description": "The version of the update.", "type": [ "null", "string" - ] + ], + "example": "1.2.3" }, "study": { "description": "Last update associated with a study", @@ -476,6 +507,7 @@ "lastUpdateDbId" ], "title": "LastUpdate", + "description": "The date and time when this study was last modified", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json index d4cc0259..ee0e15de 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json @@ -7,7 +7,8 @@ "type": [ "null", "boolean" - ] + ], + "example": true }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", @@ -19,7 +20,8 @@ "type": [ "null", "string" - ] + ], + "example": "Wheat" }, "contacts": { "description": "List of contact entities associated with this trial", @@ -52,10 +54,12 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org" }, "endDate": { "description": "The date this trial ends", + "format": "date", "type": [ "null", "string" @@ -110,6 +114,7 @@ }, "startDate": { "description": "The date this trial started", + "format": "date", "type": [ "null", "string" @@ -117,25 +122,29 @@ }, "trialDbId": { "description": "The ID which uniquely identifies a trial\n\nMIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution.", - "type": "string" + "type": "string", + "example": "1883b402" }, "trialDescription": { "description": "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail.", "type": [ "null", "string" - ] + ], + "example": "General drought resistance trial initiated in Peru before duplication in Africa" }, "trialName": { "description": "The human readable name of a trial\n\nMIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation.", - "type": "string" + "type": "string", + "example": "Peru Yield Trial 1" }, "trialPUI": { "description": "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", "type": [ "null", "string" - ] + ], + "example": "https://doi.org/101093190" }, "plates": { "title": "plates", @@ -185,6 +194,7 @@ "trialDbId" ], "title": "Trial", + "description": "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing.", "type": "object", "brapi-metadata": { "primaryModel": true @@ -197,14 +207,16 @@ "type": [ "null", "string" - ] + ], + "example": "doi:10.15454/312953986E3" }, "license": { "description": "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended.", "type": [ "null", "string" - ] + ], + "example": "https://CreativeCommons.org/licenses/by/4.0" }, "publicReleaseDate": { "description": "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described.", @@ -228,6 +240,7 @@ } }, "title": "DatasetAuthorships", + "description": "License and citation information for the data in this trial", "type": "object", "brapi-metadata": { "primaryModel": false @@ -236,16 +249,20 @@ "Publication": { "properties": { "publicationPUI": { + "description": "The permanent unique identifier of the publication.", "type": [ "null", "string" - ] + ], + "example": "doi:10.15454/312953986E3" }, "publicationReference": { + "description": "The publication reference.", "type": [ "null", "string" - ] + ], + "example": "Selby, BrAPI - An application programming interface for plant breeding applications, Bioinformatics, https://doi.org/10.1093/bioinformatics/190" }, "trial": { "description": "Publications associated with a trial", @@ -255,6 +272,7 @@ } }, "title": "Publication", + "description": "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json index fe22bfef..87ed0582 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json @@ -91,6 +91,7 @@ "variantSets" ], "title": "AlleleMatrix", + "description": "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier.", "type": "object", "brapi-metadata": { "primaryModel": true @@ -149,6 +150,7 @@ } }, "title": "DataMatrix", + "description": "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.", "type": "object", "brapi-metadata": { "primaryModel": false @@ -204,6 +206,7 @@ } }, "title": "Pagination", + "description": "Pagination info for the matrix", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json index fdb5002a..f86bcf47 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json @@ -60,12 +60,14 @@ "variantSet" ], "title": "Call", + "description": "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345.", "type": "object", "brapi-metadata": { "primaryModel": true } }, "GenotypeMetadata": { + "description": "An additional layer of metadata associated with a genotype", "properties": { "dataType": { "description": "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", @@ -110,6 +112,7 @@ } }, "title": "GenotypeMetadata", + "description": "Genotype Metadata are additional layers of metadata associated with each genotype.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json index f8010ebd..d6096f23 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json @@ -101,6 +101,7 @@ "callSetDbId" ], "title": "CallSet", + "description": "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json index a872b1fc..9228deee 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json @@ -108,6 +108,7 @@ "type" ], "title": "GenomeMap", + "description": "The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json index 3c622984..7315cd7c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json @@ -35,6 +35,7 @@ } }, "title": "MarkerPosition", + "description": "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json index 4ac45e48..76ed1fd9 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json @@ -25,11 +25,13 @@ "type": [ "null", "string" - ] + ], + "example": "11223344" }, "plateDbId": { "description": "The ID which uniquely identifies a `Plate`", - "type": "string" + "type": "string", + "example": "a106467f" }, "plateFormat": { "description": "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", @@ -45,7 +47,8 @@ }, "plateName": { "description": "A human readable name for a `Plate`", - "type": "string" + "type": "string", + "example": "Plate_123_XYZ" }, "program": { "$ref": "../BrAPI-Core/Program.json#/$defs/Program", @@ -65,7 +68,8 @@ "type": [ "null", "string" - ] + ], + "example": "TISSUE" }, "study": { "$ref": "../BrAPI-Core/Study.json#/$defs/Study", @@ -98,6 +102,7 @@ "plateName" ], "title": "Plate", + "description": "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json index 912dce94..4ab5c409 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json @@ -126,6 +126,7 @@ "referenceName" ], "title": "Reference", + "description": "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json index 8cede9b8..16650470 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json @@ -141,6 +141,7 @@ "referenceSetName" ], "title": "ReferenceSet", + "description": "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json index fcd9b09e..c99bec74 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json @@ -28,7 +28,8 @@ "type": [ "null", "integer" - ] + ], + "example": 6 }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -72,46 +73,50 @@ "type": [ "null", "string" - ] + ], + "example": "B" }, "sampleBarcode": { "description": "A unique identifier physically attached to the `Sample`", "type": [ "null", "string" - ] + ], + "example": "3a027b59" }, "sampleDescription": { "description": "Description of a `Sample`\n
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing.", "type": [ "null", "string" - ] + ], + "example": "This sample was taken from the root of a tree" }, "sampleDbId": { "description": "The ID which uniquely identifies a `Sample`\n
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample.", - "type": [ - "null", - "string" - ] + "type": "string", + "example": "cd06a61d" }, "sampleGroupId": { "description": "The ID which uniquely identifies a group of `Samples`", "type": [ "null", "string" - ] + ], + "example": "8524b436" }, "sampleName": { "description": "The human readable name of the `Sample`", - "type": "string" + "type": "string", + "example": "Sample_alpha_20191022" }, "samplePUI": { "description": "A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc)\n
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. ", "type": [ "null", "string" - ] + ], + "example": "doi:10.15454/312953986E3" }, "sampleTimestamp": { "description": "The date and time a `Sample` was collected from the field\n
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested", @@ -126,7 +131,8 @@ "type": [ "null", "string" - ] + ], + "example": "Tissue" }, "study": { "$ref": "../BrAPI-Core/Study.json#/$defs/Study", @@ -139,14 +145,16 @@ "type": [ "null", "string" - ] + ], + "example": "Bob" }, "tissueType": { "description": "The type of tissue sampled. ex. 'Leaf', 'Root', etc.\n
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology).", "type": [ "null", "string" - ] + ], + "example": "Root" }, "trial": { "$ref": "../BrAPI-Core/Trial.json#/$defs/Trial", @@ -159,13 +167,15 @@ "type": [ "null", "string" - ] + ], + "example": "B6" } }, "required": [ "sampleName" ], "title": "Sample", + "description": "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc).", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json index 8cc89e95..8c064d57 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json @@ -204,6 +204,7 @@ "variantDbId" ], "title": "Variant", + "description": "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index 7947a929..5c454ede 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -156,6 +156,7 @@ "variantSetDbId" ], "title": "VariantSet", + "description": "A VariantSet is a collection of variants and variant calls intended to be analyzed together.", "type": "object", "brapi-metadata": { "primaryModel": true @@ -228,6 +229,7 @@ "analysisDbId" ], "title": "Analysis", + "description": "An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used.", "type": "object", "brapi-metadata": { "primaryModel": false @@ -309,6 +311,7 @@ } }, "title": "AvailableFormat", + "description": "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other.", "type": "object", "brapi-metadata": { "primaryModel": false @@ -352,6 +355,7 @@ } }, "title": "MetadataField", + "description": "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard ", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json index b87ed137..9776f7d3 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json @@ -63,6 +63,7 @@ "description" ], "title": "Breeding Method", + "description": "The techniques and protocol used to produce a Cross or Germplasm", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index 22f350df..7753abbc 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -23,14 +23,16 @@ }, "crossDbId": { "description": "the unique identifier for a cross", - "type": "string" + "type": "string", + "example": "d105fd6f" }, "crossName": { "description": "the human readable name for a cross", "type": [ "null", "string" - ] + ], + "example": "my_Crosses_2018_01" }, "crossType": { "description": "the type of cross", @@ -65,12 +67,12 @@ }, "plannedCross": { "$ref": "PlannedCross.json#/$defs/PlannedCross", - "description": "the unique identifier for a planned cross", + "description": "The Cross that was used in the planning of this one.", "referencedAttribute": "crosses", "relationshipType": "many-to-one" }, "pollinationEvents": { - "description": "The list of pollination events that occurred for this cross", + "description": "The list of pollination events that occurred for this cross.", "relationshipType": "one-to-many", "referencedAttribute": "cross", "items": { @@ -102,6 +104,7 @@ "crossDbId" ], "title": "Cross", + "description": "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present.", "type": "object", "brapi-metadata": { "primaryModel": true @@ -131,6 +134,7 @@ } }, "title": "CrossAttribute", + "description": "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'", "type": "object", "brapi-metadata": { "primaryModel": false @@ -161,13 +165,14 @@ ] }, "cross": { - "description": "Pollination events associated with a cross", + "description": "The Cross associated with this Pollination Event", "$ref": "../BrAPI-Germplasm/Cross.json#/$defs/Cross", "relationshipType": "many-to-one", "referencedAttribute": "pollinationEvents" } }, "title": "PollinationEvent", + "description": "A Pollination Event that was used or attempted for a Cross.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json index bbc383a4..fc638818 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json @@ -26,6 +26,7 @@ } }, "title": "CrossParent", + "description": "The identifying information gor the parent material of a cross.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json index a971b749..0d359de9 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json @@ -11,7 +11,8 @@ "BULK_OPEN_POLLINATED", "DOUBLE_HAPLOID" ], - "type": "string" + "type": "string", + "example": "BIPARENTAL" } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json index b3ee17b9..01af5245 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json @@ -12,7 +12,8 @@ "type": [ "null", "string" - ] + ], + "example": "Cassava" }, "crossingProjectDbId": { "description": "The unique identifier for a crossing project", @@ -23,11 +24,13 @@ "type": [ "null", "string" - ] + ], + "example": "Crosses between germplasm X and germplasm Y in male nursery study X_2018 and female nursery study Y_2018" }, "crossingProjectName": { "description": "The human readable name for a crossing project", - "type": "string" + "type": "string", + "example": "Crosses_2018" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -106,6 +109,7 @@ "crossingProjectName" ], "title": "CrossingProject", + "description": "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index dc80ae08..828b7e86 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -7,7 +7,8 @@ "type": [ "null", "string" - ] + ], + "example": "A0000003" }, "acquisitionDate": { "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", @@ -50,14 +51,16 @@ "type": [ "null", "string" - ] + ], + "example": "420" }, "biologicalStatusOfAccessionDescription": { "description": "Supplemental text description for 'biologicalStatusOfAccessionCode'", "type": [ "null", "string" - ] + ], + "example": "Genetic stock" }, "breedingMethod": { "$ref": "BreedingMethod.json#/$defs/BreedingMethod", @@ -70,25 +73,29 @@ "type": [ "null", "string" - ] + ], + "example": "Rice Diversity Panel 1 (RDP1)" }, "commonCropName": { "description": "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\".", - "type": "string" + "type": "string", + "example": "Maize" }, "countryOfOriginCode": { "description": "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", "type": [ "null", "string" - ] + ], + "example": "BES" }, "defaultDisplayName": { "description": "Human readable name used for display purposes", "type": [ "null", "string" - ] + ], + "example": "A0000003" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -96,7 +103,8 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org" }, "donors": { "description": "List of donor institutes", @@ -130,15 +138,18 @@ "type": [ "null", "string" - ] + ], + "example": "Aspergillus" }, "germplasmDbId": { - "description": "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", - "type": "string" + "description": "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", + "type": "string", + "example": "d4076594" }, "germplasmName": { "description": "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space.", - "type": "string" + "type": "string", + "example": "A0000003" }, "germplasmOrigin": { "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", @@ -155,64 +166,73 @@ ] }, "germplasmPUI": { - "description": "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", - "type": "string" + "description": "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", + "type": "string", + "example": "http://pui.per/accession/A0000003" }, "germplasmPreprocessing": { "description": "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary.", "type": [ "null", "string" - ] + ], + "example": "EO:0007210; transplanted from study 2351 observation unit ID: pot:894" }, "instituteCode": { "description": "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", "type": [ "null", "string" - ] + ], + "example": "PER001" }, "instituteName": { "description": "The name of the institute that maintains the material", "type": [ "null", "string" - ] + ], + "example": "The BrAPI Institute" }, "pedigree": { "description": "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", "type": [ "null", "string" - ] + ], + "example": "A0000001/A0000002" }, "seedSource": { "description": "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available.", "type": [ "null", "string" - ] + ], + "example": "INRA:095115_inra" }, "seedSourceDescription": { "description": "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source", "type": [ "null", "string" - ] + ], + "example": "Branches were collected from a 10-year-old tree growing in a progeny trial established in a loamy brown earth soil." }, "species": { "description": "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.", "type": [ "null", "string" - ] + ], + "example": "fructus" }, "speciesAuthority": { "description": "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", "type": [ "null", "string" - ] + ], + "example": "Smith, 1822" }, "storageTypes": { "description": "The type of storage this germplasm is kept in at a genebank.", @@ -233,19 +253,20 @@ "type": [ "null", "string" - ] + ], + "example": "Aspergillus fructus A" }, "subtaxaAuthority": { "description": "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", "type": [ "null", "string" - ] + ], + "example": "Smith, 1822" }, "synonyms": { "description": "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon.", "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", "items": { "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Synonym", "description": "Synonyms" @@ -264,7 +285,6 @@ "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/TaxonId", "description": "TaxonIds" }, - "title": "TaxonIds", "type": [ "null", "array" @@ -385,6 +405,7 @@ "commonCropName" ], "title": "Germplasm", + "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.", "type": "object", "brapi-metadata": { "primaryModel": true @@ -407,13 +428,14 @@ ] }, "germplasm": { - "description": "donoers associated with a germplasm", + "description": "donors associated with a germplasm", "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", "relationshipType": "many-to-one", "referencedAttribute": "donors" } }, "title": "Donor", + "description": "Identifier assigned to an accession by the material donor.", "type": "object", "brapi-metadata": { "primaryModel": false @@ -450,6 +472,7 @@ } }, "title": "GermplasmOrigin", + "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", "type": "object", "brapi-metadata": { "primaryModel": false @@ -492,12 +515,14 @@ } }, "title": "StorageType", + "description": "The type of storage this germplasm is kept in at a genebank.", "type": "object", "brapi-metadata": { "primaryModel": false } }, "Synonym": { + "description": "Alternative way to refer to a Germplasm, Cultivar of Variety", "properties": { "synonym": { "description": "Alternative name or ID used to reference this germplasm", @@ -521,12 +546,14 @@ } }, "title": "Synonym", + "description": "Alternative names or IDs used to reference this germplasm", "type": "object", "brapi-metadata": { "primaryModel": false } }, "TaxonId": { + "description": "The Taxon of the Germplasm", "properties": { "taxonId": { "description": "The identifier (name, ID, URI) of a particular taxonomy within the source provider", @@ -548,6 +575,7 @@ "taxonId" ], "title": "TaxonId", + "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json index fb37543c..4a561657 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json @@ -26,6 +26,7 @@ } ], "title": "GermplasmAttribute", + "description": "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit", "brapi-metadata": { "primaryModel": true } diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json index 1aa344fb..9d0e75de 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json @@ -49,13 +49,15 @@ "type": [ "null", "string" - ] + ], + "example": "Present" } }, "required": [ "attribute" ], "title": "GermplasmAttributeValue", + "description": "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json index 15f2d26c..7f41b3fe 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json @@ -118,6 +118,7 @@ "germplasm" ], "title": "PedigreeNode", + "description": "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances.", "type": "object", "brapi-metadata": { "primaryModel": true @@ -147,6 +148,7 @@ "parentType" ], "title": "GermplasmParent", + "description": "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes.", "type": "object", "brapi-metadata": { "primaryModel": false @@ -176,6 +178,7 @@ "parentType" ], "title": "GermplasmChild", + "description": "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json index 57d26cde..72c5a418 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json @@ -9,7 +9,8 @@ }, "crossType": { "description": "the type of cross", - "$ref": "CrossType.json#/$defs/CrossType" + "$ref": "CrossType.json#/$defs/CrossType", + "example": "BIPARENTAL" }, "crossingProject": { "$ref": "CrossingProject.json#/$defs/CrossingProject", @@ -47,7 +48,8 @@ "type": [ "null", "string" - ] + ], + "example": "my_Crosses_2018_01" }, "status": { "description": "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", @@ -61,7 +63,8 @@ "null", "string" ], - "title": "PlannedCrossStatus" + "title": "PlannedCrossStatus", + "example": "TODO" }, "crosses": { "title": "crosses", @@ -82,6 +85,7 @@ "plannedCrossDbId" ], "title": "PlannedCross", + "description": "Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json index 0ab0c67f..586657ee 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json @@ -12,7 +12,8 @@ "type": [ "null", "number" - ] + ], + "example": 561 }, "contentMixture": { "description": "The mixture of germplasm present in the seed lot.\n
\nIf this seed lot only contains a single germplasm, the response should contain the name \nand DbId of that germplasm with a mixturePercentage value of 100\n
\nIf the seed lot contains a mixture of different germplasm, the response should contain \nthe name and DbId every germplasm present. The mixturePercentage field should contain \nthe ratio of each germplasm in the total mixture. All of the mixturePercentage values \nin this array should sum to equal 100.", @@ -71,39 +72,45 @@ }, "seedLotDbId": { "description": "Unique DbId for the Seed Lot", - "type": "string" + "type": "string", + "example": "261ecb09" }, "seedLotDescription": { "description": "A general description of this Seed Lot", "type": [ "null", "string" - ] + ], + "example": "This is a description of a seed lot" }, "seedLotName": { "description": "A human readable name for this Seed Lot", - "type": "string" + "type": "string", + "example": "Seed Lot Alpha" }, "sourceCollection": { "description": "The description of the source where this material was originally collected (wild, nursery, etc)", "type": [ "null", "string" - ] + ], + "example": "nursery" }, "storageLocation": { "description": "Description the storage location", "type": [ "null", "string" - ] + ], + "example": "The storage location is an massive, underground, bunker." }, "units": { "description": "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)", "type": [ "null", "string" - ] + ], + "example": "seeds" }, "fromSeedLotTransactions": { "title": "fromSeedLotTransactions", @@ -153,6 +160,7 @@ "seedLotName" ], "title": "SeedLot", + "description": "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program.", "type": "object", "brapi-metadata": { "primaryModel": true @@ -185,6 +193,7 @@ } }, "title": "ContentMixture", + "description": "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json index 8e7ac8a6..c3669fb1 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json @@ -12,7 +12,8 @@ "type": [ "null", "number" - ] + ], + "example": 45 }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -48,7 +49,8 @@ "type": [ "null", "string" - ] + ], + "example": "f9cd88d2" }, "transactionTimestamp": { "description": "The time stamp for when the transaction occurred", @@ -63,13 +65,15 @@ "type": [ "null", "string" - ] + ], + "example": "seeds" } }, "required": [ "transactionDbId" ], "title": "SeedLotTransaction", + "description": "The record of an event where material was moved in or out of a particular SeedLot", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json index 2b840ee4..1f61935f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json @@ -81,6 +81,7 @@ "eventType" ], "title": "Event", + "description": "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other", "type": "object", "brapi-metadata": { "primaryModel": true @@ -123,6 +124,7 @@ } }, "title": "EventDateRange", + "description": "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)", "type": "object", "brapi-metadata": { "primaryModel": false @@ -190,6 +192,7 @@ } }, "title": "EventParameter", + "description": "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event.", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index 93e43b5b..212ba910 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -4,22 +4,23 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" }, "copyright": { "description": "The copyright information of this image. Example 'Copyright 2018 Bob Robertson'", "type": [ "null", "string" - ] + ], + "example": "Copyright 2018 Bob Robertson" }, "description": { "description": "The human readable description of an image.", "type": [ "null", "string" - ] + ], + "example": "This is a picture of a tomato" }, "descriptiveOntologyTerms": { "description": "A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", @@ -29,7 +30,8 @@ "type": [ "null", "array" - ] + ], + "examples": ["doi:10.1002/0470841559", "Red", "ncbi:0300294"] }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -53,21 +55,24 @@ "type": [ "null", "string" - ] + ], + "example": "image_0000231.jpg" }, "imageFileSize": { "description": "The size of the image in Bytes.", "type": [ "null", "integer" - ] + ], + "example": 50000 }, "imageHeight": { "description": "The height of the image in Pixels.", "type": [ "null", "integer" - ] + ], + "example": 550 }, "imageLocation": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", @@ -80,7 +85,8 @@ "type": [ "null", "string" - ] + ], + "example": "Tomato Image 1" }, "imageTimeStamp": { "description": "The date and time the image was taken", @@ -95,14 +101,16 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org/images/tomato" }, "imageWidth": { "description": "The width of the image in Pixels.", "type": [ "null", "integer" - ] + ], + "example": 700 }, "mimeType": { "description": "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc", @@ -110,7 +118,8 @@ "type": [ "null", "string" - ] + ], + "example": "image/jpeg" }, "observationUnit": { "$ref": "ObservationUnit.json#/$defs/ObservationUnit", @@ -132,6 +141,7 @@ "imageDbId" ], "title": "Image", + "description": "The metadata for an image file that is connected to some phenotypic observation data.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json index 5aaae643..6f80c1a1 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json @@ -12,14 +12,16 @@ "type": [ "null", "string" - ] + ], + "example": "Smith, 1893, Really Cool Paper, Popular Journal" }, "description": { "description": "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)", "type": [ "null", "string" - ] + ], + "example": "A measuring tape was used" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -39,14 +41,16 @@ "type": [ "null", "string" - ] + ], + "example": "a^2 + b^2 = c^2" }, "methodClass": { "description": "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)", "type": [ "null", "string" - ] + ], + "example": "Measurement" }, "methodDbId": { "description": "Method unique identifier", @@ -57,14 +61,16 @@ }, "methodName": { "description": "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", - "type": "string" + "type": "string", + "example": "Measuring Tape" }, "methodPUI": { "description": "The Permanent Unique Identifier of a Method, usually in the form of a URI", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/CO_123:0000212" }, "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", @@ -73,9 +79,11 @@ } }, "required": [ + "methodDbId", "methodName" ], "title": "Method", + "description": "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". ", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json index 113d8d86..0eecbeaf 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json @@ -12,7 +12,8 @@ "type": [ "null", "string" - ] + ], + "example": "917d3ae0" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -41,7 +42,8 @@ }, "observationDbId": { "description": "The ID which uniquely identifies an observation", - "type": "string" + "type": "string", + "example": "ef24b615" }, "observationTimeStamp": { "description": "The date and time when this observation was made", @@ -64,6 +66,7 @@ "relationshipType": "many-to-one" }, "season": { + "description": "The season for this Observation", "$ref": "../BrAPI-Core/Season.json#/$defs/Season", "relationshipType": "many-to-one" }, @@ -78,14 +81,16 @@ "type": [ "null", "string" - ] + ], + "example": "a2f7f60b" }, "value": { "description": "The value of the data collected as an observation", "type": [ "null", "string" - ] + ], + "example": "2.3" }, "images": { "title": "images", @@ -106,6 +111,7 @@ "observationDbId" ], "title": "Observation", + "description": "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit.", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json index 9a7247b0..d3cda181 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -40,21 +40,24 @@ }, "observationUnitDbId": { "description": "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. ", - "type": "string" + "type": "string", + "example": "8c67503c" }, "observationUnitName": { "description": "A human readable name for an observation unit", "type": [ "null", "string" - ] + ], + "example": "Plot 1" }, "observationUnitPUI": { "description": "A Permanent Unique Identifier for an observation unit\n\nMIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible.", "type": [ "null", "string" - ] + ], + "example": "http://pui.per/plot/1a9afc14" }, "observationUnitPosition": { "description": "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section.", @@ -93,7 +96,7 @@ "relationshipType": "one-to-many", "referencedAttribute": "observationUnit", "items": { - "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/Treatment", + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationTreatment", "description": "Treatments" }, "title": "Treatments", @@ -169,6 +172,7 @@ "observationUnitDbId" ], "title": "ObservationUnit", + "description": "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples.", "type": "object", "brapi-metadata": { "primaryModel": true @@ -227,22 +231,8 @@ ] }, "positionCoordinateXType": { - "description": "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", - "enum": [ - "LONGITUDE", - "LATITUDE", - "PLANTED_ROW", - "PLANTED_INDIVIDUAL", - "GRID_ROW", - "GRID_COL", - "MEASURED_ROW", - "MEASURED_COL", - null - ], - "type": [ - "null", - "string" - ] + "description": "The type of positional coordinate used for the X coordinate of the position.", + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/PositionCoordinateType" }, "positionCoordinateY": { "description": "The Y position coordinate for an observation unit. Different systems may use different coordinate systems.", @@ -252,22 +242,8 @@ ] }, "positionCoordinateYType": { - "description": "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", - "enum": [ - "LONGITUDE", - "LATITUDE", - "PLANTED_ROW", - "PLANTED_INDIVIDUAL", - "GRID_ROW", - "GRID_COL", - "MEASURED_ROW", - "MEASURED_COL", - null - ], - "type": [ - "null", - "string" - ] + "description": "The type of positional coordinate used for the Y coordinate of the position.", + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/PositionCoordinateType" }, "observationUnit": { "description": "associated observation Unit", @@ -277,26 +253,30 @@ } }, "title": "ObservationUnitPosition", + "description": "All positional and layout information related to this Observation Unit", "type": "object", "brapi-metadata": { "primaryModel": false } }, - "Treatment": { + "ObservationTreatment": { + "description": "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor.", "properties": { "factor": { "description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.", "type": [ "null", "string" - ] + ], + "examples": ["test-factor:dia2020-2-nv.fertilizer"] }, "modality": { "description": "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ", "type": [ "null", "string" - ] + ], + "examples": ["test-factor:dia2020-2-nv.lf"] }, "observationUnit": { "description": "associated observation Unit", @@ -305,13 +285,31 @@ "referencedAttribute": "treatments" } }, - "title": "Treatment", + "title": "ObservationTreatment", "type": "object", "brapi-metadata": { "primaryModel": false } + }, + "PositionCoordinateType": { + "description": "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum": [ + "LONGITUDE", + "LATITUDE", + "PLANTED_ROW", + "PLANTED_INDIVIDUAL", + "GRID_ROW", + "GRID_COL", + "MEASURED_ROW", + "MEASURED_COL", + null + ], + "type": [ + "null", + "string" + ] } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} \ No newline at end of file diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json index 8f636d4e..69387d59 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json @@ -7,21 +7,26 @@ }, { "type": "object", + "title": "ObservationVariable", + "description": "A unique combination of Trait, Method, and Scale to define a clear context for an Observation.", "properties": { "observationVariableDbId": { "description": "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation.", - "type": "string" + "type": "string", + "example": "b9b7edd1" }, "observationVariableName": { "description": "Variable name (usually a short name)\n\nMIAPPE V1.1 (DM-84) Variable name - Name of the variable.", - "type": "string" + "type": "string", + "example": "Variable Name" }, "observationVariablePUI": { "description": "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/CO_123:0009012" }, "studies": { "title": "Studies", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json index 01e6a8f2..10e6af16 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json @@ -12,21 +12,24 @@ "type": [ "null", "string" - ] + ], + "example": "Bob Robertson, Rob Robertson" }, "copyright": { "description": "Ontology copyright", "type": [ "null", "string" - ] + ], + "example": "Copyright 1987, Bob Robertson" }, "description": { "description": "Human readable description of Ontology", "type": [ "null", "string" - ] + ], + "example": "This is an example ontology that does not exist" }, "documentationURL": { "description": "A URL to the human readable documentation of an object", @@ -34,14 +37,16 @@ "type": [ "null", "string" - ] + ], + "example": "https://wiki.brapi.org/ontology" }, "licence": { "description": "Ontology licence", "type": [ "null", "string" - ] + ], + "example": "MIT Open source licence" }, "ontologyDbId": { "description": "Ontology database unique identifier", @@ -49,14 +54,16 @@ }, "ontologyName": { "description": "Ontology name", - "type": "string" + "type": "string", + "example": "The Official Ontology" }, "version": { "description": "Ontology version (no specific format)", "type": [ "null", "string" - ] + ], + "example": "V1.3.2" } }, "required": [ @@ -64,6 +71,7 @@ "ontologyDbId" ], "title": "Ontology", + "description": "The identifier and metadata needed to reference an external controlled vocabulary", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/OntologyReference.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/OntologyReference.json index a2050bca..b39ee406 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/OntologyReference.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/OntologyReference.json @@ -40,6 +40,7 @@ "ontology" ], "title": "OntologyReference", + "description": "MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", "type": "object", "brapi-metadata": { "primaryModel": false @@ -48,6 +49,7 @@ "DocumentationLink": { "properties": { "URL": { + "description": "The URL or URI to the documentation", "format": "uri", "type": [ "null", @@ -55,6 +57,8 @@ ] }, "type": { + "description": "The type of documentation, which can be OBO Foundry, an RDF term or a webpage.", + "title": "DocumentationLinkType", "enum": [ "OBO", "RDF", @@ -74,6 +78,7 @@ } }, "title": "DocumentationLink", + "description": "Links to various ontology documentation", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json index 436304b0..ce5a8691 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json @@ -29,7 +29,8 @@ "type": [ "null", "integer" - ] + ], + "example": 2 }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -55,21 +56,24 @@ }, "scaleName": { "description": "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", - "type": "string" + "type": "string", + "example": "Meters" }, "scalePUI": { "description": "The Permanent Unique Identifier of a Scale, usually in the form of a URI", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/CO_123:0000112" }, "units": { "description": "This field can be used to describe the units used for this scale. This should be the abbreviated \nform of the units, intended to be displayed with every value using this scale. Usually this only \napplies when `dataType` is Numeric, but could also be included for other dataTypes when applicable.", "type": [ "null", "string" - ] + ], + "example": "m" }, "validValues": { "relationshipType": "one-to-one", @@ -87,12 +91,14 @@ "scaleName" ], "title": "Scale", + "description": "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\".", "type": "object", "brapi-metadata": { "primaryModel": true } }, "ValidValues": { + "description": "Defines the valid values for a Scale, which can be restricted to a list of categorical values, or a minimum and/or a maximum value.", "properties": { "categories": { "description": "List of possible values with optional labels", @@ -113,14 +119,16 @@ "type": [ "null", "string" - ] + ], + "example": "9999" }, "minimumValue": { "description": "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC.", "type": [ "null", "string" - ] + ], + "example": "2" }, "scale": { "description": "associated scale", @@ -130,12 +138,14 @@ } }, "title": "ValidValues", + "description": "Metadata describing the acceptable values for this Scale", "type": "object", "brapi-metadata": { "primaryModel": false } }, "ValidValuesCategory": { + "description": "A categorical value for a Scale.", "properties": { "label": { "description": "A text label for a category", @@ -159,6 +169,7 @@ } }, "title": "ValidValuesCategory", + "description": "If the Scale is a categorical type, these objects define the valid options", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json index bf996d19..0a4e9ed6 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json @@ -15,35 +15,40 @@ "type": [ "null", "array" - ] + ], + "examples": ["H", "PH", "H1"] }, "attribute": { "description": "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", "type": [ "null", "string" - ] + ], + "example": "height" }, "attributePUI": { "description": "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/PO:00012345" }, "entity": { "description": "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", "type": [ "null", "string" - ] + ], + "example": "Stalk" }, "entityPUI": { "description": "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/PATO:00098765" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -63,7 +68,8 @@ "type": [ "null", "string" - ] + ], + "example": "PH" }, "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", @@ -75,7 +81,8 @@ "type": [ "null", "string" - ] + ], + "example": "recommended" }, "synonyms": { "description": "Other trait names", @@ -85,14 +92,16 @@ "type": [ "null", "array" - ] + ], + "examples": ["Height", "Plant Height", "Stalk Height", "Canopy Height"] }, "traitClass": { "description": "A classification to describe the type of trait and the context it should be considered in.\n
examples- \"morphological\", \"phenological\", \"agronomical\", \"physiological\", \"abiotic stress\", \"biotic stress\", \"biochemical\", \"quality traits\", \"fertility\", etc.", "type": [ "null", "string" - ] + ], + "example": "phenological" }, "traitDbId": { "description": "The ID which uniquely identifies a trait", @@ -106,24 +115,28 @@ "type": [ "null", "string" - ] + ], + "example": "The height of the plant" }, "traitName": { "description": "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", - "type": "string" + "type": "string", + "example": "Height" }, "traitPUI": { "description": "The Permanent Unique Identifier of a Trait, usually in the form of a URI", "type": [ "null", "string" - ] + ], + "example": "http://my-traits.com/trait/CO_123:0000012" } }, "required": [ "traitName" ], "title": "Trait", + "description": "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". ", "type": "object", "brapi-metadata": { "primaryModel": true diff --git a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json index 4f536c2b..278bd6ab 100644 --- a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json +++ b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json @@ -31,7 +31,7 @@ } } }, - "example": [ + "examples": [ { "dimension": "variants", "pageSize": 500, @@ -56,7 +56,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Genotype", "Read Depth" ] @@ -67,7 +67,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "GT", "RD" ] @@ -78,7 +78,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "20:1000-35000", "20:87000-125000" ] @@ -89,7 +89,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "a03202ec", "274e4f63" ] @@ -100,7 +100,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "a03202ec", "274e4f63" ] @@ -111,7 +111,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "a03202ec", "274e4f63" ] @@ -122,7 +122,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "a03202ec", "274e4f63" ] @@ -133,7 +133,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "a03202ec", "274e4f63" ] @@ -144,7 +144,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "bba0b258", "ff97d4f0" ] @@ -155,7 +155,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "407c0508", "49e24dfc" ] diff --git a/Specification/BrAPI-Schema/Requests/CallRequest.json b/Specification/BrAPI-Schema/Requests/CallRequest.json index daf37c9a..fc1ce477 100644 --- a/Specification/BrAPI-Schema/Requests/CallRequest.json +++ b/Specification/BrAPI-Schema/Requests/CallRequest.json @@ -9,7 +9,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "a03202ec", "274e4f63" ] @@ -20,7 +20,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "bba0b258", "ff97d4f0" ] @@ -31,7 +31,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "407c0508", "49e24dfc" ] diff --git a/Specification/BrAPI-Schema/Requests/CallSetRequest.json b/Specification/BrAPI-Schema/Requests/CallSetRequest.json index 6344162d..5029078a 100644 --- a/Specification/BrAPI-Schema/Requests/CallSetRequest.json +++ b/Specification/BrAPI-Schema/Requests/CallSetRequest.json @@ -26,7 +26,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "758d3f6d", "39c0a3f7" ] @@ -37,7 +37,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Sample_123", "Sample_789" ] @@ -48,7 +48,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "6c7486b2", "49c36a73" ] @@ -59,7 +59,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Sample_123_DNA_Run_456", "Sample_789_DNA_Run_101" ] @@ -70,7 +70,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "8a9a8972", "32a2649a" ] diff --git a/Specification/BrAPI-Schema/Requests/EventRequest.json b/Specification/BrAPI-Schema/Requests/EventRequest.json index 4ebabc27..37c31d92 100644 --- a/Specification/BrAPI-Schema/Requests/EventRequest.json +++ b/Specification/BrAPI-Schema/Requests/EventRequest.json @@ -14,7 +14,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3cd0ca36", "983f3b14" ] @@ -25,7 +25,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "bba0b258", "ff97d4f0" ] diff --git a/Specification/BrAPI-Schema/Requests/GermplasmAttributeRequest.json b/Specification/BrAPI-Schema/Requests/GermplasmAttributeRequest.json index a12755fc..4ee6aada 100644 --- a/Specification/BrAPI-Schema/Requests/GermplasmAttributeRequest.json +++ b/Specification/BrAPI-Schema/Requests/GermplasmAttributeRequest.json @@ -17,7 +17,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "2ef15c9f", "318e7f7d" ] @@ -28,7 +28,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Plant Height 1", "Root Color" ] @@ -39,7 +39,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://my-traits.com/trait/CO_123:0008012", "http://my-traits.com/trait/CO_123:0007261" ] @@ -50,7 +50,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Morphological", "Physical" ] diff --git a/Specification/BrAPI-Schema/Requests/GermplasmAttributeValueRequest.json b/Specification/BrAPI-Schema/Requests/GermplasmAttributeValueRequest.json index 41f39116..e0e1e87d 100644 --- a/Specification/BrAPI-Schema/Requests/GermplasmAttributeValueRequest.json +++ b/Specification/BrAPI-Schema/Requests/GermplasmAttributeValueRequest.json @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "ca4636d0", "c8a92409" ] @@ -31,7 +31,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "2ef15c9f", "318e7f7d" ] @@ -42,7 +42,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Plant Height 1", "Root Color" ] @@ -53,7 +53,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "f44f7b23", "a26b576e" ] @@ -64,7 +64,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "07e34f83", "d3d5517a" ] @@ -75,7 +75,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "a13ecffa", "7e1afe4f" ] @@ -86,7 +86,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "ef81147b", "78d82fad" ] @@ -97,7 +97,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "morphological", "phenological", "agronomical" @@ -109,7 +109,7 @@ "$ref": "../BrAPI-Common/TraitDataType.json#/$defs/TraitDataType" }, "type": "array", - "example": [ + "examples": [ "Numerical", "Ordinal", "Text" diff --git a/Specification/BrAPI-Schema/Requests/GermplasmRequest.json b/Specification/BrAPI-Schema/Requests/GermplasmRequest.json index f2d2d6ec..d1645ca4 100644 --- a/Specification/BrAPI-Schema/Requests/GermplasmRequest.json +++ b/Specification/BrAPI-Schema/Requests/GermplasmRequest.json @@ -26,7 +26,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://pui.per/accession/A0000003", "http://pui.per/accession/A0000477" ] @@ -37,7 +37,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "A0000003", "A0000477" ] @@ -48,7 +48,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "RDP1", "MDP1" ] @@ -59,7 +59,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "fa000203", "fa009965" ] @@ -70,7 +70,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "PER001", "NOR001" ] @@ -81,7 +81,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Aspergillus fructus", "Zea mays" ] @@ -92,7 +92,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Aspergillus", "Zea" ] @@ -103,7 +103,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "fructus", "mays" ] @@ -114,7 +114,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "variety_1", "2c38f9b6" ] @@ -125,7 +125,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "72c1001f", "7346c553" ] @@ -136,7 +136,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "16e16a7e", "ce06cf9e" ] diff --git a/Specification/BrAPI-Schema/Requests/ImageRequest.json b/Specification/BrAPI-Schema/Requests/ImageRequest.json index 99881cb4..81e3eaaf 100644 --- a/Specification/BrAPI-Schema/Requests/ImageRequest.json +++ b/Specification/BrAPI-Schema/Requests/ImageRequest.json @@ -17,7 +17,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "doi:10.1002/0470841559", "Red", "ncbi:0300294" @@ -29,7 +29,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "image_01032019.jpg", "picture_field_1234.jpg" ] @@ -63,7 +63,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Image 43", "Tractor in field" ] @@ -95,7 +95,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "image/jpg", "image/jpeg", "image/gif" @@ -107,7 +107,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "47326456", "fc9823ac" ] @@ -118,7 +118,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "564b64a6", "0d122d1d" ] @@ -129,7 +129,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "f5e4b273", "328c9424" ] diff --git a/Specification/BrAPI-Schema/Requests/ListRequest.json b/Specification/BrAPI-Schema/Requests/ListRequest.json index 0256400f..f4030031 100644 --- a/Specification/BrAPI-Schema/Requests/ListRequest.json +++ b/Specification/BrAPI-Schema/Requests/ListRequest.json @@ -29,7 +29,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "55f20cf6", "3193ca3d" ] @@ -40,7 +40,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Planing List 1", "Bobs List" ] @@ -51,7 +51,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Bob Robertson", "Rob Robertson" ] @@ -62,7 +62,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "bob@bob.com", "rob@bob.com" ] @@ -73,7 +73,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "USER", "SYSTEM", "EXTERNAL" diff --git a/Specification/BrAPI-Schema/Requests/LocationRequest.json b/Specification/BrAPI-Schema/Requests/LocationRequest.json index 43931d73..f6f6c761 100644 --- a/Specification/BrAPI-Schema/Requests/LocationRequest.json +++ b/Specification/BrAPI-Schema/Requests/LocationRequest.json @@ -20,7 +20,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "L1", "LHC" ] @@ -41,7 +41,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "USA", "PER" ] @@ -52,7 +52,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "United States of America", "Peru" ] @@ -66,7 +66,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "123 Main Street", "456 Side Street" ] @@ -77,7 +77,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "The Institute", "The Other Institute" ] @@ -88,7 +88,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Nursery", "Storage Location" ] @@ -99,7 +99,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "b28911cf", "5071d1e4" ] @@ -110,7 +110,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Location Alpha", "The Large Hadron Collider" ] diff --git a/Specification/BrAPI-Schema/Requests/MarkerPositionRequest.json b/Specification/BrAPI-Schema/Requests/MarkerPositionRequest.json index f05b9bd4..300f901f 100644 --- a/Specification/BrAPI-Schema/Requests/MarkerPositionRequest.json +++ b/Specification/BrAPI-Schema/Requests/MarkerPositionRequest.json @@ -11,7 +11,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "7e6fa8aa", "bedc418c" ] @@ -22,7 +22,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Chromosome 2", "Chromosome 3" ] @@ -33,7 +33,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "a0caa928", "f8894a26" ] diff --git a/Specification/BrAPI-Schema/Requests/MethodRequest.json b/Specification/BrAPI-Schema/Requests/MethodRequest.json index 015b6674..658d7e95 100644 --- a/Specification/BrAPI-Schema/Requests/MethodRequest.json +++ b/Specification/BrAPI-Schema/Requests/MethodRequest.json @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "exampls": [ "3cd0ca36", "983f3b14" ] @@ -31,7 +31,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3cd0ca36", "983f3b14" ] diff --git a/Specification/BrAPI-Schema/Requests/ObservationRequest.json b/Specification/BrAPI-Schema/Requests/ObservationRequest.json index 4a78811a..15e3083f 100644 --- a/Specification/BrAPI-Schema/Requests/ObservationRequest.json +++ b/Specification/BrAPI-Schema/Requests/ObservationRequest.json @@ -32,7 +32,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "6a4a59d8", "3ff067e0" ] @@ -43,7 +43,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "76f559b5", "066bc5d3" ] @@ -54,7 +54,7 @@ "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevel.json#/$defs/ObservationUnitLevel" }, - "example": [ + "examples": [ { "levelName": "plot", "levelCode": "Plot_123" @@ -75,7 +75,7 @@ "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevelRelationship.json#/$defs/ObservationUnitLevelRelationship" }, - "example": [ + "examples": [ { "levelName": "field", "levelCode": "Field_1" @@ -98,7 +98,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Spring 2018", "Season A" ] diff --git a/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json b/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json index 9a7407dc..786cb4ae 100644 --- a/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json +++ b/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json @@ -32,7 +32,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "66bab7e3", "0e5e7f99" ] @@ -43,7 +43,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "FieldA_PlotB", "SpecialPlantName" ] @@ -54,7 +54,7 @@ "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevel.json#/$defs/ObservationUnitLevel" }, - "example": [ + "examples": [ { "levelName": "plot", "levelCode": "Plot_123" @@ -75,7 +75,7 @@ "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevelRelationship.json#/$defs/ObservationUnitLevelRelationship" }, - "example": [ + "examples": [ { "levelName": "field", "levelCode": "Field_1" @@ -93,7 +93,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Spring 2018", "Season A" ] diff --git a/Specification/BrAPI-Schema/Requests/Parameters/CommonCropNamesParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/CommonCropNamesParameters.json index b5922710..bd7d761f 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/CommonCropNamesParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/CommonCropNamesParameters.json @@ -9,7 +9,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Tomatillo", "Paw Paw" ] diff --git a/Specification/BrAPI-Schema/Requests/Parameters/GermplasmParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/GermplasmParameters.json index d5ca59c6..8e603bb3 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/GermplasmParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/GermplasmParameters.json @@ -9,7 +9,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "e9c6edd7", "1b1df4a6" ] @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "A0000003", "A0000477" ] diff --git a/Specification/BrAPI-Schema/Requests/Parameters/LocationParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/LocationParameters.json index 5f412286..41da14f3 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/LocationParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/LocationParameters.json @@ -9,7 +9,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "b28911cf", "5071d1e4" ] @@ -20,7 +20,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Location Alpha", "The Large Hadron Collider" ] diff --git a/Specification/BrAPI-Schema/Requests/Parameters/ObservationVariableParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/ObservationVariableParameters.json index 2e7f68fe..7eda0166 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/ObservationVariableParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/ObservationVariableParameters.json @@ -9,7 +9,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "a646187d", "6d23513b" ] @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Plant Height in meters", "Wheat rust score 1-5" ] @@ -31,7 +31,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://my-traits.com/trait/CO_123:0008012", "http://my-traits.com/trait/CO_123:0007261" ] diff --git a/Specification/BrAPI-Schema/Requests/Parameters/ProgramParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/ProgramParameters.json index 741dba50..86856961 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/ProgramParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/ProgramParameters.json @@ -9,7 +9,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "8f5de35b", "0e2d4a13" ] @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Better Breeding Program", "Best Breeding Program" ] diff --git a/Specification/BrAPI-Schema/Requests/Parameters/StudyParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/StudyParameters.json index 6489c45c..78565e4c 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/StudyParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/StudyParameters.json @@ -9,7 +9,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "cf6c4bd4", "691e69d6" ] @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "The First Bob Study 2017", "Wheat Yield Trial 246" ] diff --git a/Specification/BrAPI-Schema/Requests/Parameters/TrialParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/TrialParameters.json index 358fd316..aeb6678f 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/TrialParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/TrialParameters.json @@ -9,7 +9,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "d2593dc2", "9431a731" ] @@ -20,7 +20,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "All Yield Trials 2016", "Disease Resistance Study Comparison Group" ] diff --git a/Specification/BrAPI-Schema/Requests/Parameters/VariableBaseClassParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/VariableBaseClassParameters.json index cb906cc9..05c8ffba 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/VariableBaseClassParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/VariableBaseClassParameters.json @@ -24,7 +24,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "5bcac0ae", "7f48e22d" ] @@ -35,7 +35,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "f44f7b23", "a26b576e" ] @@ -46,7 +46,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "07e34f83", "d3d5517a" ] @@ -57,7 +57,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Measuring Tape", "Spectrometer" ] @@ -68,7 +68,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://my-traits.com/trait/CO_123:0000212", "http://my-traits.com/trait/CO_123:0003557" ] @@ -79,7 +79,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "a13ecffa", "7e1afe4f" ] @@ -90,7 +90,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Meters", "Liters" ] @@ -101,7 +101,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://my-traits.com/trait/CO_123:0000336", "http://my-traits.com/trait/CO_123:0000560" ] @@ -112,7 +112,7 @@ "$ref": "../../BrAPI-Common/TraitDataType.json#/$defs/TraitDataType" }, "type": "array", - "example": [ + "examples": [ "Numerical", "Ordinal", "Text" @@ -124,7 +124,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "morphological", "phenological", "agronomical" @@ -136,7 +136,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "ef81147b", "78d82fad" ] @@ -147,7 +147,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Stalk Height", "Root Color" ] @@ -158,7 +158,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://my-traits.com/trait/CO_123:0000456", "http://my-traits.com/trait/CO_123:0000820" ] @@ -169,7 +169,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Height", "Color" ] @@ -180,7 +180,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://my-traits.com/trait/CO_123:0008336", "http://my-traits.com/trait/CO_123:0001092" ] @@ -191,7 +191,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Stalk", "Root" ] @@ -202,7 +202,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://my-traits.com/trait/CO_123:0004098", "http://my-traits.com/trait/CO_123:0002366" ] diff --git a/Specification/BrAPI-Schema/Requests/PedigreeNodeRequest.json b/Specification/BrAPI-Schema/Requests/PedigreeNodeRequest.json index 6b2854b7..9c2808e6 100644 --- a/Specification/BrAPI-Schema/Requests/PedigreeNodeRequest.json +++ b/Specification/BrAPI-Schema/Requests/PedigreeNodeRequest.json @@ -26,7 +26,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "http://pui.per/accession/A0000003", "http://pui.per/accession/A0000477" ] @@ -37,7 +37,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "A0000003", "A0000477" ] @@ -48,7 +48,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "RDP1", "MDP1" ] @@ -59,7 +59,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "f0000203", "fa009965" ] @@ -70,7 +70,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "PER001", "NOR001" ] @@ -81,7 +81,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Aspergillus fructus", "Zea mays" ] @@ -92,7 +92,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Aspergillus", "Zea" ] @@ -103,7 +103,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "fructus", "mays" ] @@ -114,7 +114,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "variety_1", "2c38f9b6" ] diff --git a/Specification/BrAPI-Schema/Requests/PersonRequest.json b/Specification/BrAPI-Schema/Requests/PersonRequest.json index 8c413826..240ff959 100644 --- a/Specification/BrAPI-Schema/Requests/PersonRequest.json +++ b/Specification/BrAPI-Schema/Requests/PersonRequest.json @@ -17,7 +17,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "bob@bob.com", "rob@bob.com" ] @@ -28,7 +28,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Bob", "Rob" ] @@ -39,7 +39,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Robertson", "Smith" ] @@ -50,7 +50,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "123 Main Street", "456 Side Street" ] @@ -61,7 +61,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "Danger", "Fight" ] @@ -72,7 +72,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "1e7731ab", "bc28cff8" ] @@ -83,7 +83,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "9995555555", "8884444444" ] @@ -94,7 +94,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "bob", "rob" ] diff --git a/Specification/BrAPI-Schema/Requests/PlateRequest.json b/Specification/BrAPI-Schema/Requests/PlateRequest.json index 7ec737f1..5de94e33 100644 --- a/Specification/BrAPI-Schema/Requests/PlateRequest.json +++ b/Specification/BrAPI-Schema/Requests/PlateRequest.json @@ -26,7 +26,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3cd0ca36", "983f3b14" ] @@ -37,7 +37,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "0cac98b8", "b96125fb" ] @@ -48,7 +48,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "0cac98b8", "b96125fb" ] @@ -59,7 +59,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "11223344", "55667788" ] @@ -70,7 +70,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3bece2ca", "dd286cc6" ] @@ -81,7 +81,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "SA_111", "SA_222" ] @@ -92,7 +92,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "45e1e2d7", "6cc6dd28" ] @@ -103,7 +103,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "d745e1e2", "6dd28d74" ] diff --git a/Specification/BrAPI-Schema/Requests/ProgramRequest.json b/Specification/BrAPI-Schema/Requests/ProgramRequest.json index dc08fd71..f77b58b5 100644 --- a/Specification/BrAPI-Schema/Requests/ProgramRequest.json +++ b/Specification/BrAPI-Schema/Requests/ProgramRequest.json @@ -17,7 +17,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "P1", "P2" ] @@ -28,7 +28,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "d8bd96c7", "a2b9c8e7" ] @@ -39,7 +39,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Bob Robertson", "Rob Robertson" ] @@ -50,7 +50,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Objective Code One", "This is a longer objective search query" ] @@ -65,7 +65,7 @@ ] }, "type": "array", - "example": [ + "examples": [ "STANDARD", "PROJECT" ] diff --git a/Specification/BrAPI-Schema/Requests/ReferenceRequest.json b/Specification/BrAPI-Schema/Requests/ReferenceRequest.json index bd4f522f..d454acbc 100644 --- a/Specification/BrAPI-Schema/Requests/ReferenceRequest.json +++ b/Specification/BrAPI-Schema/Requests/ReferenceRequest.json @@ -26,7 +26,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "A0009283", "A0006657" ] @@ -37,7 +37,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "c2365e900c81a89cf74d83dab60df146" ] }, @@ -47,7 +47,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "04c83ea7", "d0998a34" ] @@ -58,7 +58,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "32a19dd7", "2c182c18" ] diff --git a/Specification/BrAPI-Schema/Requests/ReferenceSetRequest.json b/Specification/BrAPI-Schema/Requests/ReferenceSetRequest.json index a501d4b4..ba805ce5 100644 --- a/Specification/BrAPI-Schema/Requests/ReferenceSetRequest.json +++ b/Specification/BrAPI-Schema/Requests/ReferenceSetRequest.json @@ -26,7 +26,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "A0009283", "A0006657" ] @@ -37,7 +37,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "doi:10.15454/312953986E3", "doi:10.15454/312953986E3" ] @@ -48,7 +48,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "c2365e900c81a89cf74d83dab60df146" ] }, @@ -58,7 +58,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "32a19dd7", "2c182c18" ] diff --git a/Specification/BrAPI-Schema/Requests/SampleRequest.json b/Specification/BrAPI-Schema/Requests/SampleRequest.json index f390995e..a0a25161 100644 --- a/Specification/BrAPI-Schema/Requests/SampleRequest.json +++ b/Specification/BrAPI-Schema/Requests/SampleRequest.json @@ -26,7 +26,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3cd0ca36", "983f3b14" ] @@ -37,7 +37,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "0cac98b8", "b96125fb" ] @@ -48,7 +48,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "0cac98b8", "b96125fb" ] @@ -59,7 +59,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3bece2ca", "dd286cc6" ] @@ -70,7 +70,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "SA_111", "SA_222" ] @@ -81,7 +81,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "45e1e2d7", "6cc6dd28" ] @@ -92,7 +92,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "d745e1e2", "6dd28d74" ] diff --git a/Specification/BrAPI-Schema/Requests/ScaleRequest.json b/Specification/BrAPI-Schema/Requests/ScaleRequest.json index 4de425f5..c5e4c4c9 100644 --- a/Specification/BrAPI-Schema/Requests/ScaleRequest.json +++ b/Specification/BrAPI-Schema/Requests/ScaleRequest.json @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3cd0ca36", "983f3b14" ] @@ -31,7 +31,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3cd0ca36", "983f3b14" ] diff --git a/Specification/BrAPI-Schema/Requests/SeasonRequest.json b/Specification/BrAPI-Schema/Requests/SeasonRequest.json index 049074f7..23af5103 100644 --- a/Specification/BrAPI-Schema/Requests/SeasonRequest.json +++ b/Specification/BrAPI-Schema/Requests/SeasonRequest.json @@ -9,7 +9,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "2012", "1957-2004" ] @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Spring", "Planting_Time_7" ] @@ -31,7 +31,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Objective Code One", "This is a longer objective search query" ] @@ -42,7 +42,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "2017" ] } diff --git a/Specification/BrAPI-Schema/Requests/StudyRequest.json b/Specification/BrAPI-Schema/Requests/StudyRequest.json index d1e21695..00d11a38 100644 --- a/Specification/BrAPI-Schema/Requests/StudyRequest.json +++ b/Specification/BrAPI-Schema/Requests/StudyRequest.json @@ -37,7 +37,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Harvest Two 2017", "Summer 2018" ] @@ -48,7 +48,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Yield Trial", "Disease Resistance Trial" ] @@ -59,7 +59,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "Grape_Yield_Spring_2018", "Walnut_Kenya" ] @@ -70,7 +70,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "doi:10.155454/12349537312", "https://pui.per/d8dd35e1" ] diff --git a/Specification/BrAPI-Schema/Requests/TraitRequest.json b/Specification/BrAPI-Schema/Requests/TraitRequest.json index 8899ea96..717e0712 100644 --- a/Specification/BrAPI-Schema/Requests/TraitRequest.json +++ b/Specification/BrAPI-Schema/Requests/TraitRequest.json @@ -20,7 +20,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3cd0ca36", "983f3b14" ] @@ -31,7 +31,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3cd0ca36", "983f3b14" ] diff --git a/Specification/BrAPI-Schema/Requests/TrialRequest.json b/Specification/BrAPI-Schema/Requests/TrialRequest.json index ad1307b0..5c72151d 100644 --- a/Specification/BrAPI-Schema/Requests/TrialRequest.json +++ b/Specification/BrAPI-Schema/Requests/TrialRequest.json @@ -34,7 +34,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "e0f70c2a", "b82f0967" ] @@ -55,7 +55,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "https://doi.org/01093190", "https://doi.org/11192409" ] diff --git a/Specification/BrAPI-Schema/Requests/VarientRequest.json b/Specification/BrAPI-Schema/Requests/VarientRequest.json index 68d62037..075c7af1 100644 --- a/Specification/BrAPI-Schema/Requests/VarientRequest.json +++ b/Specification/BrAPI-Schema/Requests/VarientRequest.json @@ -24,7 +24,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "4639fe3e", "b60d900b" ] @@ -46,7 +46,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "89ab4d17", "74d3b63d" ] @@ -57,7 +57,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "d3b63d4d", "3b63d74b" ] @@ -73,7 +73,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "3b63d889", "ab4d174d" ] @@ -84,7 +84,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "ba63d810", "434d1760" ] diff --git a/Specification/BrAPI-Schema/Requests/VarientSetRequest.json b/Specification/BrAPI-Schema/Requests/VarientSetRequest.json index 35137070..af092965 100644 --- a/Specification/BrAPI-Schema/Requests/VarientSetRequest.json +++ b/Specification/BrAPI-Schema/Requests/VarientSetRequest.json @@ -23,7 +23,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "9569cfc4", "da1e888c" ] @@ -34,7 +34,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "c80f068b", "eb7c5f50" ] @@ -45,7 +45,7 @@ "items": { "type": "string" }, - "example": [ + "examples": [ "b2903842", "dcbb8558" ] @@ -56,7 +56,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "89ab4d17", "74d3b63d" ] @@ -67,7 +67,7 @@ "type": "string" }, "type": "array", - "example": [ + "examples": [ "d3b63d4d", "3b63d74b" ] diff --git a/Specification/Generated/BrAPI-Core.yaml b/Specification/Generated/BrAPI-Core.yaml new file mode 100644 index 00000000..6cf39963 --- /dev/null +++ b/Specification/Generated/BrAPI-Core.yaml @@ -0,0 +1,3271 @@ +openapi: 3.0.0 +info: + title: BrAPI-Core + version: "2.1" +servers: +- url: / +paths: + /serverinfo: + get: + tags: + - Server Info + summary: Get the list of implemented Calls + description: "Implementation Notes\n\nHaving a consistent structure for the\ + \ path string of each call is very \nimportant for teams to be able to connect\ + \ and find errors. Read more on Github.\n\nHere are the rules for the path\ + \ of each call that should be returned\n\nEvery word in the call path should\ + \ match the documentation exactly, both in \nspelling and capitalization.\ + \ Note that path strings are all lower case, but \npath parameters are camel\ + \ case.\n\nEach path should start relative to \\\"/\\\" and therefore should\ + \ not include \\\"/\\\"\n\nNo leading or trailing slashes (\\\"/\\\") \n\n\ + Path parameters are wrapped in curly braces (\\\"{}\\\"). The name of the\ + \ path parameter \nshould be spelled exactly as it is specified in the documentation.\n\ + \nExamples \n\nGOOD \"call\": \"germplasm/{germplasmDbId}/pedigree\" \n\n\ + BAD \"call\": \"germplasm/{id}/pedigree\"\n\nBAD \"call\": \"germplasm/{germplasmDBid}/pedigree\"\ + \ \n\nBAD \"call\": \"brapi/v2/germplasm/{germplasmDbId}/pedigree\" \n\n\ + BAD \"call\": \"/germplasm/{germplasmDbId}/pedigree/\" \n\nBAD \"call\"\ + : \"germplasm//pedigree\"" + parameters: + - name: contentType + in: query + description: Filter the list of endpoints based on the response content type. + required: false + style: form + explode: true + schema: + $ref: "#/components/schemas/ContentTypes" + - name: dataType + in: query + description: |- + **Deprecated in v2.1** Please use `contentType`. Github issue number #443 +
The data format supported by the call. + required: false + deprecated: true + style: form + explode: true + schema: + $ref: "#/components/schemas/ContentTypes" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + description: OK + content: + application/json: + schema: + title: ServerInfoResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ServerInfo" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /lists: + get: + tags: + - Lists + summary: Get a filtered list of List + description: Get a list of List + parameters: + - name: dateCreatedRangeStart + in: query + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + required: false + schema: + type: string + - name: dateCreatedRangeEnd + in: query + description: Define the end for an interval of time and only include Lists + that are created within this interval. + required: false + schema: + type: string + - name: dateModifiedRangeStart + in: query + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + required: false + schema: + type: string + - name: dateModifiedRangeEnd + in: query + description: Define the end for an interval of time and only include Lists + that are modified within this interval. + required: false + schema: + type: string + - name: listDbId + in: query + description: An array of primary database identifiers to identify a set of + Lists + required: false + schema: + type: string + - name: listName + in: query + description: An array of human readable names to identify a set of Lists + required: false + schema: + type: string + - name: listOwnerName + in: query + description: An array of names for the people or entities who are responsible + for a set of Lists + required: false + schema: + type: string + - name: listOwnerPersonDbId + in: query + description: An array of primary database identifiers to identify people or + entities who are responsible for a set of Lists + required: false + schema: + type: string + - name: listSource + in: query + description: "An array of terms identifying lists from different sources (ie\ + \ 'USER', 'SYSTEM', etc)" + required: false + schema: + type: string + - name: listType + in: query + required: false + schema: + $ref: "#/components/schemas/ListType" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ListListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Lists + summary: Create new List + description: Add new List to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ListNewRequest" + responses: + "200": + $ref: "#/components/responses/ListListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /locations: + get: + tags: + - Locations + summary: Get a filtered list of Location + description: Get a list of Location + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: locationName + in: query + description: A human readable names to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: abbreviation + in: query + description: A list of shortened human readable names for a set of Locations + required: false + schema: + type: string + - name: altitudeMin + in: query + description: The minimum altitude to search for + required: false + schema: + type: number + - name: altitudeMax + in: query + description: The maximum altitude to search for + required: false + schema: + type: number + - name: countryCode + in: query + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" + required: false + schema: + type: string + - name: countryName + in: query + description: The full name of the country to search for + required: false + schema: + type: string + - name: coordinate + in: query + required: false + schema: + $ref: "#/components/schemas/GeoJSONSearchArea" + - name: instituteAddress + in: query + description: The street address of the institute to search for + required: false + schema: + type: string + - name: instituteName + in: query + description: The name of the institute to search for + required: false + schema: + type: string + - name: locationType + in: query + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + required: false + schema: + type: string + - name: parentLocationDbId + in: query + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \nFor\ + \ example, an Institution might have multiple Field Stations inside it and\ + \ each Field Station might have multiple Fields." + required: false + schema: + type: string + - name: parentLocationName + in: query + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \nFor\ + \ example, an Institution might have multiple Field Stations inside it and\ + \ each Field Station might have multiple Fields." + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/LocationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Locations + summary: Create new Location + description: Add new Location to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/LocationNewRequest" + responses: + "200": + $ref: "#/components/responses/LocationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /people: + get: + tags: + - People + summary: Get a filtered list of Person + description: Get a list of Person + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: emailAddress + in: query + description: email address for this person + required: false + schema: + type: string + - name: firstName + in: query + description: Persons first name + required: false + schema: + type: string + - name: lastName + in: query + description: Persons last name + required: false + schema: + type: string + - name: mailingAddress + in: query + description: physical address of this person + required: false + schema: + type: string + - name: middleName + in: query + description: Persons middle name + required: false + schema: + type: string + - name: personDbId + in: query + description: Unique ID for this person + required: false + schema: + type: string + - name: phoneNumber + in: query + description: phone number of this person + required: false + schema: + type: string + - name: userID + in: query + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/PersonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - People + summary: Create new Person + description: Add new Person to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PersonNewRequest" + responses: + "200": + $ref: "#/components/responses/PersonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /programs: + get: + tags: + - Programs + summary: Get a filtered list of Program + description: Get a list of Program + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: abbreviation + in: query + description: A list of shortened human readable names for a set of Programs + required: false + schema: + type: string + - name: leadPersonDbId + in: query + description: The person DbIds of the program leader to search for + required: false + schema: + type: string + - name: leadPersonName + in: query + description: The names of the program leader to search for + required: false + schema: + type: string + - name: objectife + in: query + description: A program objective to search for + required: false + schema: + type: string + - name: programType + in: query + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + required: false + schema: + type: string + enum: + - STANDARD + - PROJECT + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ProgramListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Programs + summary: Create new Program + description: Add new Program to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ProgramNewRequest" + responses: + "200": + $ref: "#/components/responses/ProgramListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /seasons: + get: + tags: + - Seasons + summary: Get a filtered list of Season + description: Get a list of Season + parameters: + - name: seasonDbId + in: query + description: "The unique identifier for a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'." + required: false + schema: + type: string + - name: season + in: query + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + required: false + schema: + type: string + - name: seasonName + in: query + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + required: false + schema: + type: string + - name: year + in: query + description: The 4 digit year of a season. Example "2017" + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/SeasonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Seasons + summary: Create new Season + description: Add new Season to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/Season" + responses: + "200": + $ref: "#/components/responses/SeasonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /studies: + get: + tags: + - Studies + summary: Get a filtered list of Study + description: Get a list of Study + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: locationName + in: query + description: A human readable names to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The DbIds of Variables to search for + required: false + schema: + type: string + - name: observationVariableName + in: query + description: The names of Variables to search for + required: false + schema: + type: string + - name: observationVariablePUI + in: query + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + required: false + schema: + type: string + - name: actife + in: query + description: A flag to indicate if a Study is currently active and ongoing + required: false + schema: + type: boolean + - name: seasonDbId + in: query + description: The ID which uniquely identifies a season + required: false + schema: + type: string + - name: studyType + in: query + description: "The type of study being performed. ex. \"Yield Trial\", etc" + required: false + schema: + type: string + - name: studyCode + in: query + description: A short human readable code for a study + required: false + schema: + type: string + - name: studyPUI + in: query + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/StudyListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Studies + summary: Create new Study + description: Add new Study to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/StudyNewRequest" + responses: + "200": + $ref: "#/components/responses/StudyListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /trials: + get: + tags: + - Trials + summary: Get a filtered list of Trial + description: Get a list of Trial + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: locationName + in: query + description: A human readable names to search for + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The DbIds of Variables to search for + required: false + schema: + type: string + - name: observationVariableName + in: query + description: The names of Variables to search for + required: false + schema: + type: string + - name: observationVariablePUI + in: query + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: actife + in: query + description: A flag to indicate if a Trial is currently active and ongoing + required: false + schema: + type: boolean + - name: contactDbId + in: query + description: List of contact entities associated with this trial + required: false + schema: + type: string + - name: searchDateRangeStart + in: query + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of\ + \ the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate`\ + \ AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n\ + - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + required: false + schema: + type: string + - name: searchDateRangeEnd + in: query + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of\ + \ the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate`\ + \ AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n\ + - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + required: false + schema: + type: string + - name: trialPUI + in: query + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/TrialListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Trials + summary: Create new Trial + description: Add new Trial to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TrialNewRequest" + responses: + "200": + $ref: "#/components/responses/TrialListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /lists/{listDbId}: + get: + tags: + - Lists + summary: Get the details of a specific List + description: Get details for a List + responses: + "200": + $ref: "#/components/responses/ListSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Lists + summary: Update the details for an existing List + description: Update the details for an existing List + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ListNewRequest" + responses: + "200": + $ref: "#/components/responses/ListSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /locations/{locationDbId}: + get: + tags: + - Locations + summary: Get the details of a specific Location + description: Get details for a Location + responses: + "200": + $ref: "#/components/responses/LocationSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Locations + summary: Update the details for an existing Location + description: Update the details for an existing Location + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/LocationNewRequest" + responses: + "200": + $ref: "#/components/responses/LocationSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /people/{personDbId}: + get: + tags: + - People + summary: Get the details of a specific Person + description: Get details for a Person + responses: + "200": + $ref: "#/components/responses/PersonSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - People + summary: Update the details for an existing Person + description: Update the details for an existing Person + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PersonNewRequest" + responses: + "200": + $ref: "#/components/responses/PersonSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /programs/{programDbId}: + get: + tags: + - Programs + summary: Get the details of a specific Program + description: Get details for a Program + responses: + "200": + $ref: "#/components/responses/ProgramSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Programs + summary: Update the details for an existing Program + description: Update the details for an existing Program + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ProgramNewRequest" + responses: + "200": + $ref: "#/components/responses/ProgramSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /seasons/{seasonDbId}: + get: + tags: + - Seasons + summary: Get the details of a specific Season + description: Get details for a Season + responses: + "200": + $ref: "#/components/responses/SeasonSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Seasons + summary: Update the details for an existing Season + description: Update the details for an existing Season + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/Season" + responses: + "200": + $ref: "#/components/responses/SeasonSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /studies/{studyDbId}: + get: + tags: + - Studies + summary: Get the details of a specific Study + description: Get details for a Study + responses: + "200": + $ref: "#/components/responses/StudySingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Studies + summary: Update the details for an existing Study + description: Update the details for an existing Study + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/StudyNewRequest" + responses: + "200": + $ref: "#/components/responses/StudySingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /trials/{trialDbId}: + get: + tags: + - Trials + summary: Get the details of a specific Trial + description: Get details for a Trial + responses: + "200": + $ref: "#/components/responses/TrialSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Trials + summary: Update the details for an existing Trial + description: Update the details for an existing Trial + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TrialNewRequest" + responses: + "200": + $ref: "#/components/responses/TrialSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/lists: + post: + tags: + - Lists + summary: Submit a search request for `List` + description: "Submit a search request for `List`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ListListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/locations: + post: + tags: + - Locations + summary: Submit a search request for `Location` + description: "Submit a search request for `Location`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/location/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/LocationListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/people: + post: + tags: + - People + summary: Submit a search request for `Person` + description: "Submit a search request for `Person`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/person/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/PersonListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/programs: + post: + tags: + - Programs + summary: Submit a search request for `Program` + description: "Submit a search request for `Program`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/program/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ProgramListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/studies: + post: + tags: + - Studies + summary: Submit a search request for `Study` + description: "Submit a search request for `Study`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/StudyListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/trials: + post: + tags: + - Trials + summary: Submit a search request for `Trial` + description: "Submit a search request for `Trial`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/TrialListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/lists/{searchResultsDbId}: + get: + tags: + - Lists + summary: "Submit a search request for `List`
\nSearch requests allow a client\ + \ to send a complex query for data. However, the server may not respond with\ + \ the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `List` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/list` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ListListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/locations/{searchResultsDbId}: + get: + tags: + - Locations + summary: "Submit a search request for `Location`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/location/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Location` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/location`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/LocationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/people/{searchResultsDbId}: + get: + tags: + - People + summary: "Submit a search request for `Person`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/person/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Person` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/person` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/PersonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/programs/{searchResultsDbId}: + get: + tags: + - Programs + summary: "Submit a search request for `Program`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/program/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Program` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/program` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ProgramListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/studies/{searchResultsDbId}: + get: + tags: + - Studies + summary: "Submit a search request for `Study`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Study` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/study` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/StudyListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/trials/{searchResultsDbId}: + get: + tags: + - Trials + summary: "Submit a search request for `Trial`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Trial` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/trial` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/TrialListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" +components: + schemas: + Service: + required: + - methods + - service + - versions + type: object + properties: + service: + type: string + description: The name of the available call as recorded in the documentation + example: "germplasm/{germplasmDbId}/pedigree" + contentTypes: + type: array + description: The possible content types returned by the service endpoint + example: + - application/json + items: + $ref: "#/components/schemas/ContentTypes" + dataTypes: + type: array + description: "**Deprecated in v2.1** Please use `contentTypes`. Github issue\ + \ number #443 \n
The possible data formats returned by the available\ + \ call " + example: + - application/json + deprecated: true + items: + $ref: "#/components/schemas/ContentTypes" + methods: + type: array + description: The possible HTTP Methods to be used with the available call + example: + - GET + - POST + items: + type: string + enum: + - GET + - POST + - PUT + - DELETE + versions: + type: array + description: The supported versions of a particular call + example: + - "2.0" + - "2.1" + items: + type: string + enum: + - "2.0" + - "2.1" + - "2.2" + ServerInfo: + required: + - calls + type: object + properties: + contactEmail: + type: string + description: A contact email address for this server management + example: contact@institute.org + documentationURL: + type: string + description: A URL to the human readable documentation of an object + example: institute.org/server + organizationURL: + type: string + description: The URL of the organization that manages this server and data + example: institute.org/home + organizationName: + type: string + description: The name of the organization that manages this server and data + example: The Institute + serverName: + type: string + description: The name of this server + example: The BrAPI Test Server + serverDescription: + type: string + description: A description of this server + example: |- + The BrAPI Test Server + Web Server - Apache Tomcat 7.0.32 + Database - Postgres 10 + Supported BrAPI Version - V2.0 + location: + type: string + description: "Physical location of this server (ie. City, Country)" + example: USA + calls: + type: array + description: Array of available calls on this server + items: + $ref: "#/components/schemas/Service" + AdditionalInfo: + type: object + properties: + additionalProperties: + type: string + description: "A free space containing any additional information related to\ + \ a particular object. A data source may provide any JSON object, unrestricted\ + \ by the BrAPI specification." + Attribute: + required: + - attributeName + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeCategory: + type: string + attributeDbId: + type: string + attributeDescription: + type: string + attributeName: + type: string + attributePUI: + type: string + commonCropName: + type: string + contextOfUse: + type: array + items: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + method: + $ref: "#/components/schemas/Method" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + synonyms: + type: array + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + Contact: + required: + - contactDbId + type: object + properties: + contactDbId: + type: string + email: + type: string + instituteName: + type: string + name: + type: string + orcid: + type: string + type: + type: string + description: A persons contact information + ContentTypes: + type: string + enum: + - application/json + - text/csv + - text/tsv + - application/flapjack + Context: + title: context + type: array + description: "The JSON-LD Context is used to provide JSON-LD definitions to\ + \ each field in a JSON object. By providing an array of context file urls,\ + \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ + \ see https://w3c.github.io/json-ld-syntax/#the-context" + example: + - https://brapi.org/jsonld/context/metadata.jsonld + items: + type: string + format: uri + DataLink: + type: object + properties: + dataFormat: + type: string + description: + type: string + fileFormat: + type: string + name: + type: string + provenance: + type: string + scientificType: + type: string + url: + type: string + version: + type: string + description: "A link to extra data files associated with this study. Extra data\ + \ could include notes, images, and reference data." + DatasetAuthorships: + type: object + properties: + datasetPUI: + type: string + license: + type: string + publicReleaseDate: + type: string + submissionDate: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: License and citation information for the data in this trial + EnvironmentParameter: + required: + - description + - environmentParametersDbId + - parameterName + type: object + properties: + description: + type: string + environmentParametersDbId: + type: string + parameterName: + type: string + parameterPUI: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + unit: + type: string + unitPUI: + type: string + value: + type: string + valuePUI: + type: string + description: "Environmental parameters that were kept constant throughout the\ + \ study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57)\ + \ Environment - Environmental parameters that were kept constant throughout\ + \ the study and did not change between observation units or assays. Environment\ + \ characteristics that vary over time, i.e. environmental variables, should\ + \ be recorded as Observed Variables (see below)." + ExperimentalDesign: + type: object + properties: + PUI: + type: string + description: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: The experimental and statistical design full description plus a + category PUI taken from crop research ontology or agronomy ontology + ExternalReference: + type: object + properties: + referenceId: + type: string + referenceSource: + type: string + GeoJSON: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + type: + type: string + description: |- + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONGeometry: + oneOf: + - required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + items: + type: number + type: + type: string + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + - required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." + GeoJSONSearchArea: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + germplasmOrigin: + $ref: "#/components/schemas/GermplasmOrigin" + imageDbId: + type: string + imageName: + type: string + observationDbId: + type: string + observationUnit: + $ref: "#/components/schemas/ObservationUnitPosition" + type: + type: string + GrowthFacility: + type: object + properties: + PUI: + type: string + description: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: Short description of the facility in which the study was carried + out. + LastUpdate: + required: + - lastUpdateDbId + type: object + properties: + lastUpdateDbId: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + timestamp: + type: string + version: + type: string + description: The date and time when this study was last modified + List: + required: + - listDbId + - listName + - listType + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + dateCreated: + type: string + dateModified: + type: string + listDescription: + type: string + listName: + type: string + listOwnerName: + type: string + listSize: + type: integer + format: int32 + listSource: + type: string + listType: + $ref: "#/components/schemas/ListType" + personDbId: + type: string + description: "A List represents a collection of other BrAPI data objects. Typically\ + \ these are custom lists generated by a user to keep track of interesting\ + \ data. For example, a user might build a List of Germplasm that they have\ + \ manually marked for further study." + ListNewRequest: + required: + - listDbId + - listDbId + - listName + - listType + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + dateCreated: + type: string + dateModified: + type: string + listDbId: + type: string + listDescription: + type: string + listName: + type: string + listOwnerName: + type: string + listSize: + type: integer + format: int32 + listSource: + type: string + listType: + $ref: "#/components/schemas/ListType" + personDbId: + type: string + description: "A List represents a collection of other BrAPI data objects. Typically\ + \ these are custom lists generated by a user to keep track of interesting\ + \ data. For example, a user might build a List of Germplasm that they have\ + \ manually marked for further study." + ListSearchRequest: + type: object + properties: + dateCreatedRangeEnd: + type: string + dateCreatedRangeStart: + type: string + dateModifiedRangeEnd: + type: string + dateModifiedRangeStart: + type: string + listType: + $ref: "#/components/schemas/ListType" + description: "A List represents a collection of other BrAPI data objects. Typically\ + \ these are custom lists generated by a user to keep track of interesting\ + \ data. For example, a user might build a List of Germplasm that they have\ + \ manually marked for further study." + ListType: + type: string + description: The type of objects that are referenced in a List + enum: + - germplasm + - markers + - variants + - programs + - trials + - studies + - observationUnits + - observations + - observationVariables + - samples + Location: + required: + - locationDbId + - locationName + type: object + properties: + abbreviation: + type: string + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + childLocationDbIds: + type: array + items: + type: string + coordinateDescription: + type: string + coordinateUncertainty: + type: string + coordinates: + $ref: "#/components/schemas/GeoJSON" + countryCode: + type: string + countryName: + type: string + documentationURL: + type: string + environmentType: + type: string + exposure: + type: string + instituteAddress: + type: string + instituteName: + type: string + locationDbId: + type: string + locationName: + type: string + locationType: + type: string + siteStatus: + type: string + slope: + type: string + topography: + type: string + description: "A geographic Location on earth. This is usually used to describe\ + \ the general area where an experiment took place. For example, a natural\ + \ site, an experimental field, a greenhouse, a phenotyping facility, etc." + LocationNewRequest: + required: + - locationDbId + - locationDbId + - locationName + type: object + properties: + abbreviation: + type: string + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + childLocationDbIds: + type: array + items: + type: string + coordinateDescription: + type: string + coordinateUncertainty: + type: string + coordinates: + $ref: "#/components/schemas/GeoJSON" + countryCode: + type: string + countryName: + type: string + documentationURL: + type: string + environmentType: + type: string + exposure: + type: string + instituteAddress: + type: string + instituteName: + type: string + locationDbId: + type: string + locationName: + type: string + locationType: + type: string + siteStatus: + type: string + slope: + type: string + topography: + type: string + description: "A geographic Location on earth. This is usually used to describe\ + \ the general area where an experiment took place. For example, a natural\ + \ site, an experimental field, a greenhouse, a phenotyping facility, etc." + LocationSearchRequest: + type: object + properties: + altitudeMax: + type: number + altitudeMin: + type: number + coordinates: + $ref: "#/components/schemas/GeoJSONSearchArea" + description: "A geographic Location on earth. This is usually used to describe\ + \ the general area where an experiment took place. For example, a natural\ + \ site, an experimental field, a greenhouse, a phenotyping facility, etc." + ObservationUnitHierarchyLevel: + type: object + properties: + levelName: + type: string + levelOrder: + type: integer + format: int32 + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + OntologyTerm: + type: object + properties: + term: + type: string + termURI: + type: string + description: A pointer to an ontology used by a genomic reference + Person: + required: + - personDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + description: + type: string + emailAddress: + type: string + firstName: + type: string + lastName: + type: string + mailingAddress: + type: string + middleName: + type: string + phoneNumber: + type: string + userID: + type: string + description: "A generic object used to maintain the metadata needed to describe\ + \ a human. The Person might be a software user, a field technician, or a primary\ + \ contact for a Program." + PersonNewRequest: + required: + - personDbId + - personDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + description: + type: string + emailAddress: + type: string + firstName: + type: string + lastName: + type: string + mailingAddress: + type: string + middleName: + type: string + personDbId: + type: string + phoneNumber: + type: string + userID: + type: string + description: "A generic object used to maintain the metadata needed to describe\ + \ a human. The Person might be a software user, a field technician, or a primary\ + \ contact for a Program." + PersonSearchRequest: + type: object + properties: {} + description: "A generic object used to maintain the metadata needed to describe\ + \ a human. The Person might be a software user, a field technician, or a primary\ + \ contact for a Program." + Program: + required: + - programDbId + - programName + type: object + properties: + abbreviation: + type: string + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + documentationURL: + type: string + fundingInformation: + type: string + objective: + type: string + personDbId: + type: string + programName: + type: string + programType: + type: string + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding\ + \ " + enum: + - STANDARD + - PROJECT + description: A BrAPI Program represents the high level organization or group + who is responsible for conducting trials and studies. Things like Breeding + Programs and Funded Projects are considered BrAPI Programs. A Program can + contain multiple Trials. A Trial can contain multiple Studies. + ProgramNewRequest: + required: + - programDbId + - programDbId + - programName + type: object + properties: + abbreviation: + type: string + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + documentationURL: + type: string + fundingInformation: + type: string + objective: + type: string + personDbId: + type: string + programDbId: + type: string + programName: + type: string + programType: + type: string + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding\ + \ " + enum: + - STANDARD + - PROJECT + description: A BrAPI Program represents the high level organization or group + who is responsible for conducting trials and studies. Things like Breeding + Programs and Funded Projects are considered BrAPI Programs. A Program can + contain multiple Trials. A Trial can contain multiple Studies. + ProgramSearchRequest: + type: object + properties: {} + description: A BrAPI Program represents the high level organization or group + who is responsible for conducting trials and studies. Things like Breeding + Programs and Funded Projects are considered BrAPI Programs. A Program can + contain multiple Trials. A Trial can contain multiple Studies. + Publication: + type: object + properties: + publicationPUI: + type: string + publicationReference: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for a + literature publication where the investigation is described. Use of DOIs is + recommended. + Season: + required: + - seasonDbId + type: object + properties: + seasonDbId: + type: string + seasonName: + type: string + year: + type: integer + format: int32 + description: "A Season defines a period in time. A Season is made of two parts;\ + \ (1) the primary year and (2) a term which defines a segment of the year.\ + \ This term could be a traditional season, like \"Spring\" or \"Summer\",\ + \ or this term could be a month, like \"May\" or \"June\", or this could be\ + \ an arbitrary season name which is meaningful to the breeding Program like\ + \ \"PlantingTime_3\" or \"Season E\"." + Study: + required: + - studyDbId + - studyName + type: object + properties: + active: + type: boolean + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + contactDbIds: + type: array + items: + type: string + culturalPractices: + type: string + documentationURL: + type: string + endDate: + type: string + experimentalDesign: + $ref: "#/components/schemas/ExperimentalDesign" + growthFacility: + $ref: "#/components/schemas/GrowthFacility" + lastUpdateDbId: + type: string + license: + type: string + locationDbId: + type: string + locationName: + type: string + observationLevelDbIds: + type: array + items: + type: string + observationUnitsDescription: + type: string + observationVariableDbIds: + type: array + items: + type: string + startDate: + type: string + studyCode: + type: string + studyDescription: + type: string + studyName: + type: string + studyPUI: + type: string + studyType: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: A Study represents an experiment that has taken place at a single + location. The Study contains metadata about the parameters and design of the + experiment. It can also be used to group results and data sets generated from + the experiment. A Trial can represent a collection of one or more Studies. + StudyNewRequest: + required: + - studyDbId + - studyDbId + - studyName + type: object + properties: + active: + type: boolean + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + contactDbIds: + type: array + items: + type: string + culturalPractices: + type: string + documentationURL: + type: string + endDate: + type: string + experimentalDesign: + $ref: "#/components/schemas/ExperimentalDesign" + growthFacility: + $ref: "#/components/schemas/GrowthFacility" + lastUpdateDbId: + type: string + license: + type: string + locationDbId: + type: string + locationName: + type: string + observationLevelDbIds: + type: array + items: + type: string + observationUnitsDescription: + type: string + observationVariableDbIds: + type: array + items: + type: string + startDate: + type: string + studyCode: + type: string + studyDbId: + type: string + studyDescription: + type: string + studyName: + type: string + studyPUI: + type: string + studyType: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: A Study represents an experiment that has taken place at a single + location. The Study contains metadata about the parameters and design of the + experiment. It can also be used to group results and data sets generated from + the experiment. A Trial can represent a collection of one or more Studies. + StudySearchRequest: + type: object + properties: + active: + type: boolean + description: A Study represents an experiment that has taken place at a single + location. The Study contains metadata about the parameters and design of the + experiment. It can also be used to group results and data sets generated from + the experiment. A Trial can represent a collection of one or more Studies. + TraitDataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + Trial: + required: + - trialDbId + - trialName + type: object + properties: + active: + type: boolean + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + contacts: + type: array + items: + $ref: "#/components/schemas/Contact" + documentationURL: + type: string + endDate: + type: string + programDbId: + type: string + programName: + type: string + startDate: + type: string + studyDbIds: + type: array + items: + type: string + trialDescription: + type: string + trialName: + type: string + trialPUI: + type: string + description: "A Trial represents a collection of Study objects, and the metadata\ + \ associated with that collection. A Trial could represent a multi-location\ + \ experiment, and could contain information related to publications and data\ + \ licensing." + TrialNewRequest: + required: + - trialDbId + - trialDbId + - trialName + type: object + properties: + active: + type: boolean + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + contacts: + type: array + items: + $ref: "#/components/schemas/Contact" + documentationURL: + type: string + endDate: + type: string + programDbId: + type: string + programName: + type: string + startDate: + type: string + studyDbIds: + type: array + items: + type: string + trialDbId: + type: string + trialDescription: + type: string + trialName: + type: string + trialPUI: + type: string + description: "A Trial represents a collection of Study objects, and the metadata\ + \ associated with that collection. A Trial could represent a multi-location\ + \ experiment, and could contain information related to publications and data\ + \ licensing." + TrialSearchRequest: + type: object + properties: + active: + type: boolean + searchDateRangeEnd: + type: string + searchDateRangeStart: + type: string + description: "A Trial represents a collection of Study objects, and the metadata\ + \ associated with that collection. A Trial could represent a multi-location\ + \ experiment, and could contain information related to publications and data\ + \ licensing." + Variable: + required: + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + contextOfUse: + type: array + items: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + method: + $ref: "#/components/schemas/Method" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + synonyms: + type: array + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + description: "A unique combination of Trait, Method, and Scale to define a clear\ + \ context for an Observation." + basePagination: + required: + - currentPage + - pageSize + type: object + properties: + currentPage: + type: integer + description: The index number for the returned page of data. This should + always match the requested page number or the default page (0). + example: 0 + default: 0 + pageSize: + type: integer + description: "The number of data elements returned, aka the size of the\ + \ current page. If the requested page does not have enough elements to\ + \ fill a page at the requested page size, this field should indicate the\ + \ actual number of elements returned." + example: 1000 + default: 1000 + totalCount: + type: integer + description: The total number of elements that are available on the server + and match the requested query parameters. + example: 10 + totalPages: + type: integer + description: "The total number of pages of elements available on the server.\ + \ This should be calculated with the following formula. \n
totalPages\ + \ = CEILING( totalCount / requested_page_size)" + example: 1 + description: "The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." + dataFile: + required: + - fileURL + type: object + properties: + fileURL: + type: string + description: The absolute URL where the file is located + format: uri + example: https://wiki.brapi.org/examples/datafile.xlsx + fileName: + type: string + description: The name of the file + example: datafile.xlsx + fileSize: + type: integer + description: The size of the file in bytes + example: 4398 + fileDescription: + type: string + description: A human readable description of the file contents + example: This is an Excel data file + fileType: + type: string + description: The type or format of the file. Preferably MIME Type. + example: application/vnd.ms-excel + fileMD5Hash: + type: string + description: The MD5 Hash of the file contents to be used as a check sum + example: c2365e900c81a89cf74d83dab60df146 + description: A dataFile contains a URL and the relevant file metadata to represent + a file + metadata: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/basePagination" + metadataBase: + type: object + properties: + datafiles: + type: array + description: "The datafiles contains a list of file URLs and metadata. \n\ + These files contain additional information related to the returned object\ + \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ + \ data file, an informational file, the uploaded file where the data originated\ + \ from, a generated file representing the whole dataset in a particular\ + \ format, or any other related file. " + example: [] + items: + $ref: "#/components/schemas/dataFile" + status: + type: array + description: "The status field contains a list of informational status messages\ + \ from the server. \nIf no status is reported, an empty list should be\ + \ returned. See Error Reporting for more information." + items: + $ref: "#/components/schemas/status" + description: "An object in the BrAPI standard response model that describes\ + \ some information about the service call being performed. This includes supplementary\ + \ data, status log messages, and pagination information." + metadataTokenPagination: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/tokenPagination" + status: + required: + - message + - messageType + type: object + properties: + message: + type: string + description: A short message concerning the status of this request/response + example: "Request accepted, response successful" + messageType: + type: string + description: The logging level for the attached message + example: INFO + enum: + - DEBUG + - ERROR + - WARNING + - INFO + description: An array of status messages to convey technical logging information + from the server to the client. + tokenPagination: + allOf: + - $ref: "#/components/schemas/basePagination" + - required: + - nextPageToken + type: object + properties: + nextPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the next page of data." + example: cb668f63 + deprecated: true + currentPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the current page of data." + example: 48bc6ac1 + deprecated: true + prevPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the previous page of data." + example: 9659857e + deprecated: true + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ + \ construct an additional query and move to the next or previous page respectively.\ + \ " + example: + currentPage: 0 + pageSize: 1000 + totalCount: 10 + totalPages: 1 + responses: + "401Unauthorized": + description: Unauthorized + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization + token + "202AcceptedSearchResponse": + description: Accepted + content: + application/json: + schema: + title: 202AcceptedSearchResponse + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + type: object + properties: + searchResultsDbId: + type: string + example: 551ae08c + StudySingleResponse: + description: OK + content: + application/json: + schema: + title: StudySingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Study" + PersonListResponse: + description: OK + content: + application/json: + schema: + title: PersonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Person" + LocationListResponse: + description: OK + content: + application/json: + schema: + title: LocationListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Location" + TrialListResponse: + description: OK + content: + application/json: + schema: + title: TrialListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Trial" + "403Forbidden": + description: Forbidden + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to + perform this action + ProgramListResponse: + description: OK + content: + application/json: + schema: + title: ProgramListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Program" + TrialSingleResponse: + description: OK + content: + application/json: + schema: + title: TrialSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Trial" + ListListResponse: + description: OK + content: + application/json: + schema: + title: ListListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/List" + SeasonSingleResponse: + description: OK + content: + application/json: + schema: + title: SeasonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Season" + "400BadRequest": + description: Bad Request + content: + application/json: + schema: + type: string + example: |- + ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object + + ERROR - 2018-10-08T18:15:11Z - Invalid query parameter + + ERROR - 2018-10-08T18:15:11Z - Required parameter is missing + "404NotFound": + description: Not Found + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not + found + StudyListResponse: + description: OK + content: + application/json: + schema: + title: StudyListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Study" + LocationSingleResponse: + description: OK + content: + application/json: + schema: + title: LocationSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Location" + SeasonListResponse: + description: OK + content: + application/json: + schema: + title: SeasonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Season" + ListSingleResponse: + description: OK + content: + application/json: + schema: + title: ListSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/List" + PersonSingleResponse: + description: OK + content: + application/json: + schema: + title: PersonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Person" + ProgramSingleResponse: + description: OK + content: + application/json: + schema: + title: ProgramSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Program" + parameters: + externalReferenceID: + name: externalReferenceID + in: query + description: "**Deprecated in v2.1** Please use `externalReferenceId`. Github\ + \ issue number #460 \n
An external reference ID. Could be a simple string\ + \ or a URI. (use with `externalReferenceSource` parameter)" + required: false + deprecated: true + style: form + explode: true + schema: + type: string + externalReferenceId: + name: externalReferenceId + in: query + description: An external reference ID. Could be a simple string or a URI. (use + with `externalReferenceSource` parameter) + required: false + style: form + explode: true + schema: + type: string + externalReferenceSource: + name: externalReferenceSource + in: query + description: An identifier for the source system or database of an external + reference (use with `externalReferenceId` parameter) + required: false + style: form + explode: true + schema: + type: string + acceptHeader: + name: Accept + in: header + description: "A standard HTTP request header that is used to request a specific\ + \ content type (JSON, CSV, etc) which is \"acceptable\" to the client and\ + \ should be returned by the server" + required: true + style: simple + explode: false + schema: + $ref: "#/components/schemas/ContentTypes" + example: application/json + searchResultsDbId: + name: searchResultsDbId + in: path + description: Unique identifier which references the search results + required: true + style: simple + explode: false + schema: + type: string + pageSize: + name: pageSize + in: query + description: The size of the pages to be returned. Default is `1000`. + required: false + style: form + explode: true + schema: + type: integer + example: 1000 + page: + name: page + in: query + description: |- + Used to request a specific page of data to be returned. + + The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. + required: false + style: form + explode: true + schema: + type: integer + example: "0" + pageToken: + name: pageToken + in: query + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n
\ + \ Tokenized pages are for large data sets which can not be efficiently broken\ + \ into indexed pages. Use the nextPageToken and prevPageToken from a prior\ + \ response to construct a query and move to the next or previous page respectively. " + required: false + deprecated: true + style: form + explode: true + schema: + type: string + example: 33c27874 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX + securitySchemes: + AuthorizationToken: + type: http + description: OAuth Bearer Token - A valid Bearer token to prove authorization + scheme: bearer + bearerFormat: nonce token or JWT diff --git a/Specification/Generated/BrAPI-Genotyping.yaml b/Specification/Generated/BrAPI-Genotyping.yaml new file mode 100644 index 00000000..180d385a --- /dev/null +++ b/Specification/Generated/BrAPI-Genotyping.yaml @@ -0,0 +1,5207 @@ +openapi: 3.0.1 +info: + title: BrAPI-Genotyping + version: "2.1" +paths: + /calls: + get: + tags: + - Calls + summary: Get a filtered list of Call + description: Get a list of Call + parameters: + - name: callSetDbId + in: query + description: A list of IDs which uniquely identify `CallSets` within the given + database server + required: false + schema: + type: string + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variant` within the given + database server + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` within the + given database server + required: false + schema: + type: string + - name: expandHomozygote + in: query + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + required: false + schema: + type: boolean + - name: sepPhased + in: query + description: The string used as a separator for phased allele calls. + required: false + schema: + type: string + - name: sepUnphased + in: query + description: The string used as a separator for unphased allele calls. + required: false + schema: + type: string + - name: unknownString + in: query + description: The string used as a representation for missing data. + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/CallListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /callsets: + get: + tags: + - CallSets + summary: Get a filtered list of CallSet + description: Get a list of CallSet + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: sampleDbId + in: query + description: A list of IDs which uniquely identify `Samples` within the given + database server + required: false + schema: + type: string + - name: sampleName + in: query + description: A list of human readable names associated with `Samples` + required: false + schema: + type: string + - name: callSetDbId + in: query + description: A list of IDs which uniquely identify `CallSets` within the given + database server + required: false + schema: + type: string + - name: callSetName + in: query + description: A list of human readable names associated with `CallSets` + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` within the + given database server + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/CallSetListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /maps: + get: + tags: + - GenomeMaps + summary: Get a filtered list of GenomeMap + description: Get a list of GenomeMap + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: mapDbId + in: query + description: The ID which uniquely identifies a `GenomeMap` + required: false + schema: + type: string + - name: mapPUI + in: query + description: The DOI or other permanent identifier for a `GenomeMap` + required: false + schema: + type: string + - name: scientificName + in: query + description: "Full scientific binomial format name. This includes Genus, Species,\ + \ and Sub-species" + required: false + schema: + type: string + - name: type + in: query + description: "The type of map, usually \"Genetic\" or \"Physical\"" + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/GenomeMapListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /markerpositions: + get: + tags: + - MarkerPositions + summary: Get a filtered list of MarkerPosition + description: Get a list of MarkerPosition + parameters: + - name: mapDbId + in: query + description: A list of IDs which uniquely identify `GenomeMaps` within the + given database server + required: false + schema: + type: string + - name: linkageGroupName + in: query + description: A list of Uniquely Identifiable linkage group names + required: false + schema: + type: string + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variants` within the given + database server + required: false + schema: + type: string + - name: minPosition + in: query + description: The minimum position of markers in a given map + required: false + schema: + type: integer + format: int32 + - name: maxPosition + in: query + description: The maximum position of markers in a given map + required: false + schema: + type: integer + format: int32 + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/MarkerPositionListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /plates: + get: + tags: + - Plates + summary: Get a filtered list of Plate + description: Get a list of Plate + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: observationUnitDbId + in: query + description: The ID which uniquely identifies an observation unit + required: false + schema: + type: string + - name: plateDbId + in: query + description: The ID which uniquely identifies a plate of samples + required: false + schema: + type: string + - name: plateName + in: query + description: The human readable name of a plate of samples + required: false + schema: + type: string + - name: plateBarcode + in: query + description: A unique identifier physically attached to the plate + required: false + schema: + type: string + - name: sampleDbId + in: query + description: The ID which uniquely identifies a sample + required: false + schema: + type: string + - name: sampleName + in: query + description: The human readable name of the sample + required: false + schema: + type: string + - name: sampleGroupDbId + in: query + description: The unique identifier for a group of related Samples + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: The ID which uniquely identifies a germplasm + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/PlateListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Plates + summary: Create new Plate + description: Add new Plate to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PlateNewRequest" + responses: + "200": + $ref: "#/components/responses/PlateListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /references: + get: + tags: + - References + summary: Get a filtered list of Reference + description: Get a list of Reference + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: accession + in: query + description: "If specified, return the references for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + required: false + schema: + type: string + - name: md5checksum + in: query + description: "If specified, return the references for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + required: false + schema: + type: string + - name: referenceDbId + in: query + description: A list of IDs which uniquely identify `References` within the + given database server + required: false + schema: + type: string + - name: referenceSetDbId + in: query + description: A list of IDs which uniquely identify `ReferenceSets` within + the given database server + required: false + schema: + type: string + - name: isDerived + in: query + description: "A sequence X is said to be derived from source sequence Y, if\ + \ X and Y are of the same length and the per-base sequence divergence at\ + \ A/C/G/T bases is sufficiently small. Two sequences derived from the same\ + \ official sequence share the same coordinates and annotations, and can\ + \ be replaced with the official sequence for certain use cases." + required: false + schema: + type: boolean + - name: minLength + in: query + description: The minimum length of this `References` sequence. + required: false + schema: + type: integer + format: int32 + - name: maxLength + in: query + description: The minimum length of this `References` sequence. + required: false + schema: + type: integer + format: int32 + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ReferenceListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /referencesets: + get: + tags: + - ReferenceSets + summary: Get a filtered list of ReferenceSet + description: Get a list of ReferenceSet + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: accession + in: query + description: "If set, return the reference sets for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + required: false + schema: + type: string + - name: assemblyPUI + in: query + description: "If set, return the reference sets for which the `assemblyId`\ + \ matches this string (case-sensitive, exact match)." + required: false + schema: + type: string + - name: md5checksum + in: query + description: "If set, return the reference sets for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + required: false + schema: + type: string + - name: referenceSetDbId + in: query + description: The `ReferenceSets` to search. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ReferenceSetListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /samples: + get: + tags: + - Samples + summary: Get a filtered list of Sample + description: Get a list of Sample + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: observationUnitDbId + in: query + description: The ID which uniquely identifies an `ObservationUnit` + required: false + schema: + type: string + - name: plateDbId + in: query + description: The ID which uniquely identifies a `Plate` of `Samples` + required: false + schema: + type: string + - name: plateName + in: query + description: The human readable name of a `Plate` of `Samples` + required: false + schema: + type: string + - name: sampleDbId + in: query + description: The ID which uniquely identifies a `Sample` + required: false + schema: + type: string + - name: sampleName + in: query + description: The human readable name of the `Sample` + required: false + schema: + type: string + - name: sampleGroupDbId + in: query + description: The unique identifier for a group of related `Samples` + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: The ID which uniquely identifies a `Germplasm` + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/SampleListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Samples + summary: Update the details for an existing Sample + description: Update the details for an existing Sample + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SampleNewRequest" + responses: + "200": + $ref: "#/components/responses/SampleListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Samples + summary: Create new Sample + description: Add new Sample to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SampleNewRequest" + responses: + "200": + $ref: "#/components/responses/SampleListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variants: + get: + tags: + - Variants + summary: Get a filtered list of Variant + description: Get a list of Variant + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: callSetDbId + in: query + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue number\ + \ #474 \n
Only return variant calls which belong to call sets with these\ + \ IDs. If unspecified, return all variants and no variant call objects." + required: false + schema: + type: string + - name: end + in: query + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + required: false + schema: + type: integer + format: int32 + - name: referenceDbId + in: query + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + required: false + schema: + type: string + - name: referenceDbId + in: query + description: The unique identifier representing a genotype `Reference` + required: false + schema: + type: string + - name: referenceSetDbId + in: query + description: The unique identifier representing a genotype `ReferenceSet` + required: false + schema: + type: string + - name: start + in: query + description: "The beginning of the window (0-based, inclusive) for which overlapping\ + \ variants should be returned. Genomic positions are non-negative integers\ + \ less than reference length. Requests spanning the join of circular genomes\ + \ are represented as two requests one on each side of the join (position\ + \ 0)." + required: false + schema: + type: integer + format: int32 + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variants` + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/VariantListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variantsets: + get: + tags: + - VariantSets + summary: Get a filtered list of VariantSet + description: Get a list of VariantSet + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: callSetDbId + in: query + description: The unique identifier representing a CallSet + required: false + schema: + type: string + - name: variantDbId + in: query + description: The unique identifier representing a Variant + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: The unique identifier representing a VariantSet + required: false + schema: + type: string + - name: referenceDbId + in: query + description: The unique identifier representing a genotype Reference + required: false + schema: + type: string + - name: referenceSetDbId + in: query + description: The unique identifier representing a genotype ReferenceSet + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/VariantSetListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /callsets/{callSetDbId}: + get: + tags: + - CallSets + summary: Get the details of a specific CallSet + description: Get details for a CallSet + responses: + "200": + $ref: "#/components/responses/CallSetSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /callsets/{callSetDbId}/calls: + get: + tags: + - Calls + summary: Get a filtered list of Call + description: Get a list of Call + parameters: + - name: callSetDbId + in: query + description: A list of IDs which uniquely identify `CallSets` within the given + database server + required: false + schema: + type: string + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variant` within the given + database server + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` within the + given database server + required: false + schema: + type: string + - name: expandHomozygote + in: query + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + required: false + schema: + type: boolean + - name: sepPhased + in: query + description: The string used as a separator for phased allele calls. + required: false + schema: + type: string + - name: sepUnphased + in: query + description: The string used as a separator for unphased allele calls. + required: false + schema: + type: string + - name: unknownString + in: query + description: The string used as a representation for missing data. + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/CallListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /maps/{mapDbId}: + get: + tags: + - GenomeMaps + summary: Get the details of a specific GenomeMap + description: Get details for a GenomeMap + responses: + "200": + $ref: "#/components/responses/GenomeMapSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /plates/{plateDbId}: + get: + tags: + - Plates + summary: Get the details of a specific Plate + description: Get details for a Plate + responses: + "200": + $ref: "#/components/responses/PlateSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /references/{referenceDbId}: + get: + tags: + - References + summary: Get the details of a specific Reference + description: Get details for a Reference + responses: + "200": + $ref: "#/components/responses/ReferenceSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /referencesets/{referenceSetDbId}: + get: + tags: + - ReferenceSets + summary: Get the details of a specific ReferenceSet + description: Get details for a ReferenceSet + responses: + "200": + $ref: "#/components/responses/ReferenceSetSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /samples/{sampleDbId}: + get: + tags: + - Samples + summary: Get the details of a specific Sample + description: Get details for a Sample + responses: + "200": + $ref: "#/components/responses/SampleSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variants/{variantDbId}: + get: + tags: + - Variants + summary: Get the details of a specific Variant + description: Get details for a Variant + responses: + "200": + $ref: "#/components/responses/VariantSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variants/{variantDbId}/calls: + get: + tags: + - Calls + summary: Get a filtered list of Call + description: Get a list of Call + parameters: + - name: callSetDbId + in: query + description: A list of IDs which uniquely identify `CallSets` within the given + database server + required: false + schema: + type: string + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variant` within the given + database server + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` within the + given database server + required: false + schema: + type: string + - name: expandHomozygote + in: query + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + required: false + schema: + type: boolean + - name: sepPhased + in: query + description: The string used as a separator for phased allele calls. + required: false + schema: + type: string + - name: sepUnphased + in: query + description: The string used as a separator for unphased allele calls. + required: false + schema: + type: string + - name: unknownString + in: query + description: The string used as a representation for missing data. + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/CallListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variantsets/{variantSetDbId}: + get: + tags: + - VariantSets + summary: Get the details of a specific VariantSet + description: Get details for a VariantSet + responses: + "200": + $ref: "#/components/responses/VariantSetSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variantsets/{variantSetDbId}/calls: + get: + tags: + - Calls + summary: Get a filtered list of Call + description: Get a list of Call + parameters: + - name: callSetDbId + in: query + description: A list of IDs which uniquely identify `CallSets` within the given + database server + required: false + schema: + type: string + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variant` within the given + database server + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` within the + given database server + required: false + schema: + type: string + - name: expandHomozygote + in: query + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + required: false + schema: + type: boolean + - name: sepPhased + in: query + description: The string used as a separator for phased allele calls. + required: false + schema: + type: string + - name: sepUnphased + in: query + description: The string used as a separator for unphased allele calls. + required: false + schema: + type: string + - name: unknownString + in: query + description: The string used as a representation for missing data. + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/CallListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variantsets/{variantSetDbId}/callsets: + get: + tags: + - CallSets + summary: Get a filtered list of CallSet + description: Get a list of CallSet + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: sampleDbId + in: query + description: A list of IDs which uniquely identify `Samples` within the given + database server + required: false + schema: + type: string + - name: sampleName + in: query + description: A list of human readable names associated with `Samples` + required: false + schema: + type: string + - name: callSetDbId + in: query + description: A list of IDs which uniquely identify `CallSets` within the given + database server + required: false + schema: + type: string + - name: callSetName + in: query + description: A list of human readable names associated with `CallSets` + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` within the + given database server + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/CallSetListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variantsets/{variantSetDbId}/variants: + get: + tags: + - Variants + summary: Get a filtered list of Variant + description: Get a list of Variant + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: callSetDbId + in: query + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue number\ + \ #474 \n
Only return variant calls which belong to call sets with these\ + \ IDs. If unspecified, return all variants and no variant call objects." + required: false + schema: + type: string + - name: end + in: query + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + required: false + schema: + type: integer + format: int32 + - name: referenceDbId + in: query + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + required: false + schema: + type: string + - name: referenceDbId + in: query + description: The unique identifier representing a genotype `Reference` + required: false + schema: + type: string + - name: referenceSetDbId + in: query + description: The unique identifier representing a genotype `ReferenceSet` + required: false + schema: + type: string + - name: start + in: query + description: "The beginning of the window (0-based, inclusive) for which overlapping\ + \ variants should be returned. Genomic positions are non-negative integers\ + \ less than reference length. Requests spanning the join of circular genomes\ + \ are represented as two requests one on each side of the join (position\ + \ 0)." + required: false + schema: + type: integer + format: int32 + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variants` + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/VariantListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/allelematrix: + post: + tags: + - AlleleMatrix + summary: Submit a search request for `AlleleMatrix` + description: "Submit a search request for `AlleleMatrix`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to\ + \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/AlleleMatrixListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/calls: + post: + tags: + - Calls + summary: Submit a search request for `Call` + description: "Submit a search request for `Call`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/CallListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/callsets: + post: + tags: + - CallSets + summary: Submit a search request for `CallSet` + description: "Submit a search request for `CallSet`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/CallSetListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/markerpositions: + post: + tags: + - MarkerPositions + summary: Submit a search request for `MarkerPosition` + description: "Submit a search request for `MarkerPosition`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/MarkerPositionListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/plates: + post: + tags: + - Plates + summary: Submit a search request for `Plate` + description: "Submit a search request for `Plate`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/PlateListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/references: + post: + tags: + - References + summary: Submit a search request for `Reference` + description: "Submit a search request for `Reference`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve\ + \ the results of the search.
\nReview the Search\ + \ Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ReferenceListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/referencesets: + post: + tags: + - ReferenceSets + summary: Submit a search request for `ReferenceSet` + description: "Submit a search request for `ReferenceSet`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to\ + \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ReferenceSetListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/samples: + post: + tags: + - Samples + summary: Submit a search request for `Sample` + description: "Submit a search request for `Sample`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/sample/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/SampleListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/variants: + post: + tags: + - Variants + summary: Submit a search request for `Variant` + description: "Submit a search request for `Variant`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/variant/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/VariantListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/variantsets: + post: + tags: + - VariantSets + summary: Submit a search request for `VariantSet` + description: "Submit a search request for `VariantSet`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to\ + \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/VariantSetListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/allelematrix/{searchResultsDbId}: + get: + tags: + - AlleleMatrix + summary: "Submit a search request for `AlleleMatrix`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of\ + \ the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `AlleleMatrix` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/alleleMatrix`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/AlleleMatrixListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/calls/{searchResultsDbId}: + get: + tags: + - Calls + summary: "Submit a search request for `Call`
\nSearch requests allow a client\ + \ to send a complex query for data. However, the server may not respond with\ + \ the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Call` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/call` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/CallListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/callsets/{searchResultsDbId}: + get: + tags: + - CallSets + summary: "Submit a search request for `CallSet`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `CallSet` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/callSet` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/CallSetListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/markerpositions/{searchResultsDbId}: + get: + tags: + - MarkerPositions + summary: "Submit a search request for `MarkerPosition`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `MarkerPosition` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/markerPosition`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/MarkerPositionListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/plates/{searchResultsDbId}: + get: + tags: + - Plates + summary: "Submit a search request for `Plate`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Plate` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/plate` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/PlateListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/references/{searchResultsDbId}: + get: + tags: + - References + summary: "Submit a search request for `Reference`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/reference/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Reference` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/reference`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ReferenceListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/referencesets/{searchResultsDbId}: + get: + tags: + - ReferenceSets + summary: "Submit a search request for `ReferenceSet`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of\ + \ the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `ReferenceSet` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/referenceSet`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ReferenceSetListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/samples/{searchResultsDbId}: + get: + tags: + - Samples + summary: "Submit a search request for `Sample`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/sample/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Sample` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/sample` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/SampleListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/variants/{searchResultsDbId}: + get: + tags: + - Variants + summary: "Submit a search request for `Variant`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/variant/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Variant` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/variant` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/VariantListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/variantsets/{searchResultsDbId}: + get: + tags: + - VariantSets + summary: "Submit a search request for `VariantSet`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of\ + \ the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `VariantSet` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/variantSet`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/VariantSetListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" +components: + schemas: + AdditionalInfo: + type: object + properties: + additionalProperties: + type: string + description: "A free space containing any additional information related to\ + \ a particular object. A data source may provide any JSON object, unrestricted\ + \ by the BrAPI specification." + AlleleMatrix: + required: + - callSetDbIds + - variantSetDbIds + type: object + properties: + callSetDbIds: + type: array + items: + type: string + expandHomozygotes: + type: boolean + sepPhased: + type: string + sepUnphased: + type: string + unknownString: + type: string + variantDbIds: + type: array + items: + type: string + variantSetDbIds: + type: array + items: + type: string + description: "The AlleleMatrix object is used to describe a matrix of genotyping\ + \ results. This 2d array of data reduces the overall size of the response\ + \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ + \ data retrieval faster and easier." + AlleleMatrixSearchRequest: + type: object + properties: + expandHomozygotes: + type: boolean + preview: + type: boolean + sepPhased: + type: string + sepUnphased: + type: string + unknownString: + type: string + description: "The AlleleMatrix object is used to describe a matrix of genotyping\ + \ results. This 2d array of data reduces the overall size of the response\ + \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ + \ data retrieval faster and easier." + Analysis: + required: + - analysisDbId + type: object + properties: + analysisDbId: + type: string + analysisName: + type: string + created: + type: string + description: + type: string + software: + type: array + items: + type: string + type: + type: string + updated: + type: string + variantSetDbId: + type: string + variantSetName: + type: string + description: "An analysis contains an interpretation of one or several experiments.\ + \ (e.g. SNVs, copy number variations, methylation status) together with information\ + \ about the methodology used." + Attribute: + required: + - attributeName + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeCategory: + type: string + attributeDbId: + type: string + attributeDescription: + type: string + attributeName: + type: string + attributePUI: + type: string + commonCropName: + type: string + contextOfUse: + type: array + items: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + method: + $ref: "#/components/schemas/Method" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + synonyms: + type: array + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + AvailableFormat: + type: object + properties: + dataFormat: + type: string + description: "dataFormat defines the structure of the data within a file\ + \ (ie DartSeq, VCF, Hapmap, tabular, etc)" + enum: + - DartSeq + - VCF + - Hapmap + - tabular + - JSON + expandHomozygotes: + type: boolean + fileFormat: + type: string + description: "fileFormat defines the MIME type of the file (ie text/csv,\ + \ application/excel, application/zip). This should also be reflected in\ + \ the Accept and ContentType HTTP headers for every relevant request and\ + \ response." + enum: + - text/csv + - text/tsv + - application/excel + - application/zip + - application/json + fileURL: + type: string + sepPhased: + type: string + sepUnphased: + type: string + unknownString: + type: string + variantSetDbId: + type: string + variantSetName: + type: string + description: Each 'availableFormat' object is a pairing of dataFormat and fileFormat. + These must be communicated in pairs because they are not independent parameters + and sometimes one influences the other. + Call: + required: + - callSetDbId + - variantDbId + - variantSetDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + callSetDbId: + type: string + callSetName: + type: string + genotypeValue: + type: string + phaseSet: + type: string + variantDbId: + type: string + variantSetDbId: + type: string + variantSetName: + type: string + description: "A `Call` represents the determination of genotype with respect\ + \ to a particular `Variant`. \n\nIt may include associated information such\ + \ as quality and phasing. For example, a call might assign a probability of\ + \ 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name\ + \ NA_12345." + CallSearchRequest: + type: object + properties: + expandHomozygotes: + type: boolean + sepPhased: + type: string + sepUnphased: + type: string + unknownString: + type: string + description: "A `Call` represents the determination of genotype with respect\ + \ to a particular `Variant`. \n\nIt may include associated information such\ + \ as quality and phasing. For example, a call might assign a probability of\ + \ 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name\ + \ NA_12345." + CallSet: + required: + - callSetDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + callSetDbId: + type: string + callSetName: + type: string + created: + type: string + sampleDbId: + type: string + sampleName: + type: string + samplePUI: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + updated: + type: string + variantSetDbIds: + type: array + items: + type: string + description: A CallSet is a collection of Calls that were generated by the same + analysis of the same Sample + CallSetSearchRequest: + type: object + properties: {} + description: A CallSet is a collection of Calls that were generated by the same + analysis of the same Sample + Contact: + required: + - contactDbId + type: object + properties: + contactDbId: + type: string + email: + type: string + instituteName: + type: string + name: + type: string + orcid: + type: string + type: + type: string + description: A persons contact information + ContentTypes: + type: string + enum: + - application/json + - text/csv + - text/tsv + - application/flapjack + Context: + title: context + type: array + description: "The JSON-LD Context is used to provide JSON-LD definitions to\ + \ each field in a JSON object. By providing an array of context file urls,\ + \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ + \ see https://w3c.github.io/json-ld-syntax/#the-context" + example: + - https://brapi.org/jsonld/context/metadata.jsonld + items: + type: string + format: uri + CrossParent: + type: object + properties: + germplasm: + $ref: "#/components/schemas/Germplasm" + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + parentType: + $ref: "#/components/schemas/ParentType" + description: The identifying information gor the parent material of a cross. + CrossType: + type: string + description: "The type of cross make. Accepted values for this field are 'BIPARENTAL',\ + \ 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED'\ + \ and 'DOUBLE_HAPLOID'." + enum: + - BIPARENTAL + - SELF + - OPEN_POLLINATED + - BULK + - BULK_SELFED + - BULK_OPEN_POLLINATED + - DOUBLE_HAPLOID + DataMatrix: + type: object + properties: + alleleMatrix: + $ref: "#/components/schemas/AlleleMatrix" + dataMatrix: + type: array + items: + type: array + items: + type: string + dataMatrixAbbreviation: + type: string + dataMatrixName: + type: string + dataType: + type: string + description: The type of field represented in this data matrix. This is + intended to help parse the data out of JSON. + enum: + - string + - integer + - float + - boolean + description: "A two dimensional array that holds allele data or associated metadata.\ + \ Each matrix should be the same size and orientation, aligned with the \"\ + callSetDbIds\" as columns and the \"variantDbIds\" as rows." + ExperimentalDesign: + type: object + properties: + PUI: + type: string + description: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: The experimental and statistical design full description plus a + category PUI taken from crop research ontology or agronomy ontology + ExternalReference: + type: object + properties: + referenceId: + type: string + referenceSource: + type: string + GenomeMap: + required: + - commonCropName + - mapDbId + - type + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + comments: + type: string + commonCropName: + type: string + documentationURL: + type: string + linkageGroupCount: + type: integer + format: int32 + mapDbId: + type: string + mapName: + type: string + mapPUI: + type: string + markerCount: + type: integer + format: int32 + publishedDate: + type: string + scientificName: + type: string + type: + type: string + unit: + type: string + description: The GenomeMap represents the metadata associated with a reference + map of a particular species genome. A GenomeMap can either represent a physical + map or genetic map. + GenotypeMetadata: + type: object + properties: + call: + $ref: "#/components/schemas/Call" + dataType: + type: string + description: The type of field represented in this Genotype Field. This + is intended to help parse the data out of JSON. + enum: + - string + - integer + - float + - boolean + fieldAbbreviation: + type: string + fieldName: + type: string + fieldValue: + type: string + description: Genotype Metadata are additional layers of metadata associated + with each genotype. + GeoJSON: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + type: + type: string + description: |- + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONGeometry: + oneOf: + - required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + items: + type: number + type: + type: string + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + - required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." + GeoJSONSearchArea: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + germplasmOrigin: + $ref: "#/components/schemas/GermplasmOrigin" + imageDbId: + type: string + imageName: + type: string + observationDbId: + type: string + observationUnit: + $ref: "#/components/schemas/ObservationUnitPosition" + type: + type: string + Germplasm: + required: + - commonCropName + - germplasmDbId + - germplasmName + - germplasmPUI + type: object + properties: + accessionNumber: + type: string + acquisitionDate: + type: string + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + biologicalStatusOfAccessionCode: + type: string + description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can\ + \ be used at 3 different levels of detail: either by using the general\ + \ codes such as 100, 200, 300, 400, or by using the more specific codes\ + \ such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild\ + \ \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace\ + \ \n400) Breeding/research material \n410) Breeders line \n411) Synthetic\ + \ population \n412) Hybrid \n413) Founder stock/base population \n414)\ + \ Inbred line (parent of hybrid cultivar) \n415) Segregating population\ + \ \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion\ + \ mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome\ + \ addition/substitution, aneuploids, amphiploids) \n423) Other genetic\ + \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ + \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ + \ \n999) Other (Elaborate in REMARKS field)" + enum: + - "100" + - "110" + - "120" + - "130" + - "200" + - "300" + - "400" + - "410" + - "411" + - "412" + - "413" + - "414" + - "415" + - "416" + - "420" + - "421" + - "422" + - "423" + - "500" + - "600" + - "999" + biologicalStatusOfAccessionDescription: + type: string + breedingMethodDbId: + type: string + breedingMethodName: + type: string + collection: + type: string + commonCropName: + type: string + countryOfOriginCode: + type: string + defaultDisplayName: + type: string + documentationURL: + type: string + genus: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + germplasmPreprocessing: + type: string + instituteCode: + type: string + instituteName: + type: string + pedigree: + type: string + sampleDbIds: + type: array + items: + type: string + seedSource: + type: string + seedSourceDescription: + type: string + species: + type: string + speciesAuthority: + type: string + subtaxa: + type: string + subtaxaAuthority: + type: string + description: "The conceptual identifiers and metadata describing a genetically\ + \ unique organism that is noteworthy in some way. Depending on context, a\ + \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ + \ Germplasm is conceptual data, not necessarily associated to a real physical\ + \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ + \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ + \ a Cross may or may not create a new Germplasm, since not every Cross is\ + \ unique or noteworthy." + GermplasmOrigin: + type: object + properties: + coordinateUncertainty: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + description: "Information for material (orchard, natural sites, ...). Geographic\ + \ identification of the plants from which seeds or cutting have been taken\ + \ to produce that germplasm." + GrowthFacility: + type: object + properties: + PUI: + type: string + description: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: Short description of the facility in which the study was carried + out. + ListType: + type: string + description: The type of objects that are referenced in a List + enum: + - germplasm + - markers + - variants + - programs + - trials + - studies + - observationUnits + - observations + - observationVariables + - samples + MarkerPosition: + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + linkageGroupName: + type: string + mapDbId: + type: string + mapName: + type: string + mapPUI: + type: string + position: + type: integer + format: int32 + variantDbId: + type: string + description: A MarkerPosition describes a particular genetic marker at a specific + position on a GenomeMap. A collection of MarkerPositions make up the data + to represent a full GenomeMap. + MarkerPositionSearchRequest: + type: object + properties: + maxPosition: + type: integer + format: int32 + minPosition: + type: integer + format: int32 + description: A MarkerPosition describes a particular genetic marker at a specific + position on a GenomeMap. A collection of MarkerPositions make up the data + to represent a full GenomeMap. + MetadataField: + type: object + properties: + dataType: + type: string + description: The type of field represented in this Genotype Field. This + is intended to help parse the data out of JSON. + enum: + - string + - integer + - float + - boolean + fieldAbbreviation: + type: string + fieldName: + type: string + variantSetDbId: + type: string + variantSetName: + type: string + description: "Indicates which types of genotyping data and metadata are available\ + \ in the VariantSet. \n
When possible, these field names and abbreviations\ + \ should follow the VCF standard " + Method: + required: + - methodDbId + - methodName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + bibliographicalReference: + type: string + description: + type: string + formula: + type: string + methodClass: + type: string + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReferenceDbId: + type: string + description: "A description of the way an Observation should be collected. \n\ +
For example, an ObservationVariable might be defined with a Trait of \"\ + plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ + \ variable would be distinct from a variable with the Method \"estimation\"\ + \ or \"drone image processing\". " + ObservationUnitHierarchyLevel: + type: object + properties: + levelName: + type: string + levelOrder: + type: integer + format: int32 + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitLevel: + type: object + properties: + levelCode: + type: string + levelName: + type: string + levelOrder: + type: integer + format: int32 + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitPosition: + type: object + properties: + entryType: + type: string + description: "The type of entry for this observation unit. ex. \"CHECK\"\ + , \"TEST\", \"FILLER\"" + enum: + - CHECK + - TEST + - FILLER + observationLevel: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + positionCoordinateX: + type: string + positionCoordinateXType: + $ref: "#/components/schemas/PositionCoordinateType" + positionCoordinateY: + type: string + positionCoordinateYType: + $ref: "#/components/schemas/PositionCoordinateType" + description: All positional and layout information related to this Observation + Unit + Ontology: + required: + - ontologyDbId + - ontologyName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + authors: + type: string + copyright: + type: string + description: + type: string + documentationURL: + type: string + licence: + type: string + ontologyDbId: + type: string + ontologyName: + type: string + version: + type: string + description: The identifier and metadata needed to reference an external controlled + vocabulary + OntologyReference: + required: + - ontology + type: object + properties: + ontology: + $ref: "#/components/schemas/Ontology" + ontologyReferenceDbId: + type: string + version: + type: string + description: "MIAPPE V1.1 (DM-85) Variable accession number - Accession number\ + \ of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession\ + \ number - Accession number of the trait in a suitable controlled vocabulary\ + \ (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number\ + \ - Accession number of the method in a suitable controlled vocabulary (Crop\ + \ Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number -\ + \ Accession number of the scale in a suitable controlled vocabulary (Crop\ + \ Ontology)." + OntologyTerm: + type: object + properties: + term: + type: string + termURI: + type: string + description: A pointer to an ontology used by a genomic reference + Pagination: + type: object + properties: + alleleMatrix: + $ref: "#/components/schemas/AlleleMatrix" + dimension: + type: string + description: The dimension of the matrix being paginated + enum: + - CALLSETS + - VARIANTS + page: + type: integer + format: int32 + pageSize: + type: integer + format: int32 + totalCount: + type: integer + format: int32 + totalPages: + type: integer + format: int32 + description: Pagination info for the matrix + ParentType: + type: string + description: "The type of parent used during crossing. Accepted values for this\ + \ field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn\ + \ a pedigree record, the 'parentType' describes each parent of a particular\ + \ germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe\ + \ how this germplasm was crossed to generate a particular progeny. \\nFor\ + \ example, given a record for germplasm A, having a progeny B and C. The 'parentType'\ + \ field for progeny B item refers \\nto the 'parentType' of A toward B. The\ + \ 'parentType' field for progeny C item refers to the 'parentType' of A toward\ + \ C.\\nIn this way, A could be a male parent to B, but a female parent to\ + \ C. " + enum: + - MALE + - FEMALE + - SELF + - POPULATION + - CLONAL + Plate: + required: + - plateDbId + - plateName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + plateBarcode: + type: string + plateFormat: + type: string + description: "Enum for plate formats, usually \"PLATE_96\" for a 96 well\ + \ plate or \"TUBES\" for plateless format" + enum: + - PLATE_96 + - TUBES + plateName: + type: string + programDbId: + type: string + programName: + type: string + sampleType: + type: string + description: "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" + enum: + - DNA + - RNA + - TISSUE + - MIXED + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: "A Plate represents the metadata for a collection of Samples. The\ + \ physical Plate being represented might be a plastic tray full of Samples,\ + \ or a group of Samples stored in individual containers ie bags, test tubes,\ + \ etc. Whatever the container is, the Samples in a Plate should be related\ + \ by the same physical space, though they may or may not be related as part\ + \ of the same experiment or analysis." + PlateNewRequest: + required: + - plateDbId + - plateName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + plateBarcode: + type: string + plateDbId: + type: string + plateFormat: + type: string + description: "Enum for plate formats, usually \"PLATE_96\" for a 96 well\ + \ plate or \"TUBES\" for plateless format" + enum: + - PLATE_96 + - TUBES + plateName: + type: string + programDbId: + type: string + programName: + type: string + sampleType: + type: string + description: "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" + enum: + - DNA + - RNA + - TISSUE + - MIXED + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: "A Plate represents the metadata for a collection of Samples. The\ + \ physical Plate being represented might be a plastic tray full of Samples,\ + \ or a group of Samples stored in individual containers ie bags, test tubes,\ + \ etc. Whatever the container is, the Samples in a Plate should be related\ + \ by the same physical space, though they may or may not be related as part\ + \ of the same experiment or analysis." + PlateSearchRequest: + type: object + properties: {} + description: "A Plate represents the metadata for a collection of Samples. The\ + \ physical Plate being represented might be a plastic tray full of Samples,\ + \ or a group of Samples stored in individual containers ie bags, test tubes,\ + \ etc. Whatever the container is, the Samples in a Plate should be related\ + \ by the same physical space, though they may or may not be related as part\ + \ of the same experiment or analysis." + PositionCoordinateType: + type: string + description: "The type of positional coordinate. Must be one of the following\ + \ values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location\ + \ Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84\ + \ geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW\ + \ - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical\ + \ counted number, could be independent or within a planted row \n\nGRID_ROW\ + \ - The row index number of a square grid overlay \n\nGRID_COL - The column\ + \ index number of a square grid overlay \n\nMEASURED_ROW - The distance in\ + \ meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters\ + \ from a defined 0-th column " + enum: + - LONGITUDE + - LATITUDE + - PLANTED_ROW + - PLANTED_INDIVIDUAL + - GRID_ROW + - GRID_COL + - MEASURED_ROW + - MEASURED_COL + Reference: + required: + - referenceDbId + - referenceName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + isDerived: + type: boolean + length: + type: integer + format: int32 + md5checksum: + type: string + referenceDbId: + type: string + referenceName: + type: string + referenceSetDbId: + type: string + referenceSetName: + type: string + sourceDivergence: + type: number + sourceGermplasmDbIds: + type: array + items: + type: string + sourceURI: + type: string + species: + $ref: "#/components/schemas/OntologyTerm" + variantDbIds: + type: array + items: + type: string + description: "A `Reference` is a canonical assembled contig, intended to act\ + \ as a reference coordinate space for other genomic annotations. A single\ + \ `Reference` might represent the human chromosome 1, for instance. `References`\ + \ are designed to be immutable." + ReferenceSearchRequest: + type: object + properties: + isDerived: + type: boolean + maxLength: + type: integer + format: int32 + minLength: + type: integer + format: int32 + description: "A `Reference` is a canonical assembled contig, intended to act\ + \ as a reference coordinate space for other genomic annotations. A single\ + \ `Reference` might represent the human chromosome 1, for instance. `References`\ + \ are designed to be immutable." + ReferenceSet: + required: + - referenceSetDbId + - referenceSetName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + assemblyPUI: + type: string + commonCropName: + type: string + description: + type: string + isDerived: + type: boolean + md5checksum: + type: string + referenceDbId: + type: string + referenceName: + type: string + referenceSetName: + type: string + sourceGermplasmDbIds: + type: array + items: + type: string + sourceURI: + type: string + species: + $ref: "#/components/schemas/OntologyTerm" + variantDbIds: + type: array + items: + type: string + variantSetDbIds: + type: array + items: + type: string + description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ + \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ + \ coordinate space for comparing reference-aligned experimental data." + ReferenceSetNewRequest: + required: + - referenceSetDbId + - referenceSetDbId + - referenceSetName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + assemblyPUI: + type: string + commonCropName: + type: string + description: + type: string + isDerived: + type: boolean + md5checksum: + type: string + referenceDbId: + type: string + referenceName: + type: string + referenceSetDbId: + type: string + referenceSetName: + type: string + sourceGermplasmDbIds: + type: array + items: + type: string + sourceURI: + type: string + species: + $ref: "#/components/schemas/OntologyTerm" + variantDbIds: + type: array + items: + type: string + variantSetDbIds: + type: array + items: + type: string + description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ + \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ + \ coordinate space for comparing reference-aligned experimental data." + ReferenceSetSearchRequest: + type: object + properties: {} + description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ + \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ + \ coordinate space for comparing reference-aligned experimental data." + Sample: + required: + - sampleDbId + - sampleName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + callSetDbIds: + type: array + items: + type: string + column: + type: integer + format: int32 + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + plateDbId: + type: string + plateName: + type: string + programDbId: + type: string + programName: + type: string + row: + type: string + sampleBarcode: + type: string + sampleDescription: + type: string + sampleGroupId: + type: string + sampleName: + type: string + samplePUI: + type: string + sampleTimestamp: + type: string + sampleType: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + takenBy: + type: string + tissueType: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + well: + type: string + description: "The identifiers and metadata associated with a physical piece\ + \ of biological material collected from the field for external analysis. A\ + \ Sample can take many forms (leaf clipping, seed, DNA, etc) and might be\ + \ used for a variety of analysis procedures (spectra, genotyping, etc)." + SampleNewRequest: + required: + - sampleDbId + - sampleName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + callSetDbIds: + type: array + items: + type: string + column: + type: integer + format: int32 + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + plateDbId: + type: string + plateName: + type: string + programDbId: + type: string + programName: + type: string + row: + type: string + sampleBarcode: + type: string + sampleDbId: + type: string + sampleDescription: + type: string + sampleGroupId: + type: string + sampleName: + type: string + samplePUI: + type: string + sampleTimestamp: + type: string + sampleType: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + takenBy: + type: string + tissueType: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + well: + type: string + description: "The identifiers and metadata associated with a physical piece\ + \ of biological material collected from the field for external analysis. A\ + \ Sample can take many forms (leaf clipping, seed, DNA, etc) and might be\ + \ used for a variety of analysis procedures (spectra, genotyping, etc)." + SampleSearchRequest: + type: object + properties: {} + description: "The identifiers and metadata associated with a physical piece\ + \ of biological material collected from the field for external analysis. A\ + \ Sample can take many forms (leaf clipping, seed, DNA, etc) and might be\ + \ used for a variety of analysis procedures (spectra, genotyping, etc)." + Scale: + required: + - scaleDbId + - scaleName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + dataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + decimalPlaces: + type: integer + format: int32 + ontologyReferenceDbId: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + units: + type: string + validValues: + $ref: "#/components/schemas/ValidValues" + description: "A Scale describes the units and acceptable values for an ObservationVariable.\ + \ \n
For example, an ObservationVariable might be defined with a Trait\ + \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ + . This variable would be distinct from a variable with the Scale \"inches\"\ + \ or \"pixels\"." + Trait: + required: + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attribute: + type: string + attributePUI: + type: string + entity: + type: string + entityPUI: + type: string + mainAbbreviation: + type: string + ontologyReferenceDbId: + type: string + status: + type: string + traitClass: + type: string + traitDbId: + type: string + traitDescription: + type: string + traitName: + type: string + traitPUI: + type: string + description: "A Trait describes what property is being observed. \n
For example,\ + \ an ObservationVariable might be defined with a Trait of \"plant height\"\ + , a Scale of \"meters\", and a Method of \"tape measure\". This variable would\ + \ be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\"\ + . " + TraitDataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + ValidValues: + type: object + properties: + maximumValue: + type: string + minimumValue: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + description: Metadata describing the acceptable values for this Scale + Variable: + required: + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + contextOfUse: + type: array + items: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + method: + $ref: "#/components/schemas/Method" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + synonyms: + type: array + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + description: "A unique combination of Trait, Method, and Scale to define a clear\ + \ context for an Observation." + Variant: + required: + - variantDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + created: + type: string + end: + type: integer + format: int32 + filtersApplied: + type: boolean + filtersPassed: + type: boolean + referenceBases: + type: string + referenceDbId: + type: string + referenceName: + type: string + referenceSetDbId: + type: string + referenceSetName: + type: string + start: + type: integer + format: int32 + svlen: + type: integer + format: int32 + updated: + type: string + variantDbId: + type: string + variantSetDbId: + type: string + variantSetName: + type: string + variantType: + type: string + description: "A `Variant` represents a change in DNA sequence relative to some\ + \ reference. For example, a variant could represent a classic marker, a SNP,\ + \ or an insertion. This is equivalent to a row in VCF." + VariantSearchRequest: + type: object + properties: + end: + type: integer + format: int32 + referenceDbId: + type: string + start: + type: integer + format: int32 + description: "A `Variant` represents a change in DNA sequence relative to some\ + \ reference. For example, a variant could represent a classic marker, a SNP,\ + \ or an insertion. This is equivalent to a row in VCF." + VariantSet: + required: + - variantSetDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + analysiDbIds: + type: array + items: + type: string + callSetCount: + type: integer + format: int32 + referenceSetDbId: + type: string + referenceSetName: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + variantCount: + type: integer + format: int32 + variantSetDbId: + type: string + variantSetName: + type: string + description: A VariantSet is a collection of variants and variant calls intended + to be analyzed together. + VariantSetSearchRequest: + type: object + properties: {} + description: A VariantSet is a collection of variants and variant calls intended + to be analyzed together. + basePagination: + required: + - currentPage + - pageSize + type: object + properties: + currentPage: + type: integer + description: The index number for the returned page of data. This should + always match the requested page number or the default page (0). + example: 0 + default: 0 + pageSize: + type: integer + description: "The number of data elements returned, aka the size of the\ + \ current page. If the requested page does not have enough elements to\ + \ fill a page at the requested page size, this field should indicate the\ + \ actual number of elements returned." + example: 1000 + default: 1000 + totalCount: + type: integer + description: The total number of elements that are available on the server + and match the requested query parameters. + example: 10 + totalPages: + type: integer + description: "The total number of pages of elements available on the server.\ + \ This should be calculated with the following formula. \n
totalPages\ + \ = CEILING( totalCount / requested_page_size)" + example: 1 + description: "The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." + dataFile: + required: + - fileURL + type: object + properties: + fileURL: + type: string + description: The absolute URL where the file is located + format: uri + example: https://wiki.brapi.org/examples/datafile.xlsx + fileName: + type: string + description: The name of the file + example: datafile.xlsx + fileSize: + type: integer + description: The size of the file in bytes + example: 4398 + fileDescription: + type: string + description: A human readable description of the file contents + example: This is an Excel data file + fileType: + type: string + description: The type or format of the file. Preferably MIME Type. + example: application/vnd.ms-excel + fileMD5Hash: + type: string + description: The MD5 Hash of the file contents to be used as a check sum + example: c2365e900c81a89cf74d83dab60df146 + description: A dataFile contains a URL and the relevant file metadata to represent + a file + metadata: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/basePagination" + metadataBase: + type: object + properties: + datafiles: + type: array + description: "The datafiles contains a list of file URLs and metadata. \n\ + These files contain additional information related to the returned object\ + \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ + \ data file, an informational file, the uploaded file where the data originated\ + \ from, a generated file representing the whole dataset in a particular\ + \ format, or any other related file. " + example: [] + items: + $ref: "#/components/schemas/dataFile" + status: + type: array + description: "The status field contains a list of informational status messages\ + \ from the server. \nIf no status is reported, an empty list should be\ + \ returned. See Error Reporting for more information." + items: + $ref: "#/components/schemas/status" + description: "An object in the BrAPI standard response model that describes\ + \ some information about the service call being performed. This includes supplementary\ + \ data, status log messages, and pagination information." + metadataTokenPagination: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/tokenPagination" + status: + required: + - message + - messageType + type: object + properties: + message: + type: string + description: A short message concerning the status of this request/response + example: "Request accepted, response successful" + messageType: + type: string + description: The logging level for the attached message + example: INFO + enum: + - DEBUG + - ERROR + - WARNING + - INFO + description: An array of status messages to convey technical logging information + from the server to the client. + tokenPagination: + allOf: + - $ref: "#/components/schemas/basePagination" + - required: + - nextPageToken + type: object + properties: + nextPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the next page of data." + example: cb668f63 + deprecated: true + currentPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the current page of data." + example: 48bc6ac1 + deprecated: true + prevPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the previous page of data." + example: 9659857e + deprecated: true + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ + \ construct an additional query and move to the next or previous page respectively.\ + \ " + example: + currentPage: 0 + pageSize: 1000 + totalCount: 10 + totalPages: 1 + responses: + SeedLotSingleResponse: + description: OK + content: + application/json: + schema: + title: SeedLotSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/SeedLot" + VariantSingleResponse: + description: OK + content: + application/json: + schema: + title: VariantSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Variant" + "202AcceptedSearchResponse": + description: Accepted + content: + application/json: + schema: + title: 202AcceptedSearchResponse + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + type: object + properties: + searchResultsDbId: + type: string + example: 551ae08c + StudySingleResponse: + description: OK + content: + application/json: + schema: + title: StudySingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Study" + MarkerPositionListResponse: + description: OK + content: + application/json: + schema: + title: MarkerPositionListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/MarkerPosition" + TrialListResponse: + description: OK + content: + application/json: + schema: + title: TrialListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Trial" + SeedLotListResponse: + description: OK + content: + application/json: + schema: + title: SeedLotListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/SeedLot" + VariantSetListResponse: + description: OK + content: + application/json: + schema: + title: VariantSetListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/VariantSet" + SampleSingleResponse: + description: OK + content: + application/json: + schema: + title: SampleSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Sample" + CallSetListResponse: + description: OK + content: + application/json: + schema: + title: CallSetListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/CallSet" + CallSetSingleResponse: + description: OK + content: + application/json: + schema: + title: CallSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/CallSet" + VariantSetSingleResponse: + description: OK + content: + application/json: + schema: + title: VariantSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/VariantSet" + ReferenceSetSingleResponse: + description: OK + content: + application/json: + schema: + title: ReferenceSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ReferenceSet" + CrossListResponse: + description: OK + content: + application/json: + schema: + title: CrossListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Cross" + PlateListResponse: + description: OK + content: + application/json: + schema: + title: PlateListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Plate" + SeasonListResponse: + description: OK + content: + application/json: + schema: + title: SeasonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Season" + ReferenceListResponse: + description: OK + content: + application/json: + schema: + title: ReferenceListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Reference" + AlleleMatrixListResponse: + description: OK + content: + application/json: + schema: + title: AlleleMatrixListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/AlleleMatrix" + GenomeMapSingleResponse: + description: OK + content: + application/json: + schema: + title: GenomeMapSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GenomeMap" + PersonListResponse: + description: OK + content: + application/json: + schema: + title: PersonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Person" + PlannedCrossListResponse: + description: OK + content: + application/json: + schema: + title: PlannedCrossListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/PlannedCross" + LocationListResponse: + description: OK + content: + application/json: + schema: + title: LocationListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Location" + "403Forbidden": + description: Forbidden + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to + perform this action + ProgramListResponse: + description: OK + content: + application/json: + schema: + title: ProgramListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Program" + ListListResponse: + description: OK + content: + application/json: + schema: + title: ListListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/List" + "400BadRequest": + description: Bad Request + content: + application/json: + schema: + type: string + example: |- + ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object + + ERROR - 2018-10-08T18:15:11Z - Invalid query parameter + + ERROR - 2018-10-08T18:15:11Z - Required parameter is missing + CrossingProjectListResponse: + description: OK + content: + application/json: + schema: + title: CrossingProjectListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/CrossingProject" + GermplasmAttributeSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GermplasmAttribute" + "401Unauthorized": + description: Unauthorized + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization + token + GermplasmAttributeListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/GermplasmAttribute" + GermplasmListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Germplasm" + CrossingProjectSingleResponse: + description: OK + content: + application/json: + schema: + title: CrossingProjectSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/CrossingProject" + SampleListResponse: + description: OK + content: + application/json: + schema: + title: SampleListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Sample" + ReferenceSetListResponse: + description: OK + content: + application/json: + schema: + title: ReferenceSetListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/ReferenceSet" + TrialSingleResponse: + description: OK + content: + application/json: + schema: + title: TrialSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Trial" + GermplasmSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Germplasm" + SeasonSingleResponse: + description: OK + content: + application/json: + schema: + title: SeasonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Season" + ReferenceSingleResponse: + description: OK + content: + application/json: + schema: + title: ReferenceSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Reference" + "404NotFound": + description: Not Found + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not + found + StudyListResponse: + description: OK + content: + application/json: + schema: + title: StudyListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Study" + BreedingMethodSingleResponse: + description: OK + content: + application/json: + schema: + title: BreedingMethodSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/BreedingMethod" + CallListResponse: + description: OK + content: + application/json: + schema: + title: CallListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Call" + LocationSingleResponse: + description: OK + content: + application/json: + schema: + title: LocationSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Location" + PersonSingleResponse: + description: OK + content: + application/json: + schema: + title: PersonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Person" + VariantListResponse: + description: OK + content: + application/json: + schema: + title: VariantListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Variant" + PlateSingleResponse: + description: OK + content: + application/json: + schema: + title: PlateSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Plate" + GermplasmAttributeValueListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeValueListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/GermplasmAttributeValue" + BreedingMethodListResponse: + description: OK + content: + application/json: + schema: + title: BreedingMethodListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/BreedingMethod" + GermplasmAttributeValueSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeValueSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GermplasmAttributeValue" + GenomeMapListResponse: + description: OK + content: + application/json: + schema: + title: GenomeMapListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/GenomeMap" + PedigreeNodeListResponse: + description: OK + content: + application/json: + schema: + title: PedigreeNodeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/PedigreeNode" + ListSingleResponse: + description: OK + content: + application/json: + schema: + title: ListSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/List" + ProgramSingleResponse: + description: OK + content: + application/json: + schema: + title: ProgramSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Program" + parameters: + externalReferenceID: + name: externalReferenceID + in: query + description: "**Deprecated in v2.1** Please use `externalReferenceId`. Github\ + \ issue number #460 \n
An external reference ID. Could be a simple string\ + \ or a URI. (use with `externalReferenceSource` parameter)" + required: false + deprecated: true + style: form + explode: true + schema: + type: string + externalReferenceId: + name: externalReferenceId + in: query + description: An external reference ID. Could be a simple string or a URI. (use + with `externalReferenceSource` parameter) + required: false + style: form + explode: true + schema: + type: string + externalReferenceSource: + name: externalReferenceSource + in: query + description: An identifier for the source system or database of an external + reference (use with `externalReferenceId` parameter) + required: false + style: form + explode: true + schema: + type: string + acceptHeader: + name: Accept + in: header + description: "A standard HTTP request header that is used to request a specific\ + \ content type (JSON, CSV, etc) which is \"acceptable\" to the client and\ + \ should be returned by the server" + required: true + style: simple + explode: false + schema: + $ref: "#/components/schemas/ContentTypes" + example: application/json + searchResultsDbId: + name: searchResultsDbId + in: path + description: Unique identifier which references the search results + required: true + style: simple + explode: false + schema: + type: string + pageSize: + name: pageSize + in: query + description: The size of the pages to be returned. Default is `1000`. + required: false + style: form + explode: true + schema: + type: integer + example: 1000 + page: + name: page + in: query + description: |- + Used to request a specific page of data to be returned. + + The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. + required: false + style: form + explode: true + schema: + type: integer + example: "0" + pageToken: + name: pageToken + in: query + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n
\ + \ Tokenized pages are for large data sets which can not be efficiently broken\ + \ into indexed pages. Use the nextPageToken and prevPageToken from a prior\ + \ response to construct a query and move to the next or previous page respectively. " + required: false + deprecated: true + style: form + explode: true + schema: + type: string + example: 33c27874 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX + securitySchemes: + AuthorizationToken: + type: http + description: OAuth Bearer Token - A valid Bearer token to prove authorization + scheme: bearer + bearerFormat: nonce token or JWT diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml new file mode 100644 index 00000000..59d8621c --- /dev/null +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -0,0 +1,3965 @@ +openapi: 3.0.1 +info: + title: BrAPI-Germplasm + version: "2.1" +paths: + /breedingmethods: + get: + tags: + - Germplasm + summary: Get a filtered list of BreedingMethod + description: Get a list of BreedingMethod + parameters: [] + responses: + "200": + $ref: "#/components/responses/BreedingMethodListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /crosses: + get: + tags: + - Crosses + summary: Get a filtered list of Cross + description: Get a list of Cross + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: crossingProjectDbId + in: query + description: Search for Crossing Projects with this unique id + required: false + schema: + type: string + - name: crossingProjectName + in: query + description: The human readable name for a crossing project + required: false + schema: + type: string + - name: crossDbId + in: query + description: Search for Cross with this unique id + required: false + schema: + type: string + - name: crossName + in: query + description: Search for Cross with this human readable name + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/CrossListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Crosses + summary: Update the details for an existing Cross + description: Update the details for an existing Cross + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CrossNewRequest" + responses: + "200": + $ref: "#/components/responses/CrossListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Crosses + summary: Create new Cross + description: Add new Cross to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CrossNewRequest" + responses: + "200": + $ref: "#/components/responses/CrossListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /crossingprojects: + get: + tags: + - CrossingProjects + summary: Get a filtered list of CrossingProject + description: Get a list of CrossingProject + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: crossingProjectDbId + in: query + description: Search for Crossing Projects with this unique id + required: false + schema: + type: string + - name: crossingProjectName + in: query + description: The human readable name for a crossing project + required: false + schema: + type: string + - name: includePotentialParent + in: query + description: "If the parameter 'includePotentialParents' is false, the array\ + \ 'potentialParents' should be empty, null, or excluded from the response\ + \ object." + required: false + schema: + type: boolean + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/CrossingProjectListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - CrossingProjects + summary: Create new CrossingProject + description: Add new CrossingProject to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CrossingProjectNewRequest" + responses: + "200": + $ref: "#/components/responses/CrossingProjectListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /germplasm: + get: + tags: + - Germplasm + summary: Get a filtered list of Germplasm + description: Get a list of Germplasm + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: germplasmPUI + in: query + description: List of Permanent Unique Identifiers to identify germplasm + required: false + schema: + type: string + - name: accessionNumber + in: query + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + required: false + schema: + type: string + - name: collection + in: query + description: A specific panel/collection/population name this germplasm belongs + to. + required: false + schema: + type: string + - name: familyCode + in: query + description: A familyCode representing the family this germplasm belongs to. + required: false + schema: + type: string + - name: instituteCode + in: query + description: "The code for the institute that maintains the material. \n
\ + \ MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession\ + \ is maintained. The codes consist of the 3-letter ISO 3166 country code\ + \ of the country where the institute is located plus a number (e.g. PER001).\ + \ The current set of institute codes is available from http://www.fao.org/wiews.\ + \ For those institutes not yet having an FAO Code, or for those with \"\ + obsolete\" codes, see \"Common formatting rules (v)\"." + required: false + schema: + type: string + - name: binomialName + in: query + description: List of the full binomial name (scientific name) to identify + a germplasm + required: false + schema: + type: string + - name: genu + in: query + description: List of Genus names to identify germplasm + required: false + schema: + type: string + - name: specy + in: query + description: List of Species names to identify germplasm + required: false + schema: + type: string + - name: synonym + in: query + description: List of alternative names or IDs used to reference this germplasm + required: false + schema: + type: string + - name: parentDbId + in: query + description: Search for Germplasm with these parents + required: false + schema: + type: string + - name: progenyDbId + in: query + description: Search for Germplasm with these children + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/GermplasmListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Germplasm + summary: Create new Germplasm + description: Add new Germplasm to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmNewRequest" + responses: + "200": + $ref: "#/components/responses/GermplasmListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /attributes: + get: + tags: + - GermplasmAttributes + summary: Get a filtered list of GermplasmAttribute + description: Get a list of GermplasmAttribute + parameters: + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: methodDbId + in: query + description: List of methods to filter search results + required: false + schema: + type: string + - name: methodName + in: query + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + required: false + schema: + type: string + - name: methodPUI + in: query + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + required: false + schema: + type: string + - name: scaleDbId + in: query + description: The unique identifier for a Scale + required: false + schema: + type: string + - name: scaleName + in: query + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + required: false + schema: + type: string + - name: scalePUI + in: query + description: "The Permanent Unique Identifier of a Scale, usually in the form\ + \ of a URI" + required: false + schema: + type: string + - name: traitDbId + in: query + description: The unique identifier for a Trait + required: false + schema: + type: string + - name: traitName + in: query + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + required: false + schema: + type: string + - name: traitPUI + in: query + description: "The Permanent Unique Identifier of a Trait, usually in the form\ + \ of a URI" + required: false + schema: + type: string + - name: attributeDbId + in: query + description: List of Germplasm Attribute IDs to search for + required: false + schema: + type: string + - name: attributeName + in: query + description: List of human readable Germplasm Attribute names to search for + required: false + schema: + type: string + - name: attributePUI + in: query + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + required: false + schema: + type: string + - name: attributeCategory + in: query + description: General category for the attribute. very similar to Trait class. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - GermplasmAttributes + summary: Create new GermplasmAttribute + description: Add new GermplasmAttribute to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmAttributeNewRequest" + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /attributevalues: + get: + tags: + - GermplasmAttributeValues + summary: Get a filtered list of GermplasmAttributeValue + description: Get a list of GermplasmAttributeValue + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: attributeValueDbId + in: query + description: List of Germplasm Attribute Value IDs to search for + required: false + schema: + type: string + - name: attributeDbId + in: query + description: List of Germplasm Attribute IDs to search for + required: false + schema: + type: string + - name: attributeName + in: query + description: List of human readable Germplasm Attribute names to search for + required: false + schema: + type: string + - name: ontologyDbId + in: query + description: List of ontology IDs to search for + required: false + schema: + type: string + - name: methodDbId + in: query + description: List of methods to filter search results + required: false + schema: + type: string + - name: scaleDbId + in: query + description: List of scales to filter search results + required: false + schema: + type: string + - name: traitDbId + in: query + description: List of trait unique ID to filter search results + required: false + schema: + type: string + - name: traitClass + in: query + description: List of trait classes to filter search results + required: false + schema: + type: string + - name: dataType + in: query + description: List of scale data types to filter search results + required: false + schema: + $ref: "#/components/schemas/TraitDataType" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeValueListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - GermplasmAttributeValues + summary: Create new GermplasmAttributeValue + description: Add new GermplasmAttributeValue to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmAttributeValueNewRequest" + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeValueListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /pedigree: + get: + tags: + - PedigreeNodes + summary: Get a filtered list of PedigreeNode + description: Get a list of PedigreeNode + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: germplasmPUI + in: query + description: List of Permanent Unique Identifiers to identify germplasm + required: false + schema: + type: string + - name: accessionNumber + in: query + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + required: false + schema: + type: string + - name: collection + in: query + description: A specific panel/collection/population name this germplasm belongs + to. + required: false + schema: + type: string + - name: familyCode + in: query + description: A familyCode representing the family this germplasm belongs to. + required: false + schema: + type: string + - name: instituteCode + in: query + description: "The code for the institute that maintains the material. \n
\ + \ MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession\ + \ is maintained. The codes consist of the 3-letter ISO 3166 country code\ + \ of the country where the institute is located plus a number (e.g. PER001).\ + \ The current set of institute codes is available from http://www.fao.org/wiews.\ + \ For those institutes not yet having an FAO Code, or for those with \"\ + obsolete\" codes, see \"Common formatting rules (v)\"." + required: false + schema: + type: string + - name: binomialName + in: query + description: List of the full binomial name (scientific name) to identify + a germplasm + required: false + schema: + type: string + - name: genu + in: query + description: List of Genus names to identify germplasm + required: false + schema: + type: string + - name: specy + in: query + description: List of Species names to identify germplasm + required: false + schema: + type: string + - name: synonym + in: query + description: List of alternative names or IDs used to reference this germplasm + required: false + schema: + type: string + - name: includeParent + in: query + description: "If this parameter is true, include the array of parents in the\ + \ response" + required: false + schema: + type: boolean + - name: includeSibling + in: query + description: "If this parameter is true, include the array of siblings in\ + \ the response" + required: false + schema: + type: boolean + - name: includeProgeny + in: query + description: "If this parameter is true, include the array of progeny in the\ + \ response" + required: false + schema: + type: boolean + - name: includeFullTree + in: query + description: "If this parameter is true, recursively include ALL of the nodes\ + \ available in this pedigree tree" + required: false + schema: + type: boolean + - name: pedigreeDepth + in: query + description: "Recursively include this number of levels up the tree in the\ + \ response (parents, grand-parents, great-grand-parents, etc)" + required: false + schema: + type: integer + format: int32 + - name: progenyDepth + in: query + description: "Recursively include this number of levels down the tree in the\ + \ response (children, grand-children, great-grand-children, etc)" + required: false + schema: + type: integer + format: int32 + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/PedigreeNodeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - PedigreeNodes + summary: Create new PedigreeNode + description: Add new PedigreeNode to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PedigreeNode" + responses: + "200": + $ref: "#/components/responses/PedigreeNodeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /plannedcrosses: + get: + tags: + - Crosses + summary: Get a filtered list of PlannedCross + description: Get a list of PlannedCross + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: crossingProjectDbId + in: query + description: Search for Crossing Projects with this unique id + required: false + schema: + type: string + - name: crossingProjectName + in: query + description: The human readable name for a crossing project + required: false + schema: + type: string + - name: plannedCrossDbId + in: query + description: Search for Planned Cross with this unique id + required: false + schema: + type: string + - name: plannedCrossName + in: query + description: Search for Planned Cross with this human readable name + required: false + schema: + type: string + - name: status + in: query + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not been\ + \ done on purpose ('SKIPPED')." + required: false + schema: + type: string + enum: + - TODO + - DONE + - SKIPPED + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/PlannedCrossListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Crosses + summary: Update the details for an existing PlannedCross + description: Update the details for an existing PlannedCross + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PlannedCross" + responses: + "200": + $ref: "#/components/responses/PlannedCrossListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Crosses + summary: Create new PlannedCross + description: Add new PlannedCross to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PlannedCross" + responses: + "200": + $ref: "#/components/responses/PlannedCrossListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /seedlots: + get: + tags: + - SeedLots + summary: Get a filtered list of SeedLot + description: Get a list of SeedLot + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: seedLotDbId + in: query + description: Unique id for a seed lot on this server + required: false + schema: + type: string + - name: crossDbId + in: query + description: Search for Cross with this unique id + required: false + schema: + type: string + - name: crossName + in: query + description: Search for Cross with this human readable name + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/SeedLotListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - SeedLots + summary: Create new SeedLot + description: Add new SeedLot to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SeedLotNewRequest" + responses: + "200": + $ref: "#/components/responses/SeedLotListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /breedingmethods/{breedingMethodDbId}: + get: + tags: + - Germplasm + summary: Get the details of a specific BreedingMethod + description: Get details for a BreedingMethod + responses: + "200": + $ref: "#/components/responses/BreedingMethodSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /crossingprojects/{crossingProjectDbId}: + get: + tags: + - CrossingProjects + summary: Get the details of a specific CrossingProject + description: Get details for a CrossingProject + responses: + "200": + $ref: "#/components/responses/CrossingProjectSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - CrossingProjects + summary: Update the details for an existing CrossingProject + description: Update the details for an existing CrossingProject + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CrossingProjectNewRequest" + responses: + "200": + $ref: "#/components/responses/CrossingProjectSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /germplasm/{germplasmDbId}: + get: + tags: + - Germplasm + summary: Get the details of a specific Germplasm + description: Get details for a Germplasm + responses: + "200": + $ref: "#/components/responses/GermplasmSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Germplasm + summary: Update the details for an existing Germplasm + description: Update the details for an existing Germplasm + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmNewRequest" + responses: + "200": + $ref: "#/components/responses/GermplasmSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /attributes/{attributeDbId}: + get: + tags: + - GermplasmAttributes + summary: Get the details of a specific GermplasmAttribute + description: Get details for a GermplasmAttribute + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - GermplasmAttributes + summary: Update the details for an existing GermplasmAttribute + description: Update the details for an existing GermplasmAttribute + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmAttributeNewRequest" + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /attributevalues/{attributeValueDbId}: + get: + tags: + - GermplasmAttributeValues + summary: Get the details of a specific GermplasmAttributeValue + description: Get details for a GermplasmAttributeValue + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeValueSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - GermplasmAttributeValues + summary: Update the details for an existing GermplasmAttributeValue + description: Update the details for an existing GermplasmAttributeValue + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmAttributeValueNewRequest" + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeValueSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /seedlots/{seedLotDbId}: + get: + tags: + - SeedLots + summary: Get the details of a specific SeedLot + description: Get details for a SeedLot + responses: + "200": + $ref: "#/components/responses/SeedLotSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - SeedLots + summary: Update the details for an existing SeedLot + description: Update the details for an existing SeedLot + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SeedLotNewRequest" + responses: + "200": + $ref: "#/components/responses/SeedLotSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/germplasm: + post: + tags: + - Germplasm + summary: Submit a search request for `Germplasm` + description: "Submit a search request for `Germplasm`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve\ + \ the results of the search.
\nReview the Search\ + \ Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/GermplasmListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/attributes: + post: + tags: + - GermplasmAttributes + summary: Submit a search request for `GermplasmAttribute` + description: "Submit a search request for `GermplasmAttribute`
\nSearch\ + \ requests allow a client to send a complex query for data. However, the server\ + \ may not respond with the search results immediately. \nIf a server needs\ + \ more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/attributevalues: + post: + tags: + - GermplasmAttributeValues + summary: Submit a search request for `GermplasmAttributeValue` + description: "Submit a search request for `GermplasmAttributeValue`
\nSearch\ + \ requests allow a client to send a complex query for data. However, the server\ + \ may not respond with the search results immediately. \nIf a server needs\ + \ more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeValueListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/pedigree: + post: + tags: + - PedigreeNodes + summary: Submit a search request for `PedigreeNode` + description: "Submit a search request for `PedigreeNode`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to\ + \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/PedigreeNodeListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/germplasm/{searchResultsDbId}: + get: + tags: + - Germplasm + summary: "Submit a search request for `Germplasm`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Germplasm` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/germplasm`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/GermplasmListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/attributes/{searchResultsDbId}: + get: + tags: + - GermplasmAttributes + summary: "Submit a search request for `GermplasmAttribute`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `GermplasmAttribute` search request
\n\ + Clients should submit a search request using the corresponding `POST /search/germplasmAttribute`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/attributevalues/{searchResultsDbId}: + get: + tags: + - GermplasmAttributeValues + summary: "Submit a search request for `GermplasmAttributeValue`
\nSearch\ + \ requests allow a client to send a complex query for data. However, the server\ + \ may not respond with the search results immediately. \nIf a server needs\ + \ more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `GermplasmAttributeValue` search request\ + \
\nClients should submit a search request using the corresponding `POST\ + \ /search/germplasmAttributeValue` endpoint.\nSearch requests allow a client\ + \ to send a complex query for data. However, the server may not respond with\ + \ the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse this endpoint\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeValueListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/pedigree/{searchResultsDbId}: + get: + tags: + - PedigreeNodes + summary: "Submit a search request for `PedigreeNode`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of\ + \ the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `PedigreeNode` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/pedigreeNode`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/PedigreeNodeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" +components: + schemas: + AdditionalInfo: + type: object + properties: + additionalProperties: + type: string + description: "A free space containing any additional information related to\ + \ a particular object. A data source may provide any JSON object, unrestricted\ + \ by the BrAPI specification." + Attribute: + required: + - attributeName + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeCategory: + type: string + attributeDbId: + type: string + attributeDescription: + type: string + attributeName: + type: string + attributePUI: + type: string + commonCropName: + type: string + contextOfUse: + type: array + items: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + method: + $ref: "#/components/schemas/Method" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + synonyms: + type: array + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + BreedingMethod: + required: + - abbreviation + - breedingMethodDbId + - breedingMethodName + - description + type: object + properties: + abbreviation: + type: string + breedingMethodDbId: + type: string + breedingMethodName: + type: string + description: + type: string + description: The techniques and protocol used to produce a Cross or Germplasm + Contact: + required: + - contactDbId + type: object + properties: + contactDbId: + type: string + email: + type: string + instituteName: + type: string + name: + type: string + orcid: + type: string + type: + type: string + description: A persons contact information + ContentMixture: + type: object + properties: + crossDbId: + type: string + crossName: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + mixturePercentage: + type: integer + format: int32 + seedLotDbId: + type: string + seedLotName: + type: string + description: "The mixture of germplasm present in the seed lot. \n
If this\ + \ seed lot only contains a single germplasm, the response should contain the\ + \ name and DbId of that germplasm with a mixturePercentage value of 100 \n\ +
If the seed lot contains a mixture of different germplasm, the response\ + \ should contain the name and DbId every germplasm present. The mixturePercentage\ + \ field should contain the ratio of each germplasm in the total mixture. All\ + \ of the mixturePercentage values in this array should sum to equal 100." + ContentTypes: + type: string + enum: + - application/json + - text/csv + - text/tsv + - application/flapjack + Context: + title: context + type: array + description: "The JSON-LD Context is used to provide JSON-LD definitions to\ + \ each field in a JSON object. By providing an array of context file urls,\ + \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ + \ see https://w3c.github.io/json-ld-syntax/#the-context" + example: + - https://brapi.org/jsonld/context/metadata.jsonld + items: + type: string + format: uri + Cross: + required: + - crossDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + crossName: + type: string + crossType: + $ref: "#/components/schemas/CrossType" + crossingProjectDbId: + type: string + crossingProjectName: + type: string + parent1: + $ref: "#/components/schemas/CrossParent" + parent2: + $ref: "#/components/schemas/CrossParent" + plannedCrossDbId: + type: string + plannedCrossName: + type: string + description: The identifiers and metadata represent that specific organisms + have mated to produce offspring with particular traits or genes. The offspring + of a Cross might be developed into a Germplasm if the desired traits are present. + CrossAttribute: + type: object + properties: + crossAttributeName: + type: string + crossAttributeValue: + type: string + crossDbId: + type: string + crossName: + type: string + description: "A custom attribute associated with a cross. For example, if the\ + \ crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative\ + \ Humidity', 'crossAttributeValue':'80%'" + CrossNewRequest: + required: + - crossDbId + - crossDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + crossDbId: + type: string + crossName: + type: string + crossType: + $ref: "#/components/schemas/CrossType" + crossingProjectDbId: + type: string + crossingProjectName: + type: string + parent1: + $ref: "#/components/schemas/CrossParent" + parent2: + $ref: "#/components/schemas/CrossParent" + plannedCrossDbId: + type: string + plannedCrossName: + type: string + description: The identifiers and metadata represent that specific organisms + have mated to produce offspring with particular traits or genes. The offspring + of a Cross might be developed into a Germplasm if the desired traits are present. + CrossParent: + type: object + properties: + germplasm: + $ref: "#/components/schemas/Germplasm" + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + parentType: + $ref: "#/components/schemas/ParentType" + description: The identifying information gor the parent material of a cross. + CrossType: + type: string + description: "The type of cross make. Accepted values for this field are 'BIPARENTAL',\ + \ 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED'\ + \ and 'DOUBLE_HAPLOID'." + enum: + - BIPARENTAL + - SELF + - OPEN_POLLINATED + - BULK + - BULK_SELFED + - BULK_OPEN_POLLINATED + - DOUBLE_HAPLOID + CrossingProject: + required: + - crossingProjectDbId + - crossingProjectName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + crossingProjectDescription: + type: string + crossingProjectName: + type: string + programDbId: + type: string + programName: + type: string + description: "A project structure where a list of PlannedCrosses is generated,\ + \ the crossing events occur in the field, and the resulting actual Crosses\ + \ can documented." + CrossingProjectNewRequest: + required: + - crossingProjectDbId + - crossingProjectDbId + - crossingProjectName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + crossingProjectDbId: + type: string + crossingProjectDescription: + type: string + crossingProjectName: + type: string + programDbId: + type: string + programName: + type: string + description: "A project structure where a list of PlannedCrosses is generated,\ + \ the crossing events occur in the field, and the resulting actual Crosses\ + \ can documented." + Donor: + type: object + properties: + donorAccessionNumber: + type: string + donorInstituteCode: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + description: Identifier assigned to an accession by the material donor. + ExperimentalDesign: + type: object + properties: + PUI: + type: string + description: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: The experimental and statistical design full description plus a + category PUI taken from crop research ontology or agronomy ontology + ExternalReference: + type: object + properties: + referenceId: + type: string + referenceSource: + type: string + GeoJSON: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + type: + type: string + description: |- + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONGeometry: + oneOf: + - required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + items: + type: number + type: + type: string + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + - required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." + GeoJSONSearchArea: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + germplasmOrigin: + $ref: "#/components/schemas/GermplasmOrigin" + imageDbId: + type: string + imageName: + type: string + observationDbId: + type: string + observationUnit: + $ref: "#/components/schemas/ObservationUnitPosition" + type: + type: string + Germplasm: + required: + - commonCropName + - germplasmDbId + - germplasmName + - germplasmPUI + type: object + properties: + accessionNumber: + type: string + acquisitionDate: + type: string + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + biologicalStatusOfAccessionCode: + type: string + description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can\ + \ be used at 3 different levels of detail: either by using the general\ + \ codes such as 100, 200, 300, 400, or by using the more specific codes\ + \ such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild\ + \ \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace\ + \ \n400) Breeding/research material \n410) Breeders line \n411) Synthetic\ + \ population \n412) Hybrid \n413) Founder stock/base population \n414)\ + \ Inbred line (parent of hybrid cultivar) \n415) Segregating population\ + \ \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion\ + \ mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome\ + \ addition/substitution, aneuploids, amphiploids) \n423) Other genetic\ + \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ + \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ + \ \n999) Other (Elaborate in REMARKS field)" + enum: + - "100" + - "110" + - "120" + - "130" + - "200" + - "300" + - "400" + - "410" + - "411" + - "412" + - "413" + - "414" + - "415" + - "416" + - "420" + - "421" + - "422" + - "423" + - "500" + - "600" + - "999" + biologicalStatusOfAccessionDescription: + type: string + breedingMethodDbId: + type: string + breedingMethodName: + type: string + collection: + type: string + commonCropName: + type: string + countryOfOriginCode: + type: string + defaultDisplayName: + type: string + documentationURL: + type: string + genus: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + germplasmPreprocessing: + type: string + instituteCode: + type: string + instituteName: + type: string + pedigree: + type: string + sampleDbIds: + type: array + items: + type: string + seedSource: + type: string + seedSourceDescription: + type: string + species: + type: string + speciesAuthority: + type: string + subtaxa: + type: string + subtaxaAuthority: + type: string + description: "The conceptual identifiers and metadata describing a genetically\ + \ unique organism that is noteworthy in some way. Depending on context, a\ + \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ + \ Germplasm is conceptual data, not necessarily associated to a real physical\ + \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ + \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ + \ a Cross may or may not create a new Germplasm, since not every Cross is\ + \ unique or noteworthy." + GermplasmAttribute: + required: + - attributeDbId + - attributeName + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeCategory: + type: string + attributeDescription: + type: string + attributeName: + type: string + attributePUI: + type: string + attributeValueDbIds: + type: array + items: + type: string + commonCropName: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReferenceDbId: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string + description: "The Trait-Method-Scale definition for a variable, specifically\ + \ variables related to Germplasm. Similar to an ObservationVariable, but related\ + \ to a Germplasm instead of an ObservationUnit" + GermplasmAttributeNewRequest: + required: + - attributeDbId + - attributeName + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeCategory: + type: string + attributeDbId: + type: string + attributeDescription: + type: string + attributeName: + type: string + attributePUI: + type: string + attributeValueDbIds: + type: array + items: + type: string + commonCropName: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReferenceDbId: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string + description: "The Trait-Method-Scale definition for a variable, specifically\ + \ variables related to Germplasm. Similar to an ObservationVariable, but related\ + \ to a Germplasm instead of an ObservationUnit" + GermplasmAttributeSearchRequest: + type: object + properties: {} + description: "The Trait-Method-Scale definition for a variable, specifically\ + \ variables related to Germplasm. Similar to an ObservationVariable, but related\ + \ to a Germplasm instead of an ObservationUnit" + GermplasmAttributeValue: + required: + - attributeName + - attributeValueDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeDbId: + type: string + attributeName: + type: string + attributePUI: + type: string + determinedDate: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + value: + type: string + description: "The value recorded for a particular Trait/Attribute and a particular\ + \ Germplasm. Similar to an Observation value, but more concrete, applying\ + \ to the whole Germplasm instead of a single ObservationUnit." + GermplasmAttributeValueNewRequest: + required: + - attributeName + - attributeValueDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeDbId: + type: string + attributeName: + type: string + attributePUI: + type: string + attributeValueDbId: + type: string + determinedDate: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + value: + type: string + description: "The value recorded for a particular Trait/Attribute and a particular\ + \ Germplasm. Similar to an Observation value, but more concrete, applying\ + \ to the whole Germplasm instead of a single ObservationUnit." + GermplasmAttributeValueSearchRequest: + type: object + properties: {} + description: "The value recorded for a particular Trait/Attribute and a particular\ + \ Germplasm. Similar to an Observation value, but more concrete, applying\ + \ to the whole Germplasm instead of a single ObservationUnit." + GermplasmChild: + required: + - germplasmDbId + - germplasmName + - germplasmPUI + - parentType + type: object + properties: + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + parentType: + $ref: "#/components/schemas/ParentType" + pedigreeNodeDbId: + type: string + description: "A germplasm reference that is a direct child of this germplasm.\ + \ These represent edges in the tree, connecting to other nodes." + GermplasmNewRequest: + required: + - commonCropName + - germplasmDbId + - germplasmDbId + - germplasmName + - germplasmPUI + type: object + properties: + accessionNumber: + type: string + acquisitionDate: + type: string + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + biologicalStatusOfAccessionCode: + type: string + description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can\ + \ be used at 3 different levels of detail: either by using the general\ + \ codes such as 100, 200, 300, 400, or by using the more specific codes\ + \ such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild\ + \ \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace\ + \ \n400) Breeding/research material \n410) Breeders line \n411) Synthetic\ + \ population \n412) Hybrid \n413) Founder stock/base population \n414)\ + \ Inbred line (parent of hybrid cultivar) \n415) Segregating population\ + \ \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion\ + \ mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome\ + \ addition/substitution, aneuploids, amphiploids) \n423) Other genetic\ + \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ + \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ + \ \n999) Other (Elaborate in REMARKS field)" + enum: + - "100" + - "110" + - "120" + - "130" + - "200" + - "300" + - "400" + - "410" + - "411" + - "412" + - "413" + - "414" + - "415" + - "416" + - "420" + - "421" + - "422" + - "423" + - "500" + - "600" + - "999" + biologicalStatusOfAccessionDescription: + type: string + breedingMethodDbId: + type: string + breedingMethodName: + type: string + collection: + type: string + commonCropName: + type: string + countryOfOriginCode: + type: string + defaultDisplayName: + type: string + documentationURL: + type: string + genus: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + germplasmPreprocessing: + type: string + instituteCode: + type: string + instituteName: + type: string + pedigree: + type: string + sampleDbIds: + type: array + items: + type: string + seedSource: + type: string + seedSourceDescription: + type: string + species: + type: string + speciesAuthority: + type: string + subtaxa: + type: string + subtaxaAuthority: + type: string + description: "The conceptual identifiers and metadata describing a genetically\ + \ unique organism that is noteworthy in some way. Depending on context, a\ + \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ + \ Germplasm is conceptual data, not necessarily associated to a real physical\ + \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ + \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ + \ a Cross may or may not create a new Germplasm, since not every Cross is\ + \ unique or noteworthy." + GermplasmOrigin: + type: object + properties: + coordinateUncertainty: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + description: "Information for material (orchard, natural sites, ...). Geographic\ + \ identification of the plants from which seeds or cutting have been taken\ + \ to produce that germplasm." + GermplasmParent: + required: + - germplasmDbId + - germplasmName + - germplasmPUI + - parentType + type: object + properties: + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + parentType: + $ref: "#/components/schemas/ParentType" + pedigreeNodeDbId: + type: string + description: "A germplasm reference that is a direct parent of this germplasm.\ + \ These represent edges in the tree, connecting to other nodes." + GermplasmSearchRequest: + type: object + properties: {} + description: "The conceptual identifiers and metadata describing a genetically\ + \ unique organism that is noteworthy in some way. Depending on context, a\ + \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ + \ Germplasm is conceptual data, not necessarily associated to a real physical\ + \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ + \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ + \ a Cross may or may not create a new Germplasm, since not every Cross is\ + \ unique or noteworthy." + GrowthFacility: + type: object + properties: + PUI: + type: string + description: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: Short description of the facility in which the study was carried + out. + ListType: + type: string + description: The type of objects that are referenced in a List + enum: + - germplasm + - markers + - variants + - programs + - trials + - studies + - observationUnits + - observations + - observationVariables + - samples + Method: + required: + - methodDbId + - methodName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + bibliographicalReference: + type: string + description: + type: string + formula: + type: string + methodClass: + type: string + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReferenceDbId: + type: string + description: "A description of the way an Observation should be collected. \n\ +
For example, an ObservationVariable might be defined with a Trait of \"\ + plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ + \ variable would be distinct from a variable with the Method \"estimation\"\ + \ or \"drone image processing\". " + ObservationUnitHierarchyLevel: + type: object + properties: + levelName: + type: string + levelOrder: + type: integer + format: int32 + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitPosition: + type: object + properties: + entryType: + type: string + description: "The type of entry for this observation unit. ex. \"CHECK\"\ + , \"TEST\", \"FILLER\"" + enum: + - CHECK + - TEST + - FILLER + observationLevel: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + positionCoordinateX: + type: string + positionCoordinateXType: + $ref: "#/components/schemas/PositionCoordinateType" + positionCoordinateY: + type: string + positionCoordinateYType: + $ref: "#/components/schemas/PositionCoordinateType" + description: All positional and layout information related to this Observation + Unit + OntologyReference: + required: + - ontology + type: object + properties: + ontology: + $ref: "#/components/schemas/Ontology" + ontologyReferenceDbId: + type: string + version: + type: string + description: "MIAPPE V1.1 (DM-85) Variable accession number - Accession number\ + \ of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession\ + \ number - Accession number of the trait in a suitable controlled vocabulary\ + \ (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number\ + \ - Accession number of the method in a suitable controlled vocabulary (Crop\ + \ Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number -\ + \ Accession number of the scale in a suitable controlled vocabulary (Crop\ + \ Ontology)." + OntologyTerm: + type: object + properties: + term: + type: string + termURI: + type: string + description: A pointer to an ontology used by a genomic reference + ParentType: + type: string + description: "The type of parent used during crossing. Accepted values for this\ + \ field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn\ + \ a pedigree record, the 'parentType' describes each parent of a particular\ + \ germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe\ + \ how this germplasm was crossed to generate a particular progeny. \\nFor\ + \ example, given a record for germplasm A, having a progeny B and C. The 'parentType'\ + \ field for progeny B item refers \\nto the 'parentType' of A toward B. The\ + \ 'parentType' field for progeny C item refers to the 'parentType' of A toward\ + \ C.\\nIn this way, A could be a male parent to B, but a female parent to\ + \ C. " + enum: + - MALE + - FEMALE + - SELF + - POPULATION + - CLONAL + PedigreeNode: + required: + - germplasmDbId + - germplasmName + - germplasmPUI + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + breedingMethodDbId: + type: string + breedingMethodName: + type: string + crossingProjectDbId: + type: string + crossingProjectName: + type: string + crossingYear: + type: integer + format: int32 + defaultDisplayName: + type: string + familyCode: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + pedigreeNodeDbId: + type: string + pedigreeString: + type: string + siblingDbIds: + type: array + items: + type: string + description: "A representation of a particular Germplasm within a pedigree tree,\ + \ and all the links to its parents, siblings, and children. From a list of\ + \ PedigreeNode objects, a client application should have all the information\ + \ it needs to draw a pedigree tree visualization, or calculate genetic distances." + PedigreeNodeSearchRequest: + type: object + properties: + includeFullTree: + type: boolean + includeParents: + type: boolean + includeProgeny: + type: boolean + includeSiblings: + type: boolean + pedigreeDepth: + type: integer + format: int32 + progenyDepth: + type: integer + format: int32 + description: "A representation of a particular Germplasm within a pedigree tree,\ + \ and all the links to its parents, siblings, and children. From a list of\ + \ PedigreeNode objects, a client application should have all the information\ + \ it needs to draw a pedigree tree visualization, or calculate genetic distances." + PlannedCross: + required: + - plannedCrossDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + crossType: + $ref: "#/components/schemas/CrossType" + crossingProjectDbId: + type: string + crossingProjectName: + type: string + parent1: + $ref: "#/components/schemas/CrossParent" + parent2: + $ref: "#/components/schemas/CrossParent" + plannedCrossDbId: + type: string + plannedCrossName: + type: string + status: + type: string + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ + \ been done on purpose ('SKIPPED')." + enum: + - TODO + - DONE + - SKIPPED + description: Information regarding the intention to mate specific organisms + together to produce offspring with desired traits. A PlannedCross becomes + an actual Cross when the desired mating event actually occurs in the field. + PollinationEvent: + type: object + properties: + crossDbId: + type: string + crossName: + type: string + pollinationNumber: + type: string + pollinationSuccessful: + type: boolean + pollinationTimeStamp: + type: string + description: A Pollination Event that was used or attempted for a Cross. + Scale: + required: + - scaleDbId + - scaleName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + dataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + decimalPlaces: + type: integer + format: int32 + ontologyReferenceDbId: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + units: + type: string + validValues: + $ref: "#/components/schemas/ValidValues" + description: "A Scale describes the units and acceptable values for an ObservationVariable.\ + \ \n
For example, an ObservationVariable might be defined with a Trait\ + \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ + . This variable would be distinct from a variable with the Scale \"inches\"\ + \ or \"pixels\"." + SeedLot: + required: + - seedLotDbId + - seedLotName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + amount: + type: number + createdDate: + type: string + lastUpdated: + type: string + locationDbId: + type: string + locationName: + type: string + programDbId: + type: string + programName: + type: string + seedLotDescription: + type: string + seedLotName: + type: string + sourceCollection: + type: string + storageLocation: + type: string + units: + type: string + description: "A SeedLot, also known as an InventoryLot, is a collection of starting\ + \ material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The\ + \ amount of material available for each Germplasm can be increased by seed\ + \ production and decreased by planting or trading with another breeding Program." + SeedLotNewRequest: + required: + - seedLotDbId + - seedLotDbId + - seedLotName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + amount: + type: number + createdDate: + type: string + lastUpdated: + type: string + locationDbId: + type: string + locationName: + type: string + programDbId: + type: string + programName: + type: string + seedLotDbId: + type: string + seedLotDescription: + type: string + seedLotName: + type: string + sourceCollection: + type: string + storageLocation: + type: string + units: + type: string + description: "A SeedLot, also known as an InventoryLot, is a collection of starting\ + \ material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The\ + \ amount of material available for each Germplasm can be increased by seed\ + \ production and decreased by planting or trading with another breeding Program." + SeedLotTransaction: + required: + - transactionDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + amount: + type: number + seedLotDbId: + type: string + seedLotName: + type: string + transactionDbId: + type: string + transactionDescription: + type: string + transactionTimestamp: + type: string + units: + type: string + description: The record of an event where material was moved in or out of a + particular SeedLot + StorageType: + type: object + properties: + code: + type: string + description: "The 2 digit code representing the type of storage this germplasm\ + \ is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm\ + \ is maintained under different types of storage, multiple choices are\ + \ allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI\ + \ Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection\ + \ \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection\ + \ \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA\ + \ collection \n99) Other (elaborate in REMARKS field)" + enum: + - "10" + - "11" + - "12" + - "13" + - "20" + - "30" + - "40" + - "50" + - "99" + description: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + description: The type of storage this germplasm is kept in at a genebank. + Synonym: + type: object + properties: + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + synonym: + type: string + type: + type: string + description: Alternative names or IDs used to reference this germplasm + TaxonId: + required: + - sourceName + - taxonId + type: object + properties: + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + sourceName: + type: string + taxonId: + type: string + description: "The list of IDs for this SPECIES from different sources. If present,\ + \ NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl.\ + \ The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism\ + \ - An identifier for the organism at the species level. Use of the NCBI taxon\ + \ ID is recommended." + Trait: + required: + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attribute: + type: string + attributePUI: + type: string + entity: + type: string + entityPUI: + type: string + mainAbbreviation: + type: string + ontologyReferenceDbId: + type: string + status: + type: string + traitClass: + type: string + traitDbId: + type: string + traitDescription: + type: string + traitName: + type: string + traitPUI: + type: string + description: "A Trait describes what property is being observed. \n
For example,\ + \ an ObservationVariable might be defined with a Trait of \"plant height\"\ + , a Scale of \"meters\", and a Method of \"tape measure\". This variable would\ + \ be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\"\ + . " + TraitDataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + Variable: + required: + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + contextOfUse: + type: array + items: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + method: + $ref: "#/components/schemas/Method" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + synonyms: + type: array + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + description: "A unique combination of Trait, Method, and Scale to define a clear\ + \ context for an Observation." + basePagination: + required: + - currentPage + - pageSize + type: object + properties: + currentPage: + type: integer + description: The index number for the returned page of data. This should + always match the requested page number or the default page (0). + example: 0 + default: 0 + pageSize: + type: integer + description: "The number of data elements returned, aka the size of the\ + \ current page. If the requested page does not have enough elements to\ + \ fill a page at the requested page size, this field should indicate the\ + \ actual number of elements returned." + example: 1000 + default: 1000 + totalCount: + type: integer + description: The total number of elements that are available on the server + and match the requested query parameters. + example: 10 + totalPages: + type: integer + description: "The total number of pages of elements available on the server.\ + \ This should be calculated with the following formula. \n
totalPages\ + \ = CEILING( totalCount / requested_page_size)" + example: 1 + description: "The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." + dataFile: + required: + - fileURL + type: object + properties: + fileURL: + type: string + description: The absolute URL where the file is located + format: uri + example: https://wiki.brapi.org/examples/datafile.xlsx + fileName: + type: string + description: The name of the file + example: datafile.xlsx + fileSize: + type: integer + description: The size of the file in bytes + example: 4398 + fileDescription: + type: string + description: A human readable description of the file contents + example: This is an Excel data file + fileType: + type: string + description: The type or format of the file. Preferably MIME Type. + example: application/vnd.ms-excel + fileMD5Hash: + type: string + description: The MD5 Hash of the file contents to be used as a check sum + example: c2365e900c81a89cf74d83dab60df146 + description: A dataFile contains a URL and the relevant file metadata to represent + a file + metadata: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/basePagination" + metadataBase: + type: object + properties: + datafiles: + type: array + description: "The datafiles contains a list of file URLs and metadata. \n\ + These files contain additional information related to the returned object\ + \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ + \ data file, an informational file, the uploaded file where the data originated\ + \ from, a generated file representing the whole dataset in a particular\ + \ format, or any other related file. " + example: [] + items: + $ref: "#/components/schemas/dataFile" + status: + type: array + description: "The status field contains a list of informational status messages\ + \ from the server. \nIf no status is reported, an empty list should be\ + \ returned. See Error Reporting for more information." + items: + $ref: "#/components/schemas/status" + description: "An object in the BrAPI standard response model that describes\ + \ some information about the service call being performed. This includes supplementary\ + \ data, status log messages, and pagination information." + metadataTokenPagination: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/tokenPagination" + status: + required: + - message + - messageType + type: object + properties: + message: + type: string + description: A short message concerning the status of this request/response + example: "Request accepted, response successful" + messageType: + type: string + description: The logging level for the attached message + example: INFO + enum: + - DEBUG + - ERROR + - WARNING + - INFO + description: An array of status messages to convey technical logging information + from the server to the client. + tokenPagination: + allOf: + - $ref: "#/components/schemas/basePagination" + - required: + - nextPageToken + type: object + properties: + nextPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the next page of data." + example: cb668f63 + deprecated: true + currentPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the current page of data." + example: 48bc6ac1 + deprecated: true + prevPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the previous page of data." + example: 9659857e + deprecated: true + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ + \ construct an additional query and move to the next or previous page respectively.\ + \ " + example: + currentPage: 0 + pageSize: 1000 + totalCount: 10 + totalPages: 1 + responses: + "401Unauthorized": + description: Unauthorized + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization + token + GermplasmAttributeListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/GermplasmAttribute" + GermplasmListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Germplasm" + SeedLotSingleResponse: + description: OK + content: + application/json: + schema: + title: SeedLotSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/SeedLot" + "202AcceptedSearchResponse": + description: Accepted + content: + application/json: + schema: + title: 202AcceptedSearchResponse + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + type: object + properties: + searchResultsDbId: + type: string + example: 551ae08c + StudySingleResponse: + description: OK + content: + application/json: + schema: + title: StudySingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Study" + CrossingProjectSingleResponse: + description: OK + content: + application/json: + schema: + title: CrossingProjectSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/CrossingProject" + TrialListResponse: + description: OK + content: + application/json: + schema: + title: TrialListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Trial" + SeedLotListResponse: + description: OK + content: + application/json: + schema: + title: SeedLotListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/SeedLot" + TrialSingleResponse: + description: OK + content: + application/json: + schema: + title: TrialSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Trial" + GermplasmSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Germplasm" + SeasonSingleResponse: + description: OK + content: + application/json: + schema: + title: SeasonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Season" + "404NotFound": + description: Not Found + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not + found + StudyListResponse: + description: OK + content: + application/json: + schema: + title: StudyListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Study" + CrossListResponse: + description: OK + content: + application/json: + schema: + title: CrossListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Cross" + BreedingMethodSingleResponse: + description: OK + content: + application/json: + schema: + title: BreedingMethodSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/BreedingMethod" + LocationSingleResponse: + description: OK + content: + application/json: + schema: + title: LocationSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Location" + SeasonListResponse: + description: OK + content: + application/json: + schema: + title: SeasonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Season" + PersonSingleResponse: + description: OK + content: + application/json: + schema: + title: PersonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Person" + PersonListResponse: + description: OK + content: + application/json: + schema: + title: PersonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Person" + PlannedCrossListResponse: + description: OK + content: + application/json: + schema: + title: PlannedCrossListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/PlannedCross" + LocationListResponse: + description: OK + content: + application/json: + schema: + title: LocationListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Location" + GermplasmAttributeValueListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeValueListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/GermplasmAttributeValue" + "403Forbidden": + description: Forbidden + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to + perform this action + BreedingMethodListResponse: + description: OK + content: + application/json: + schema: + title: BreedingMethodListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/BreedingMethod" + GermplasmAttributeValueSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeValueSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GermplasmAttributeValue" + ProgramListResponse: + description: OK + content: + application/json: + schema: + title: ProgramListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Program" + ListListResponse: + description: OK + content: + application/json: + schema: + title: ListListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/List" + "400BadRequest": + description: Bad Request + content: + application/json: + schema: + type: string + example: |- + ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object + + ERROR - 2018-10-08T18:15:11Z - Invalid query parameter + + ERROR - 2018-10-08T18:15:11Z - Required parameter is missing + CrossingProjectListResponse: + description: OK + content: + application/json: + schema: + title: CrossingProjectListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/CrossingProject" + PedigreeNodeListResponse: + description: OK + content: + application/json: + schema: + title: PedigreeNodeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/PedigreeNode" + ListSingleResponse: + description: OK + content: + application/json: + schema: + title: ListSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/List" + ProgramSingleResponse: + description: OK + content: + application/json: + schema: + title: ProgramSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Program" + GermplasmAttributeSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GermplasmAttribute" + parameters: + externalReferenceID: + name: externalReferenceID + in: query + description: "**Deprecated in v2.1** Please use `externalReferenceId`. Github\ + \ issue number #460 \n
An external reference ID. Could be a simple string\ + \ or a URI. (use with `externalReferenceSource` parameter)" + required: false + deprecated: true + style: form + explode: true + schema: + type: string + externalReferenceId: + name: externalReferenceId + in: query + description: An external reference ID. Could be a simple string or a URI. (use + with `externalReferenceSource` parameter) + required: false + style: form + explode: true + schema: + type: string + externalReferenceSource: + name: externalReferenceSource + in: query + description: An identifier for the source system or database of an external + reference (use with `externalReferenceId` parameter) + required: false + style: form + explode: true + schema: + type: string + acceptHeader: + name: Accept + in: header + description: "A standard HTTP request header that is used to request a specific\ + \ content type (JSON, CSV, etc) which is \"acceptable\" to the client and\ + \ should be returned by the server" + required: true + style: simple + explode: false + schema: + $ref: "#/components/schemas/ContentTypes" + example: application/json + searchResultsDbId: + name: searchResultsDbId + in: path + description: Unique identifier which references the search results + required: true + style: simple + explode: false + schema: + type: string + pageSize: + name: pageSize + in: query + description: The size of the pages to be returned. Default is `1000`. + required: false + style: form + explode: true + schema: + type: integer + example: 1000 + page: + name: page + in: query + description: |- + Used to request a specific page of data to be returned. + + The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. + required: false + style: form + explode: true + schema: + type: integer + example: "0" + pageToken: + name: pageToken + in: query + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n
\ + \ Tokenized pages are for large data sets which can not be efficiently broken\ + \ into indexed pages. Use the nextPageToken and prevPageToken from a prior\ + \ response to construct a query and move to the next or previous page respectively. " + required: false + deprecated: true + style: form + explode: true + schema: + type: string + example: 33c27874 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX + securitySchemes: + AuthorizationToken: + type: http + description: OAuth Bearer Token - A valid Bearer token to prove authorization + scheme: bearer + bearerFormat: nonce token or JWT diff --git a/Specification/Generated/BrAPI-Phenotyping.yaml b/Specification/Generated/BrAPI-Phenotyping.yaml new file mode 100644 index 00000000..d7a04c78 --- /dev/null +++ b/Specification/Generated/BrAPI-Phenotyping.yaml @@ -0,0 +1,4871 @@ +openapi: 3.0.1 +info: + title: BrAPI-Phenotyping + version: "2.1" +paths: + /events: + get: + tags: + - Events + summary: Get a filtered list of Event + description: Get a list of Event + parameters: + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: observationUnitDbId + in: query + description: The ID which uniquely identifies an observation unit. + required: false + schema: + type: string + - name: eventDbId + in: query + description: Filter based on an Event DbId. + required: false + schema: + type: string + - name: eventType + in: query + description: Filter based on an Event Type + required: false + schema: + type: string + - name: dateRangeStart + in: query + description: Filter based on an Event start date. + required: false + schema: + type: string + - name: dateRangeEnd + in: query + description: Filter based on an Event start date. + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/EventListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /images: + get: + tags: + - Images + summary: Get a filtered list of Image + description: Get a list of Image + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: descriptiveOntologyTerm + in: query + description: "A list of terms to formally describe the image to search for.\ + \ Each item could be a simple Tag, an Ontology reference Id, or a full ontology\ + \ URL." + required: false + schema: + type: string + - name: imageFileName + in: query + description: Image file names to search for. + required: false + schema: + type: string + - name: imageFileSizeMax + in: query + description: A maximum image file size to search for. + required: false + schema: + type: integer + format: int32 + - name: imageFileSizeMin + in: query + description: A minimum image file size to search for. + required: false + schema: + type: integer + format: int32 + - name: imageHeightMax + in: query + description: A maximum image height to search for. + required: false + schema: + type: integer + format: int32 + - name: imageHeightMin + in: query + description: A minimum image height to search for. + required: false + schema: + type: integer + format: int32 + - name: imageLocation + in: query + required: false + schema: + $ref: "#/components/schemas/GeoJSONSearchArea" + - name: imageName + in: query + description: Human readable names to search for. + required: false + schema: + type: string + - name: imageTimeStampRangeEnd + in: query + description: The latest timestamp to search for. + required: false + schema: + type: string + - name: imageTimeStampRangeStart + in: query + description: The earliest timestamp to search for. + required: false + schema: + type: string + - name: imageWidthMax + in: query + description: A maximum image width to search for. + required: false + schema: + type: integer + format: int32 + - name: imageWidthMin + in: query + description: A minimum image width to search for. + required: false + schema: + type: integer + format: int32 + - name: mimeType + in: query + description: A set of image file types to search for. + required: false + schema: + type: string + - name: observationDbId + in: query + description: A list of observation Ids this image is associated with to search + for + required: false + schema: + type: string + - name: imageDbId + in: query + description: A list of image Ids to search for + required: false + schema: + type: string + - name: observationUnitDbId + in: query + description: A set of observation unit identifiers to search for. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ImageListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Images + summary: Create new Image + description: Add new Image to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ImageNewRequest" + responses: + "200": + $ref: "#/components/responses/ImageListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /methods: + get: + tags: + - Methods + summary: Get a filtered list of Method + description: Get a list of Method + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: ontologyDbId + in: query + description: "The unique identifier for an ontology definition. Use this parameter\ + \ to filter results based on a specific ontology \n\n Use `GET /ontologies`\ + \ to find the list of available ontologies on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: scaleDbId + in: query + description: The unique identifier for a method. + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The unique identifier for an observation variable. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/MethodListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Methods + summary: Create new Method + description: Add new Method to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/MethodNewRequest" + responses: + "200": + $ref: "#/components/responses/MethodListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /observations: + get: + tags: + - Observations + summary: Get a filtered list of Observation + description: Get a list of Observation + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: locationName + in: query + description: A human readable names to search for + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The DbIds of Variables to search for + required: false + schema: + type: string + - name: observationVariableName + in: query + description: The names of Variables to search for + required: false + schema: + type: string + - name: observationVariablePUI + in: query + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: observationDbId + in: query + description: The unique id of an Observation + required: false + schema: + type: string + - name: observationUnitDbId + in: query + description: The unique id of an Observation Unit + required: false + schema: + type: string + - name: observationLevel + in: query + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + required: false + schema: + $ref: "#/components/schemas/ObservationUnitLevel" + - name: observationLevelRelationship + in: query + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + required: false + schema: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + - name: observationTimeStampRangeEnd + in: query + description: Timestamp range end + required: false + schema: + type: string + - name: observationTimeStampRangeStart + in: query + description: Timestamp range start + required: false + schema: + type: string + - name: seasonDbId + in: query + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ObservationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Observations + summary: Update the details for an existing Observation + description: Update the details for an existing Observation + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationNewRequest" + responses: + "200": + $ref: "#/components/responses/ObservationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Observations + summary: Create new Observation + description: Add new Observation to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationNewRequest" + responses: + "200": + $ref: "#/components/responses/ObservationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /observationunits: + get: + tags: + - ObservationUnits + summary: Get a filtered list of ObservationUnit + description: Get a list of ObservationUnit + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: locationName + in: query + description: A human readable names to search for + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The DbIds of Variables to search for + required: false + schema: + type: string + - name: observationVariableName + in: query + description: The names of Variables to search for + required: false + schema: + type: string + - name: observationVariablePUI + in: query + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: observationUnitDbId + in: query + description: The unique id of an observation unit + required: false + schema: + type: string + - name: observationUnitName + in: query + description: The human readable identifier for an Observation Unit + required: false + schema: + type: string + - name: observationLevel + in: query + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + required: false + schema: + $ref: "#/components/schemas/ObservationUnitLevel" + - name: observationLevelRelationship + in: query + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + required: false + schema: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + - name: includeObservation + in: query + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at your\ + \ own risk. It may return large, unpaginated lists of observation data.\ + \ Only set this value to True if you are sure you need to." + required: false + schema: + type: boolean + - name: seasonDbId + in: query + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ObservationUnitListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - ObservationUnits + summary: Update the details for an existing ObservationUnit + description: Update the details for an existing ObservationUnit + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationUnitNewRequest" + responses: + "200": + $ref: "#/components/responses/ObservationUnitListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - ObservationUnits + summary: Create new ObservationUnit + description: Add new ObservationUnit to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationUnitNewRequest" + responses: + "200": + $ref: "#/components/responses/ObservationUnitListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variables: + get: + tags: + - ObservationVariables + summary: Get a filtered list of ObservationVariable + description: Get a list of ObservationVariable + parameters: + - name: observationVariableDbId + in: query + description: The DbIds of Variables to search for + required: false + schema: + type: string + - name: observationVariableName + in: query + description: The names of Variables to search for + required: false + schema: + type: string + - name: observationVariablePUI + in: query + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + required: false + schema: + type: string + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: studyDbId + in: query + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + required: false + schema: + type: string + - name: ontologyDbId + in: query + description: List of ontology IDs to search for + required: false + schema: + type: string + - name: methodDbId + in: query + description: List of methods to filter search results + required: false + schema: + type: string + - name: methodName + in: query + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + required: false + schema: + type: string + - name: methodPUI + in: query + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + required: false + schema: + type: string + - name: scaleDbId + in: query + description: The unique identifier for a Scale + required: false + schema: + type: string + - name: scaleName + in: query + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + required: false + schema: + type: string + - name: scalePUI + in: query + description: "The Permanent Unique Identifier of a Scale, usually in the form\ + \ of a URI" + required: false + schema: + type: string + - name: dataType + in: query + description: List of scale data types to filter search results + required: false + schema: + $ref: "#/components/schemas/TraitDataType" + - name: traitClass + in: query + description: List of trait classes to filter search results + required: false + schema: + type: string + - name: traitDbId + in: query + description: The unique identifier for a Trait + required: false + schema: + type: string + - name: traitName + in: query + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + required: false + schema: + type: string + - name: traitPUI + in: query + description: "The Permanent Unique Identifier of a Trait, usually in the form\ + \ of a URI" + required: false + schema: + type: string + - name: traitAttribute + in: query + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + required: false + schema: + type: string + - name: traitAttributePUI + in: query + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + required: false + schema: + type: string + - name: traitEntity + in: query + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + required: false + schema: + type: string + - name: traitEntityPUI + in: query + description: "The Permanent Unique Identifier of a Trait Entity, usually in\ + \ the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\"\ + \ + \"Attribute\", the entity is the part of the plant that the trait refers\ + \ to e.g., for \"grain colour\", entity = \"grain\" " + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ObservationVariableListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - ObservationVariables + summary: Create new ObservationVariable + description: Add new ObservationVariable to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationVariableNewRequest" + responses: + "200": + $ref: "#/components/responses/ObservationVariableListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /ontologies: + get: + tags: + - Ontologies + summary: Get a filtered list of Ontology + description: Get a list of Ontology + parameters: + - name: ontologyDbId + in: query + description: "The unique identifier for an ontology definition. Use this parameter\ + \ to filter results based on a specific ontology \n\n Use `GET /ontologies`\ + \ to find the list of available ontologies on a server." + required: false + schema: + type: string + - name: ontologyName + in: query + description: The human readable identifier for an ontology definition. + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/OntologyListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Ontologies + summary: Create new Ontology + description: Add new Ontology to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/OntologyNewRequest" + responses: + "200": + $ref: "#/components/responses/OntologyListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /scales: + get: + tags: + - Scales + summary: Get a filtered list of Scale + description: Get a list of Scale + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: ontologyDbId + in: query + description: "The unique identifier for an ontology definition. Use this parameter\ + \ to filter results based on a specific ontology \n\n Use `GET /ontologies`\ + \ to find the list of available ontologies on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: scaleDbId + in: query + description: The unique identifier for a scale. + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The unique identifier for an observation variable. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ScaleListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Scales + summary: Create new Scale + description: Add new Scale to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ScaleNewRequest" + responses: + "200": + $ref: "#/components/responses/ScaleListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /traits: + get: + tags: + - Traits + summary: Get a filtered list of Trait + description: Get a list of Trait + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: ontologyDbId + in: query + description: "The unique identifier for an ontology definition. Use this parameter\ + \ to filter results based on a specific ontology \n\n Use `GET /ontologies`\ + \ to find the list of available ontologies on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: traitDbId + in: query + description: The unique identifier for a trait. + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The unique identifier for an observation variable. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/TraitListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Traits + summary: Create new Trait + description: Add new Trait to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TraitNewRequest" + responses: + "200": + $ref: "#/components/responses/TraitListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /images/{imageDbId}: + get: + tags: + - Images + summary: Get the details of a specific Image + description: Get details for a Image + responses: + "200": + $ref: "#/components/responses/ImageSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Images + summary: Update the details for an existing Image + description: Update the details for an existing Image + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ImageNewRequest" + responses: + "200": + $ref: "#/components/responses/ImageSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /methods/{methodDbId}: + get: + tags: + - Methods + summary: Get the details of a specific Method + description: Get details for a Method + responses: + "200": + $ref: "#/components/responses/MethodSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Methods + summary: Update the details for an existing Method + description: Update the details for an existing Method + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/MethodNewRequest" + responses: + "200": + $ref: "#/components/responses/MethodSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /observations/{observationDbId}: + get: + tags: + - Observations + summary: Get the details of a specific Observation + description: Get details for a Observation + responses: + "200": + $ref: "#/components/responses/ObservationSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /observationunits/{observationUnitDbId}: + get: + tags: + - ObservationUnits + summary: Get the details of a specific ObservationUnit + description: Get details for a ObservationUnit + responses: + "200": + $ref: "#/components/responses/ObservationUnitSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variables/{observationVariableDbId}: + get: + tags: + - ObservationVariables + summary: Get the details of a specific ObservationVariable + description: Get details for a ObservationVariable + responses: + "200": + $ref: "#/components/responses/ObservationVariableSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - ObservationVariables + summary: Update the details for an existing ObservationVariable + description: Update the details for an existing ObservationVariable + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationVariableNewRequest" + responses: + "200": + $ref: "#/components/responses/ObservationVariableSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /ontologies/{ontologyDbId}: + get: + tags: + - Ontologies + summary: Get the details of a specific Ontology + description: Get details for a Ontology + responses: + "200": + $ref: "#/components/responses/OntologySingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Ontologies + summary: Update the details for an existing Ontology + description: Update the details for an existing Ontology + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/OntologyNewRequest" + responses: + "200": + $ref: "#/components/responses/OntologySingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /scales/{scaleDbId}: + get: + tags: + - Scales + summary: Get the details of a specific Scale + description: Get details for a Scale + responses: + "200": + $ref: "#/components/responses/ScaleSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Scales + summary: Update the details for an existing Scale + description: Update the details for an existing Scale + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ScaleNewRequest" + responses: + "200": + $ref: "#/components/responses/ScaleSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /traits/{traitDbId}: + get: + tags: + - Traits + summary: Get the details of a specific Trait + description: Get details for a Trait + responses: + "200": + $ref: "#/components/responses/TraitSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + put: + tags: + - Traits + summary: Update the details for an existing Trait + description: Update the details for an existing Trait + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TraitNewRequest" + responses: + "200": + $ref: "#/components/responses/TraitSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/images: + post: + tags: + - Images + summary: Submit a search request for `Image` + description: "Submit a search request for `Image`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ImageListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/observations: + post: + tags: + - Observations + summary: Submit a search request for `Observation` + description: "Submit a search request for `Observation`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to\ + \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ObservationListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/observationunits: + post: + tags: + - ObservationUnits + summary: Submit a search request for `ObservationUnit` + description: "Submit a search request for `ObservationUnit`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ObservationUnitListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/variables: + post: + tags: + - ObservationVariables + summary: Submit a search request for `ObservationVariable` + description: "Submit a search request for `ObservationVariable`
\nSearch\ + \ requests allow a client to send a complex query for data. However, the server\ + \ may not respond with the search results immediately. \nIf a server needs\ + \ more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ObservationVariableListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/images/{searchResultsDbId}: + get: + tags: + - Images + summary: "Submit a search request for `Image`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Image` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/image` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ImageListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/observations/{searchResultsDbId}: + get: + tags: + - Observations + summary: "Submit a search request for `Observation`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/observation/{searchResultsDbId}` to retrieve the results of\ + \ the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Observation` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/observation`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ObservationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/observationunits/{searchResultsDbId}: + get: + tags: + - ObservationUnits + summary: "Submit a search request for `ObservationUnit`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `ObservationUnit` search request
\n\ + Clients should submit a search request using the corresponding `POST /search/observationUnit`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ObservationUnitListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/variables/{searchResultsDbId}: + get: + tags: + - ObservationVariables + summary: "Submit a search request for `ObservationVariable`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}`\ + \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `ObservationVariable` search request
\n\ + Clients should submit a search request using the corresponding `POST /search/observationVariable`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + responses: + "200": + $ref: "#/components/responses/ObservationVariableListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" +components: + schemas: + AdditionalInfo: + type: object + properties: + additionalProperties: + type: string + description: "A free space containing any additional information related to\ + \ a particular object. A data source may provide any JSON object, unrestricted\ + \ by the BrAPI specification." + AlleleMatrix: + required: + - callSetDbIds + - variantSetDbIds + type: object + properties: + callSetDbIds: + type: array + items: + type: string + expandHomozygotes: + type: boolean + sepPhased: + type: string + sepUnphased: + type: string + unknownString: + type: string + variantDbIds: + type: array + items: + type: string + variantSetDbIds: + type: array + items: + type: string + description: "The AlleleMatrix object is used to describe a matrix of genotyping\ + \ results. This 2d array of data reduces the overall size of the response\ + \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ + \ data retrieval faster and easier." + Attribute: + required: + - attributeName + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeCategory: + type: string + attributeDbId: + type: string + attributeDescription: + type: string + attributeName: + type: string + attributePUI: + type: string + commonCropName: + type: string + contextOfUse: + type: array + items: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + method: + $ref: "#/components/schemas/Method" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + synonyms: + type: array + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + Call: + required: + - callSetDbId + - variantDbId + - variantSetDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + callSetDbId: + type: string + callSetName: + type: string + genotypeValue: + type: string + phaseSet: + type: string + variantDbId: + type: string + variantSetDbId: + type: string + variantSetName: + type: string + description: "A `Call` represents the determination of genotype with respect\ + \ to a particular `Variant`. \n\nIt may include associated information such\ + \ as quality and phasing. For example, a call might assign a probability of\ + \ 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name\ + \ NA_12345." + Contact: + required: + - contactDbId + type: object + properties: + contactDbId: + type: string + email: + type: string + instituteName: + type: string + name: + type: string + orcid: + type: string + type: + type: string + description: A persons contact information + ContentTypes: + type: string + enum: + - application/json + - text/csv + - text/tsv + - application/flapjack + Context: + title: context + type: array + description: "The JSON-LD Context is used to provide JSON-LD definitions to\ + \ each field in a JSON object. By providing an array of context file urls,\ + \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ + \ see https://w3c.github.io/json-ld-syntax/#the-context" + example: + - https://brapi.org/jsonld/context/metadata.jsonld + items: + type: string + format: uri + CrossParent: + type: object + properties: + germplasm: + $ref: "#/components/schemas/Germplasm" + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + parentType: + $ref: "#/components/schemas/ParentType" + description: The identifying information gor the parent material of a cross. + CrossType: + type: string + description: "The type of cross make. Accepted values for this field are 'BIPARENTAL',\ + \ 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED'\ + \ and 'DOUBLE_HAPLOID'." + enum: + - BIPARENTAL + - SELF + - OPEN_POLLINATED + - BULK + - BULK_SELFED + - BULK_OPEN_POLLINATED + - DOUBLE_HAPLOID + DocumentationLink: + type: object + properties: + URL: + type: string + ontologyReferenceDbId: + type: string + type: + type: string + description: "The type of documentation, which can be OBO Foundry, an RDF\ + \ term or a webpage." + enum: + - OBO + - RDF + - WEBPAGE + description: Links to various ontology documentation + Event: + required: + - eventDbId + - eventType + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + eventDbId: + type: string + eventDescription: + type: string + eventType: + type: string + eventTypeDbId: + type: string + observationUnitDbIds: + type: array + items: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: "An event is discrete occurrence at a particular time in the experiment.\ + \ Events may be the realization of Treatments or parts of Treatments, or may\ + \ be confounding to Treatments. \n
ICASA Management Events allow for the\ + \ following types -> planting, fertilizer, irrigation, tillage, organic_material,\ + \ harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation,\ + \ weeding, puddling, flood_level, other" + EventDateRange: + type: object + properties: + discreteDates: + type: array + items: + type: string + endDate: + type: string + eventDbId: + type: string + startDate: + type: string + description: "An object describing when a particular Event has taken place.\ + \ An Event can occur at one or more discrete time points (`discreteDates`)\ + \ or an event can happen continuously over a longer period of time (`startDate`,\ + \ `endDate`)" + EventParameter: + type: object + properties: + code: + type: string + description: + type: string + eventDbId: + type: string + name: + type: string + units: + type: string + value: + type: string + valueDescription: + type: string + valuesByDate: + type: array + items: + type: string + description: "Additional metadata to describe an event, based on the ICASA standard\ + \ model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep),\ + \ and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters\ + \ for a Tillage event." + ExperimentalDesign: + type: object + properties: + PUI: + type: string + description: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: The experimental and statistical design full description plus a + category PUI taken from crop research ontology or agronomy ontology + ExternalReference: + type: object + properties: + referenceId: + type: string + referenceSource: + type: string + GeoJSON: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + type: + type: string + description: |- + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONGeometry: + oneOf: + - required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + items: + type: number + type: + type: string + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + - required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." + GeoJSONSearchArea: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + germplasmOrigin: + $ref: "#/components/schemas/GermplasmOrigin" + imageDbId: + type: string + imageName: + type: string + observationDbId: + type: string + observationUnit: + $ref: "#/components/schemas/ObservationUnitPosition" + type: + type: string + Germplasm: + required: + - commonCropName + - germplasmDbId + - germplasmName + - germplasmPUI + type: object + properties: + accessionNumber: + type: string + acquisitionDate: + type: string + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + biologicalStatusOfAccessionCode: + type: string + description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can\ + \ be used at 3 different levels of detail: either by using the general\ + \ codes such as 100, 200, 300, 400, or by using the more specific codes\ + \ such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild\ + \ \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace\ + \ \n400) Breeding/research material \n410) Breeders line \n411) Synthetic\ + \ population \n412) Hybrid \n413) Founder stock/base population \n414)\ + \ Inbred line (parent of hybrid cultivar) \n415) Segregating population\ + \ \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion\ + \ mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome\ + \ addition/substitution, aneuploids, amphiploids) \n423) Other genetic\ + \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ + \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ + \ \n999) Other (Elaborate in REMARKS field)" + enum: + - "100" + - "110" + - "120" + - "130" + - "200" + - "300" + - "400" + - "410" + - "411" + - "412" + - "413" + - "414" + - "415" + - "416" + - "420" + - "421" + - "422" + - "423" + - "500" + - "600" + - "999" + biologicalStatusOfAccessionDescription: + type: string + breedingMethodDbId: + type: string + breedingMethodName: + type: string + collection: + type: string + commonCropName: + type: string + countryOfOriginCode: + type: string + defaultDisplayName: + type: string + documentationURL: + type: string + genus: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + germplasmPreprocessing: + type: string + instituteCode: + type: string + instituteName: + type: string + pedigree: + type: string + sampleDbIds: + type: array + items: + type: string + seedSource: + type: string + seedSourceDescription: + type: string + species: + type: string + speciesAuthority: + type: string + subtaxa: + type: string + subtaxaAuthority: + type: string + description: "The conceptual identifiers and metadata describing a genetically\ + \ unique organism that is noteworthy in some way. Depending on context, a\ + \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ + \ Germplasm is conceptual data, not necessarily associated to a real physical\ + \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ + \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ + \ a Cross may or may not create a new Germplasm, since not every Cross is\ + \ unique or noteworthy." + GermplasmOrigin: + type: object + properties: + coordinateUncertainty: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + description: "Information for material (orchard, natural sites, ...). Geographic\ + \ identification of the plants from which seeds or cutting have been taken\ + \ to produce that germplasm." + GrowthFacility: + type: object + properties: + PUI: + type: string + description: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + description: Short description of the facility in which the study was carried + out. + Image: + required: + - imageDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + copyright: + type: string + description: + type: string + imageFileName: + type: string + imageFileSize: + type: integer + format: int32 + imageHeight: + type: integer + format: int32 + imageLocation: + $ref: "#/components/schemas/GeoJSON" + imageName: + type: string + imageTimeStamp: + type: string + imageURL: + type: string + imageWidth: + type: integer + format: int32 + mimeType: + type: string + observationDbIds: + type: array + items: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + description: The metadata for an image file that is connected to some phenotypic + observation data. + ImageNewRequest: + required: + - imageDbId + - imageDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + copyright: + type: string + description: + type: string + imageDbId: + type: string + imageFileName: + type: string + imageFileSize: + type: integer + format: int32 + imageHeight: + type: integer + format: int32 + imageLocation: + $ref: "#/components/schemas/GeoJSON" + imageName: + type: string + imageTimeStamp: + type: string + imageURL: + type: string + imageWidth: + type: integer + format: int32 + mimeType: + type: string + observationDbIds: + type: array + items: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + description: The metadata for an image file that is connected to some phenotypic + observation data. + ImageSearchRequest: + type: object + properties: + imageFileSizeMax: + type: integer + format: int32 + imageFileSizeMin: + type: integer + format: int32 + imageHeightMax: + type: integer + format: int32 + imageHeightMin: + type: integer + format: int32 + imageLocation: + $ref: "#/components/schemas/GeoJSONSearchArea" + imageTimeStampRangeEnd: + type: string + imageTimeStampRangeStart: + type: string + imageWidthMax: + type: integer + format: int32 + imageWidthMin: + type: integer + format: int32 + description: The metadata for an image file that is connected to some phenotypic + observation data. + ListType: + type: string + description: The type of objects that are referenced in a List + enum: + - germplasm + - markers + - variants + - programs + - trials + - studies + - observationUnits + - observations + - observationVariables + - samples + Method: + required: + - methodDbId + - methodName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + bibliographicalReference: + type: string + description: + type: string + formula: + type: string + methodClass: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReferenceDbId: + type: string + description: "A description of the way an Observation should be collected. \n\ +
For example, an ObservationVariable might be defined with a Trait of \"\ + plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ + \ variable would be distinct from a variable with the Method \"estimation\"\ + \ or \"drone image processing\". " + MethodNewRequest: + required: + - methodDbId + - methodDbId + - methodName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + bibliographicalReference: + type: string + description: + type: string + formula: + type: string + methodClass: + type: string + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReferenceDbId: + type: string + description: "A description of the way an Observation should be collected. \n\ +
For example, an ObservationVariable might be defined with a Trait of \"\ + plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ + \ variable would be distinct from a variable with the Method \"estimation\"\ + \ or \"drone image processing\". " + Observation: + required: + - observationDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + collector: + type: string + geoCoordinates: + $ref: "#/components/schemas/GeoJSON" + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + observationTimeStamp: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + observationVariableDbId: + type: string + observationVariableName: + type: string + observationVariablePUI: + type: string + seasonDbId: + type: string + seasonName: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + uploadedBy: + type: string + value: + type: string + description: A value assigned for a specific ObservationVariable when observing + a specific ObservationUnit. + ObservationNewRequest: + required: + - observationDbId + - observationDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + collector: + type: string + geoCoordinates: + $ref: "#/components/schemas/GeoJSON" + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + observationDbId: + type: string + observationTimeStamp: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + observationVariableDbId: + type: string + observationVariableName: + type: string + observationVariablePUI: + type: string + seasonDbId: + type: string + seasonName: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + uploadedBy: + type: string + value: + type: string + description: A value assigned for a specific ObservationVariable when observing + a specific ObservationUnit. + ObservationSearchRequest: + type: object + properties: + observationTimeStampRangeEnd: + type: string + observationTimeStampRangeStart: + type: string + description: A value assigned for a specific ObservationVariable when observing + a specific ObservationUnit. + ObservationTreatment: + type: object + properties: + factor: + type: string + modality: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + description: A Treatment applied an Observation Unit at a given Modality/Level + for a specific Factor. + ObservationUnit: + required: + - observationUnitDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + crossDbId: + type: string + crossName: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + locationDbId: + type: string + locationName: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + programDbId: + type: string + programName: + type: string + seedLotDbId: + type: string + seedLotName: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: "A representation of the physical entity being observed during\ + \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ + \ but it could include things like Fields, Blocks, or Samples." + ObservationUnitHierarchyLevel: + type: object + properties: + levelName: + type: string + levelOrder: + type: integer + format: int32 + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitLevel: + type: object + properties: + levelCode: + type: string + levelName: + type: string + levelOrder: + type: integer + format: int32 + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitLevelRelationship: + type: object + properties: + levelCode: + type: string + levelName: + type: string + levelOrder: + type: integer + format: int32 + observationUnit: + $ref: "#/components/schemas/ObservationUnit" + description: "Observation levels indicate the granularity level at which the\ + \ measurements are taken. `levelName` \ndefines the level, `levelOrder` defines\ + \ where that level exists in the hierarchy of levels. \n`levelOrder`s lower\ + \ numbers are at the top of the hierarchy (ie field > 0) and higher numbers\ + \ are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID\ + \ code for this level tag. Identify \nthis observation unit by each level\ + \ of the hierarchy where it exists. \n\nFor more information on Observation\ + \ Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study,\ + \ field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** " + ObservationUnitNewRequest: + required: + - observationUnitDbId + - observationUnitDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + crossDbId: + type: string + crossName: + type: string + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + locationDbId: + type: string + locationName: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + programDbId: + type: string + programName: + type: string + seedLotDbId: + type: string + seedLotName: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: "A representation of the physical entity being observed during\ + \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ + \ but it could include things like Fields, Blocks, or Samples." + ObservationUnitPosition: + type: object + properties: + entryType: + type: string + description: "The type of entry for this observation unit. ex. \"CHECK\"\ + , \"TEST\", \"FILLER\"" + enum: + - CHECK + - TEST + - FILLER + observationLevel: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + positionCoordinateX: + type: string + positionCoordinateXType: + $ref: "#/components/schemas/PositionCoordinateType" + positionCoordinateY: + type: string + positionCoordinateYType: + $ref: "#/components/schemas/PositionCoordinateType" + description: All positional and layout information related to this Observation + Unit + ObservationUnitSearchRequest: + type: object + properties: + includeObservations: + type: boolean + description: "A representation of the physical entity being observed during\ + \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ + \ but it could include things like Fields, Blocks, or Samples." + ObservationVariable: + required: + - methodDbId + - methodName + - observationVariableDbId + - observationVariableName + - scaleDbId + - scaleName + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + observationVariableName: + type: string + observationVariablePUI: + type: string + ontologyReferenceDbId: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string + ObservationVariableNewRequest: + required: + - methodDbId + - methodName + - observationVariableDbId + - observationVariableDbId + - observationVariableName + - scaleDbId + - scaleName + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + observationVariableDbId: + type: string + observationVariableName: + type: string + observationVariablePUI: + type: string + ontologyReferenceDbId: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string + ObservationVariableSearchRequest: + type: object + properties: {} + Ontology: + required: + - ontologyDbId + - ontologyName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + authors: + type: string + copyright: + type: string + description: + type: string + documentationURL: + type: string + licence: + type: string + ontologyName: + type: string + version: + type: string + description: The identifier and metadata needed to reference an external controlled + vocabulary + OntologyNewRequest: + required: + - ontologyDbId + - ontologyDbId + - ontologyName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + authors: + type: string + copyright: + type: string + description: + type: string + documentationURL: + type: string + licence: + type: string + ontologyDbId: + type: string + ontologyName: + type: string + version: + type: string + description: The identifier and metadata needed to reference an external controlled + vocabulary + OntologyReference: + required: + - ontology + type: object + properties: + ontology: + $ref: "#/components/schemas/Ontology" + ontologyReferenceDbId: + type: string + version: + type: string + description: "MIAPPE V1.1 (DM-85) Variable accession number - Accession number\ + \ of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession\ + \ number - Accession number of the trait in a suitable controlled vocabulary\ + \ (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number\ + \ - Accession number of the method in a suitable controlled vocabulary (Crop\ + \ Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number -\ + \ Accession number of the scale in a suitable controlled vocabulary (Crop\ + \ Ontology)." + OntologyTerm: + type: object + properties: + term: + type: string + termURI: + type: string + description: A pointer to an ontology used by a genomic reference + ParentType: + type: string + description: "The type of parent used during crossing. Accepted values for this\ + \ field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn\ + \ a pedigree record, the 'parentType' describes each parent of a particular\ + \ germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe\ + \ how this germplasm was crossed to generate a particular progeny. \\nFor\ + \ example, given a record for germplasm A, having a progeny B and C. The 'parentType'\ + \ field for progeny B item refers \\nto the 'parentType' of A toward B. The\ + \ 'parentType' field for progeny C item refers to the 'parentType' of A toward\ + \ C.\\nIn this way, A could be a male parent to B, but a female parent to\ + \ C. " + enum: + - MALE + - FEMALE + - SELF + - POPULATION + - CLONAL + PositionCoordinateType: + type: string + description: "The type of positional coordinate. Must be one of the following\ + \ values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location\ + \ Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84\ + \ geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW\ + \ - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical\ + \ counted number, could be independent or within a planted row \n\nGRID_ROW\ + \ - The row index number of a square grid overlay \n\nGRID_COL - The column\ + \ index number of a square grid overlay \n\nMEASURED_ROW - The distance in\ + \ meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters\ + \ from a defined 0-th column " + enum: + - LONGITUDE + - LATITUDE + - PLANTED_ROW + - PLANTED_INDIVIDUAL + - GRID_ROW + - GRID_COL + - MEASURED_ROW + - MEASURED_COL + Scale: + required: + - scaleDbId + - scaleName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + dataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + decimalPlaces: + type: integer + format: int32 + ontologyReferenceDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + units: + type: string + validValues: + $ref: "#/components/schemas/ValidValues" + description: "A Scale describes the units and acceptable values for an ObservationVariable.\ + \ \n
For example, an ObservationVariable might be defined with a Trait\ + \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ + . This variable would be distinct from a variable with the Scale \"inches\"\ + \ or \"pixels\"." + ScaleNewRequest: + required: + - scaleDbId + - scaleDbId + - scaleName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + dataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + decimalPlaces: + type: integer + format: int32 + ontologyReferenceDbId: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + units: + type: string + validValues: + $ref: "#/components/schemas/ValidValues" + description: "A Scale describes the units and acceptable values for an ObservationVariable.\ + \ \n
For example, an ObservationVariable might be defined with a Trait\ + \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ + . This variable would be distinct from a variable with the Scale \"inches\"\ + \ or \"pixels\"." + Trait: + required: + - traitDbId + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attribute: + type: string + attributePUI: + type: string + entity: + type: string + entityPUI: + type: string + mainAbbreviation: + type: string + ontologyReferenceDbId: + type: string + status: + type: string + traitClass: + type: string + traitDescription: + type: string + traitName: + type: string + traitPUI: + type: string + description: "A Trait describes what property is being observed. \n
For example,\ + \ an ObservationVariable might be defined with a Trait of \"plant height\"\ + , a Scale of \"meters\", and a Method of \"tape measure\". This variable would\ + \ be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\"\ + . " + TraitDataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + TraitNewRequest: + required: + - traitDbId + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attribute: + type: string + attributePUI: + type: string + entity: + type: string + entityPUI: + type: string + mainAbbreviation: + type: string + ontologyReferenceDbId: + type: string + status: + type: string + traitClass: + type: string + traitDbId: + type: string + traitDescription: + type: string + traitName: + type: string + traitPUI: + type: string + description: "A Trait describes what property is being observed. \n
For example,\ + \ an ObservationVariable might be defined with a Trait of \"plant height\"\ + , a Scale of \"meters\", and a Method of \"tape measure\". This variable would\ + \ be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\"\ + . " + ValidValues: + type: object + properties: + maximumValue: + type: string + minimumValue: + type: string + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + description: Metadata describing the acceptable values for this Scale + ValidValuesCategory: + type: object + properties: + label: + type: string + validValues: + $ref: "#/components/schemas/ValidValues" + value: + type: string + description: "If the Scale is a categorical type, these objects define the valid\ + \ options" + Variable: + required: + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + contextOfUse: + type: array + items: + type: string + defaultValue: + type: string + documentationURL: + type: string + growthStage: + type: string + institution: + type: string + language: + type: string + method: + $ref: "#/components/schemas/Method" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + status: + type: string + submissionTimestamp: + type: string + synonyms: + type: array + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + description: "A unique combination of Trait, Method, and Scale to define a clear\ + \ context for an Observation." + basePagination: + required: + - currentPage + - pageSize + type: object + properties: + currentPage: + type: integer + description: The index number for the returned page of data. This should + always match the requested page number or the default page (0). + example: 0 + default: 0 + pageSize: + type: integer + description: "The number of data elements returned, aka the size of the\ + \ current page. If the requested page does not have enough elements to\ + \ fill a page at the requested page size, this field should indicate the\ + \ actual number of elements returned." + example: 1000 + default: 1000 + totalCount: + type: integer + description: The total number of elements that are available on the server + and match the requested query parameters. + example: 10 + totalPages: + type: integer + description: "The total number of pages of elements available on the server.\ + \ This should be calculated with the following formula. \n
totalPages\ + \ = CEILING( totalCount / requested_page_size)" + example: 1 + description: "The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." + dataFile: + required: + - fileURL + type: object + properties: + fileURL: + type: string + description: The absolute URL where the file is located + format: uri + example: https://wiki.brapi.org/examples/datafile.xlsx + fileName: + type: string + description: The name of the file + example: datafile.xlsx + fileSize: + type: integer + description: The size of the file in bytes + example: 4398 + fileDescription: + type: string + description: A human readable description of the file contents + example: This is an Excel data file + fileType: + type: string + description: The type or format of the file. Preferably MIME Type. + example: application/vnd.ms-excel + fileMD5Hash: + type: string + description: The MD5 Hash of the file contents to be used as a check sum + example: c2365e900c81a89cf74d83dab60df146 + description: A dataFile contains a URL and the relevant file metadata to represent + a file + metadata: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/basePagination" + metadataBase: + type: object + properties: + datafiles: + type: array + description: "The datafiles contains a list of file URLs and metadata. \n\ + These files contain additional information related to the returned object\ + \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ + \ data file, an informational file, the uploaded file where the data originated\ + \ from, a generated file representing the whole dataset in a particular\ + \ format, or any other related file. " + example: [] + items: + $ref: "#/components/schemas/dataFile" + status: + type: array + description: "The status field contains a list of informational status messages\ + \ from the server. \nIf no status is reported, an empty list should be\ + \ returned. See Error Reporting for more information." + items: + $ref: "#/components/schemas/status" + description: "An object in the BrAPI standard response model that describes\ + \ some information about the service call being performed. This includes supplementary\ + \ data, status log messages, and pagination information." + metadataTokenPagination: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/tokenPagination" + status: + required: + - message + - messageType + type: object + properties: + message: + type: string + description: A short message concerning the status of this request/response + example: "Request accepted, response successful" + messageType: + type: string + description: The logging level for the attached message + example: INFO + enum: + - DEBUG + - ERROR + - WARNING + - INFO + description: An array of status messages to convey technical logging information + from the server to the client. + tokenPagination: + allOf: + - $ref: "#/components/schemas/basePagination" + - required: + - nextPageToken + type: object + properties: + nextPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the next page of data." + example: cb668f63 + deprecated: true + currentPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the current page of data." + example: 48bc6ac1 + deprecated: true + prevPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the previous page of data." + example: 9659857e + deprecated: true + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ + \ construct an additional query and move to the next or previous page respectively.\ + \ " + example: + currentPage: 0 + pageSize: 1000 + totalCount: 10 + totalPages: 1 + responses: + ObservationVariableSingleResponse: + description: OK + content: + application/json: + schema: + title: ObservationVariableSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ObservationVariable" + SeedLotSingleResponse: + description: OK + content: + application/json: + schema: + title: SeedLotSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/SeedLot" + VariantSingleResponse: + description: OK + content: + application/json: + schema: + title: VariantSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Variant" + "202AcceptedSearchResponse": + description: Accepted + content: + application/json: + schema: + title: 202AcceptedSearchResponse + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + type: object + properties: + searchResultsDbId: + type: string + example: 551ae08c + StudySingleResponse: + description: OK + content: + application/json: + schema: + title: StudySingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Study" + MarkerPositionListResponse: + description: OK + content: + application/json: + schema: + title: MarkerPositionListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/MarkerPosition" + TrialListResponse: + description: OK + content: + application/json: + schema: + title: TrialListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Trial" + MethodSingleResponse: + description: OK + content: + application/json: + schema: + title: MethodSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Method" + SeedLotListResponse: + description: OK + content: + application/json: + schema: + title: SeedLotListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/SeedLot" + VariantSetListResponse: + description: OK + content: + application/json: + schema: + title: VariantSetListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/VariantSet" + SampleSingleResponse: + description: OK + content: + application/json: + schema: + title: SampleSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Sample" + CallSetListResponse: + description: OK + content: + application/json: + schema: + title: CallSetListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/CallSet" + CallSetSingleResponse: + description: OK + content: + application/json: + schema: + title: CallSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/CallSet" + VariantSetSingleResponse: + description: OK + content: + application/json: + schema: + title: VariantSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/VariantSet" + ReferenceSetSingleResponse: + description: OK + content: + application/json: + schema: + title: ReferenceSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ReferenceSet" + ObservationVariableListResponse: + description: OK + content: + application/json: + schema: + title: ObservationVariableListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/ObservationVariable" + CrossListResponse: + description: OK + content: + application/json: + schema: + title: CrossListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Cross" + ImageSingleResponse: + description: OK + content: + application/json: + schema: + title: ImageSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Image" + PlateListResponse: + description: OK + content: + application/json: + schema: + title: PlateListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Plate" + SeasonListResponse: + description: OK + content: + application/json: + schema: + title: SeasonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Season" + ObservationUnitListResponse: + description: OK + content: + application/json: + schema: + title: ObservationUnitListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/ObservationUnit" + ReferenceListResponse: + description: OK + content: + application/json: + schema: + title: ReferenceListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Reference" + ObservationListResponse: + description: OK + content: + application/json: + schema: + title: ObservationListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Observation" + AlleleMatrixListResponse: + description: OK + content: + application/json: + schema: + title: AlleleMatrixListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/AlleleMatrix" + GenomeMapSingleResponse: + description: OK + content: + application/json: + schema: + title: GenomeMapSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GenomeMap" + PersonListResponse: + description: OK + content: + application/json: + schema: + title: PersonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Person" + PlannedCrossListResponse: + description: OK + content: + application/json: + schema: + title: PlannedCrossListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/PlannedCross" + LocationListResponse: + description: OK + content: + application/json: + schema: + title: LocationListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Location" + "403Forbidden": + description: Forbidden + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to + perform this action + OntologySingleResponse: + description: OK + content: + application/json: + schema: + title: OntologySingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Ontology" + ProgramListResponse: + description: OK + content: + application/json: + schema: + title: ProgramListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Program" + ObservationUnitSingleResponse: + description: OK + content: + application/json: + schema: + title: ObservationUnitSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ObservationUnit" + ScaleListResponse: + description: OK + content: + application/json: + schema: + title: ScaleListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Scale" + ListListResponse: + description: OK + content: + application/json: + schema: + title: ListListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/List" + "400BadRequest": + description: Bad Request + content: + application/json: + schema: + type: string + example: |- + ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object + + ERROR - 2018-10-08T18:15:11Z - Invalid query parameter + + ERROR - 2018-10-08T18:15:11Z - Required parameter is missing + MethodListResponse: + description: OK + content: + application/json: + schema: + title: MethodListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Method" + CrossingProjectListResponse: + description: OK + content: + application/json: + schema: + title: CrossingProjectListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/CrossingProject" + GermplasmAttributeSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GermplasmAttribute" + TraitSingleResponse: + description: OK + content: + application/json: + schema: + title: TraitSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Trait" + "401Unauthorized": + description: Unauthorized + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization + token + GermplasmAttributeListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/GermplasmAttribute" + GermplasmListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Germplasm" + CrossingProjectSingleResponse: + description: OK + content: + application/json: + schema: + title: CrossingProjectSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/CrossingProject" + EventListResponse: + description: OK + content: + application/json: + schema: + title: EventListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Event" + TraitListResponse: + description: OK + content: + application/json: + schema: + title: TraitListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Trait" + SampleListResponse: + description: OK + content: + application/json: + schema: + title: SampleListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Sample" + ReferenceSetListResponse: + description: OK + content: + application/json: + schema: + title: ReferenceSetListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/ReferenceSet" + TrialSingleResponse: + description: OK + content: + application/json: + schema: + title: TrialSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Trial" + GermplasmSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Germplasm" + SeasonSingleResponse: + description: OK + content: + application/json: + schema: + title: SeasonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Season" + ReferenceSingleResponse: + description: OK + content: + application/json: + schema: + title: ReferenceSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Reference" + OntologyListResponse: + description: OK + content: + application/json: + schema: + title: OntologyListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Ontology" + "404NotFound": + description: Not Found + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not + found + StudyListResponse: + description: OK + content: + application/json: + schema: + title: StudyListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Study" + ScaleSingleResponse: + description: OK + content: + application/json: + schema: + title: ScaleSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Scale" + BreedingMethodSingleResponse: + description: OK + content: + application/json: + schema: + title: BreedingMethodSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/BreedingMethod" + CallListResponse: + description: OK + content: + application/json: + schema: + title: CallListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Call" + LocationSingleResponse: + description: OK + content: + application/json: + schema: + title: LocationSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Location" + PersonSingleResponse: + description: OK + content: + application/json: + schema: + title: PersonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Person" + ImageListResponse: + description: OK + content: + application/json: + schema: + title: ImageListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Image" + VariantListResponse: + description: OK + content: + application/json: + schema: + title: VariantListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Variant" + PlateSingleResponse: + description: OK + content: + application/json: + schema: + title: PlateSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Plate" + GermplasmAttributeValueListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeValueListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/GermplasmAttributeValue" + BreedingMethodListResponse: + description: OK + content: + application/json: + schema: + title: BreedingMethodListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/BreedingMethod" + GermplasmAttributeValueSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeValueSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GermplasmAttributeValue" + GenomeMapListResponse: + description: OK + content: + application/json: + schema: + title: GenomeMapListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/GenomeMap" + PedigreeNodeListResponse: + description: OK + content: + application/json: + schema: + title: PedigreeNodeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/PedigreeNode" + ObservationSingleResponse: + description: OK + content: + application/json: + schema: + title: ObservationSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Observation" + ListSingleResponse: + description: OK + content: + application/json: + schema: + title: ListSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/List" + ProgramSingleResponse: + description: OK + content: + application/json: + schema: + title: ProgramSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Program" + parameters: + externalReferenceID: + name: externalReferenceID + in: query + description: "**Deprecated in v2.1** Please use `externalReferenceId`. Github\ + \ issue number #460 \n
An external reference ID. Could be a simple string\ + \ or a URI. (use with `externalReferenceSource` parameter)" + required: false + deprecated: true + style: form + explode: true + schema: + type: string + externalReferenceId: + name: externalReferenceId + in: query + description: An external reference ID. Could be a simple string or a URI. (use + with `externalReferenceSource` parameter) + required: false + style: form + explode: true + schema: + type: string + externalReferenceSource: + name: externalReferenceSource + in: query + description: An identifier for the source system or database of an external + reference (use with `externalReferenceId` parameter) + required: false + style: form + explode: true + schema: + type: string + acceptHeader: + name: Accept + in: header + description: "A standard HTTP request header that is used to request a specific\ + \ content type (JSON, CSV, etc) which is \"acceptable\" to the client and\ + \ should be returned by the server" + required: true + style: simple + explode: false + schema: + $ref: "#/components/schemas/ContentTypes" + example: application/json + searchResultsDbId: + name: searchResultsDbId + in: path + description: Unique identifier which references the search results + required: true + style: simple + explode: false + schema: + type: string + pageSize: + name: pageSize + in: query + description: The size of the pages to be returned. Default is `1000`. + required: false + style: form + explode: true + schema: + type: integer + example: 1000 + page: + name: page + in: query + description: |- + Used to request a specific page of data to be returned. + + The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. + required: false + style: form + explode: true + schema: + type: integer + example: "0" + pageToken: + name: pageToken + in: query + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n
\ + \ Tokenized pages are for large data sets which can not be efficiently broken\ + \ into indexed pages. Use the nextPageToken and prevPageToken from a prior\ + \ response to construct a query and move to the next or previous page respectively. " + required: false + deprecated: true + style: form + explode: true + schema: + type: string + example: 33c27874 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX + securitySchemes: + AuthorizationToken: + type: http + description: OAuth Bearer Token - A valid Bearer token to prove authorization + scheme: bearer + bearerFormat: nonce token or JWT diff --git a/Specification/Generated/README.md b/Specification/Generated/README.md index a02590a3..88f3155d 100644 --- a/Specification/Generated/README.md +++ b/Specification/Generated/README.md @@ -1,6 +1,32 @@ # Generated -The files in this directory are automatically generated by the [Schema Tools](../../generator/README.md) using +The files in this directory are automatically generated by the [Schema Tools](https://github.com/plantbreeding/brapi-schema-tools) using a github [action](../../.github/workflows/generate-schema.yml). +## Open API + +The generated OpenAPI YAML files by module are +* [BrAPI-Core.yaml](BrAPI-Core.yaml) +* [BrAPI-Genotyping.yaml](BrAPI-Genotyping.yaml) +* [BrAPI-Germplasm.yaml](BrAPI-Germplasm.yaml) +* [BrAPI-Phenotyping.yaml](BrAPI-Phenotyping.yaml) + +The generated single JSON file from the [JSON Schema](../BrAPI-Schema) is +* [brapi_generated.json](brapi_generated.json) + +The compiled single JSON file from the [YML specification files](../) is +* [brapi_generated.json](brapi_generated.json) + +The comparison between the generated and compiled JSON file can be found here +* [brapi_openapi_comparison.md](brapi_openapi_comparison.md) + +## GraphQL + +The generated GraphQL file from the [JSON Schema](../BrAPI-Schema) is +* [brapi_generated.graphqls](brapi_generated.graphqls) + +## OWL Turtle + +The generated OWL Turtle from the [JSON Schema](../BrAPI-Schema) is +* [brapi_generated.ttl](brapi_generated.ttl) diff --git a/Specification/Generated/brapi_generated.graphqls b/Specification/Generated/brapi_generated.graphqls index 4cfd68aa..2886e710 100644 --- a/Specification/Generated/brapi_generated.graphqls +++ b/Specification/Generated/brapi_generated.graphqls @@ -118,6 +118,7 @@ interface ObservationUnitHierarchyLevel { levelOrder: Int } +"A unique combination of Trait, Method, and Scale to define a clear context for an Observation." interface Variable { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -178,9 +179,11 @@ union GeoJSONGeometry = GeoJSONPoint | GeoJSONPolygon "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." type AdditionalInfo { + "A free space containing any additional information related to a particular object." additionalProperties: String } +"The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." type AlleleMatrix { "A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case." callSets(callSetsInput: CallSetsInput, paging: PageInput): CallSetListResponse @@ -207,6 +210,7 @@ type AlleleMatrixListResponse { page: PageInfo } +"An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used." type Analysis { "Unique identifier for this analysis description" analysisDbId: String @@ -226,6 +230,7 @@ type Analysis { variantSet: VariantSet } +"Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other." type AvailableFormat { "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)" dataFormat: DataFormat @@ -245,6 +250,7 @@ type AvailableFormat { variantSet: VariantSet } +"The techniques and protocol used to produce a Cross or Germplasm" type BreedingMethod { "A shortened version of the human readable name for a Breeding Method" abbreviation: String @@ -260,6 +266,11 @@ type BreedingMethodListResponse { data: [BreedingMethod] } +""" +A `Call` represents the determination of genotype with respect to a particular `Variant`. + +It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. +""" type Call { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -289,6 +300,7 @@ type CallListResponse { page: PageInfo } +"A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" type CallSet { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -327,6 +339,7 @@ type CallsSearchResponse { searchResultsDbId: String } +"A persons contact information" type Contact { """ The ID which uniquely identifies this contact @@ -366,6 +379,11 @@ type Contact { type: String } +""" +The mixture of germplasm present in the seed lot. +
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 +
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100. +""" type ContentMixture { "The cross for the germplasm using in this content mixture" cross: Cross @@ -377,6 +395,7 @@ type ContentMixture { seedLot: SeedLot } +"The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." type Cross { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -396,12 +415,13 @@ type Cross { parent1: CrossParent "the second parent used in the cross" parent2: CrossParent - "the unique identifier for a planned cross" + "The Cross that was used in the planning of this one." plannedCross: PlannedCross - "The list of pollination events that occurred for this cross" + "The list of pollination events that occurred for this cross." pollinationEvents: [PollinationEvent] } +"A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'" type CrossAttribute { "a custom attributes associated with a cross" cross: Cross @@ -416,6 +436,7 @@ type CrossListResponse { page: PageInfo } +"The identifying information gor the parent material of a cross." type CrossParent { "the germplasm of the cross parent" germplasm: Germplasm @@ -425,6 +446,7 @@ type CrossParent { parentType: ParentType } +"A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." type CrossingProject { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -457,6 +479,7 @@ type CrossingProjectsSearchResponse { searchResultsDbId: String } +"A link to extra data files associated with this study. Extra data could include notes, images, and reference data." type DataLink { """ The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy) @@ -500,6 +523,7 @@ type DataLink { version: String } +"A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." type DataMatrix { "Data matrices associated with an alleleMatrix" alleleMatrix: AlleleMatrix @@ -519,6 +543,7 @@ type DataMatrix { dataType: DataType } +"License and citation information for the data in this trial" type DatasetAuthorships { "The DOI or other permanent unique identifier for this published dataset" datasetPUI: String @@ -532,13 +557,17 @@ type DatasetAuthorships { trial: Trial } +"Links to various ontology documentation" type DocumentationLink { + "The URL or URI to the documentation" URL: String "associated ontology reference" ontologyReference: OntologyReference - type: Type + "The type of documentation, which can be OBO Foundry, an RDF term or a webpage." + type: DocumentationLinkType } +"Identifier assigned to an accession by the material donor." type Donor { """ The accession number assigned by the donor @@ -551,11 +580,16 @@ type Donor {
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. """ donorInstituteCode: String - "donoers associated with a germplasm" + "donors associated with a germplasm" germplasm: Germplasm } -type EnvironmentParameters { +""" +Environmental parameters that were kept constant throughout the study and did not change between observation units. + +MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). +""" +type EnvironmentParameter { "Human-readable value of the environment parameter (defined above) constant within the experiment" description: String "Human-readable value of the environment parameter (defined above) constant within the experiment" @@ -584,6 +618,10 @@ type EnvironmentParameters { valuePUI: String } +""" +An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. +
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other +""" type Event { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -616,6 +654,7 @@ type Event { study: Study } +"An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" type EventDateRange { """ A list of dates when the event occurred @@ -641,6 +680,7 @@ type EventListResponse { page: PageInfo } +"Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event." type EventParameter { """ The shortened code name of an event parameter @@ -677,6 +717,7 @@ type EventsSearchResponse { searchResultsDbId: String } +"The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" type ExperimentalDesign { "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology." PUI: String @@ -693,6 +734,7 @@ type ExternalReference { referenceSource: String } +"The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map." type GenomeMap { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -734,6 +776,7 @@ type GenomeMapsSearchResponse { searchResultsDbId: String } +"Genotype Metadata are additional layers of metadata associated with each genotype." type GenotypeMetadata { "Genotype metadata associated with a call" call: Call @@ -794,6 +837,7 @@ type GeoJSONPolygon { type: String } +"The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." type Germplasm { """ The unique identifier for a material or germplasm within a genebank @@ -871,7 +915,7 @@ type Germplasm { genus: String """ The ID which uniquely identifies a germplasm within the given database server -
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. +
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. """ germplasmDbId: String """ @@ -885,7 +929,7 @@ type Germplasm { """ The Permanent Unique Identifier which represents a germplasm - MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. MIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source @@ -963,6 +1007,7 @@ type Germplasm { taxonIds: [TaxonId] } +"The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" type GermplasmAttribute { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1036,6 +1081,7 @@ type GermplasmAttributeListResponse { page: PageInfo } +"The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." type GermplasmAttributeValue { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1068,6 +1114,7 @@ type GermplasmAttributesSearchResponse { searchResultsDbId: String } +"A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes." type GermplasmChild { "The child germplasm" childGermplasm: Germplasm @@ -1091,6 +1138,7 @@ type GermplasmListResponse { page: PageInfo } +"Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." type GermplasmOrigin { "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." coordinateUncertainty: String @@ -1107,6 +1155,7 @@ type GermplasmOrigin { germplasm: Germplasm } +"A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." type GermplasmParent { "The parent germplasm" parentGermplasm: Germplasm @@ -1130,6 +1179,7 @@ type GermplasmSearchResponse { searchResultsDbId: String } +"Short description of the facility in which the study was carried out." type GrowthFacility { "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology." PUI: String @@ -1139,6 +1189,7 @@ type GrowthFacility { study: Study } +"The metadata for an image file that is connected to some phenotypic observation data." type Image { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1193,15 +1244,19 @@ type ImagesSearchResponse { searchResultsDbId: String } +"The date and time when this study was last modified" type LastUpdate { "The date and time when this study was last modified" lastUpdateDbId: String "Last update associated with a study" study: Study + "The timestamp of the update." timestamp: String + "The version of the update." version: String } +"A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." type List { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1241,6 +1296,7 @@ type ListsSearchResponse { searchResultsDbId: String } +"A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." type Location { "A shortened version of the human readable name for a Location" abbreviation: String @@ -1321,6 +1377,7 @@ type LocationsSearchResponse { searchResultsDbId: String } +"A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." type MarkerPosition { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1350,6 +1407,10 @@ type MarkerPositionsSearchResponse { searchResultsDbId: String } +""" +Indicates which types of genotyping data and metadata are available in the VariantSet. +
When possible, these field names and abbreviations should follow the VCF standard +""" type MetadataField { "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." dataType: DataType @@ -1361,6 +1422,10 @@ type MetadataField { variantSet: VariantSet } +""" +A description of the way an Observation should be collected. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". +""" type Method { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1515,6 +1580,7 @@ type Mutation { updateVariantSet(variantSetInput: VariantSetInput): VariantSet } +"A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." type Observation { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1541,6 +1607,7 @@ type Observation { observationUnit: ObservationUnit "The ID which uniquely identifies an observation variable" observationVariable: ObservationVariable + "The season for this Observation" season: Season "The ID which uniquely identifies a study within the given database server" study: Study @@ -1555,6 +1622,25 @@ type ObservationListResponse { page: PageInfo } +"A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor." +type ObservationTreatment { + """ + The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc + + MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor. + """ + factor: String + """ + The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc + + MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. + """ + modality: String + "associated observation Unit" + observationUnit: ObservationUnit +} + +"A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." type ObservationUnit { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1599,7 +1685,7 @@ type ObservationUnit { MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. """ - treatments: [Treatment] + treatments: [ObservationTreatment] "The ID which uniquely identifies a trial" trial: Trial } @@ -1683,6 +1769,7 @@ type ObservationUnitListResponse { page: PageInfo } +"All positional and layout information related to this Observation Unit" type ObservationUnitPosition { "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"" entryType: EntryType @@ -1721,48 +1808,12 @@ type ObservationUnitPosition { observationUnit: ObservationUnit "The X position coordinate for an observation unit. Different systems may use different coordinate systems." positionCoordinateX: String - """ - The type of positional coordinate used. Must be one of the following values - - LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - - LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - - PLANTED_ROW - The physical planted row number - - PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row - - GRID_ROW - The row index number of a square grid overlay - - GRID_COL - The column index number of a square grid overlay - - MEASURED_ROW - The distance in meters from a defined 0-th row - - MEASURED_COL - The distance in meters from a defined 0-th column - """ - positionCoordinateXType: PositionCoordinateXType + "The type of positional coordinate used for the X coordinate of the position." + positionCoordinateXType: PositionCoordinateType "The Y position coordinate for an observation unit. Different systems may use different coordinate systems." positionCoordinateY: String - """ - The type of positional coordinate used. Must be one of the following values - - LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - - LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - - PLANTED_ROW - The physical planted row number - - PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row - - GRID_ROW - The row index number of a square grid overlay - - GRID_COL - The column index number of a square grid overlay - - MEASURED_ROW - The distance in meters from a defined 0-th row - - MEASURED_COL - The distance in meters from a defined 0-th column - """ - positionCoordinateYType: PositionCoordinateYType + "The type of positional coordinate used for the Y coordinate of the position." + positionCoordinateYType: PositionCoordinateType } type ObservationUnitsSearchResponse { @@ -1855,6 +1906,7 @@ type ObservationsSearchResponse { searchResultsDbId: String } +"The identifier and metadata needed to reference an external controlled vocabulary" type Ontology { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1881,6 +1933,12 @@ type OntologyListResponse { page: PageInfo } +""" +MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology +MIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). +MIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). +MIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). +""" type OntologyReference { "links to various ontology documentation" documentationLinks: [DocumentationLink] @@ -1892,6 +1950,7 @@ type OntologyReference { version: String } +"A pointer to an ontology used by a genomic reference" type OntologyTerm { "Ontology term - the label of the ontology term the termId is pointing to." term: String @@ -1906,6 +1965,7 @@ type PageInfo { totalPages: Int } +"Pagination info for the matrix" type Pagination { "Pagination associated with an alleleMatrix" alleleMatrix: AlleleMatrix @@ -1924,6 +1984,7 @@ type Pagination { totalPages: Int } +"A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances." type PedigreeNode { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -1981,6 +2042,7 @@ type PeopleSearchResponse { searchResultsDbId: String } +"A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." type Person { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2011,6 +2073,7 @@ type PersonListResponse { page: PageInfo } +"Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field." type PlannedCross { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2042,6 +2105,7 @@ type PlannedCrossesSearchResponse { searchResultsDbId: String } +"A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." type Plate { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2075,8 +2139,9 @@ type PlatesSearchResponse { searchResultsDbId: String } +"A Pollination Event that was used or attempted for a Cross." type PollinationEvent { - "Pollination events associated with a cross" + "The Cross associated with this Pollination Event" cross: Cross "The unique identifier for this pollination event" pollinationNumber: String @@ -2086,6 +2151,7 @@ type PollinationEvent { pollinationTimeStamp: String } +"A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." type Program { "A shortened version of the human readable name for a Program" abbreviation: String @@ -2125,8 +2191,11 @@ type ProgramsSearchResponse { searchResultsDbId: String } +"MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." type Publication { + "The permanent unique identifier of the publication." publicationPUI: String + "The publication reference." publicationReference: String "Publications associated with a trial" trial: Trial @@ -2321,6 +2390,7 @@ type Query { variantsSearch(variantInput: VariantsInput): VariantsSearchResponse } +"A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." type Reference { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2359,6 +2429,7 @@ type ReferenceListResponse { page: PageInfo } +"A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." type ReferenceSet { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2416,6 +2487,7 @@ type ReferencesSearchResponse { searchResultsDbId: String } +"The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." type Sample { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2487,6 +2559,10 @@ type SamplesSearchResponse { searchResultsDbId: String } +""" +A Scale describes the units and acceptable values for an ObservationVariable. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". +""" type Scale { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2540,6 +2616,7 @@ type ScaleListResponse { page: PageInfo } +"A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"." type Season { "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'" seasonDbId: String @@ -2559,6 +2636,7 @@ type SeasonsSearchResponse { searchResultsDbId: String } +"A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." type SeedLot { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2609,6 +2687,7 @@ type SeedLotListResponse { page: PageInfo } +"The record of an event where material was moved in or out of a particular SeedLot" type SeedLotTransaction { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2635,6 +2714,7 @@ type SeedLotsSearchResponse { searchResultsDbId: String } +"The type of storage this germplasm is kept in at a genebank." type StorageType { """ The 2 digit code representing the type of storage this germplasm is kept in at a genebank. @@ -2663,6 +2743,7 @@ type StudiesSearchResponse { searchResultsDbId: String } +"A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." type Study { "A flag to indicate if a Study is currently active and ongoing" active: Boolean @@ -2689,7 +2770,7 @@ type Study { MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). """ - environmentParameters: [EnvironmentParameters] + environmentParameters: [EnvironmentParameter] "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" experimentalDesign: ExperimentalDesign "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." @@ -2762,6 +2843,7 @@ type StudyListResponse { page: PageInfo } +"Alternative names or IDs used to reference this germplasm" type Synonym { "associated germplasm" germplasm: Germplasm @@ -2771,6 +2853,11 @@ type Synonym { type: String } +""" +The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. + +MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. +""" type TaxonId { "associated germplasm" germplasm: Germplasm @@ -2780,6 +2867,10 @@ type TaxonId { taxonId: String } +""" +A Trait describes what property is being observed. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". +""" type Trait { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -2842,23 +2933,7 @@ type TraitListResponse { page: PageInfo } -type Treatment { - """ - The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc - - MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor. - """ - factor: String - """ - The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc - - MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. - """ - modality: String - "associated observation Unit" - observationUnit: ObservationUnit -} - +"A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." type Trial { "A flag to indicate if a Trial is currently active and ongoing" active: Boolean @@ -2915,6 +2990,7 @@ type TrialsSearchResponse { searchResultsDbId: String } +"Metadata describing the acceptable values for this Scale" type ValidValues { "List of possible values with optional labels" categories: [ValidValuesCategory] @@ -2926,6 +3002,7 @@ type ValidValues { scale: Scale } +"If the Scale is a categorical type, these objects define the valid options" type ValidValuesCategory { "A text label for a category" label: String @@ -2935,6 +3012,7 @@ type ValidValuesCategory { value: String } +"A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." type Variant { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -3007,6 +3085,7 @@ type VariantListResponse { page: PageInfo } +"A VariantSet is a collection of variants and variant calls intended to be analyzed together." type VariantSet { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo @@ -3148,6 +3227,13 @@ enum Dimension { VARIANTS } +"The type of documentation, which can be OBO Foundry, an RDF term or a webpage." +enum DocumentationLinkType { + OBO + RDF + WEBPAGE +} + "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"" enum EntryType { CHECK @@ -3201,7 +3287,7 @@ enum PlateFormat { } """ -The type of positional coordinate used. Must be one of the following values +The type of positional coordinate. Must be one of the following values LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details @@ -3219,37 +3305,7 @@ MEASURED_ROW - The distance in meters from a defined 0-th row MEASURED_COL - The distance in meters from a defined 0-th column """ -enum PositionCoordinateXType { - GRID_COL - GRID_ROW - LATITUDE - LONGITUDE - MEASURED_COL - MEASURED_ROW - PLANTED_INDIVIDUAL - PLANTED_ROW -} - -""" -The type of positional coordinate used. Must be one of the following values - -LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - -LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - -PLANTED_ROW - The physical planted row number - -PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row - -GRID_ROW - The row index number of a square grid overlay - -GRID_COL - The column index number of a square grid overlay - -MEASURED_ROW - The distance in meters from a defined 0-th row - -MEASURED_COL - The distance in meters from a defined 0-th column -""" -enum PositionCoordinateYType { +enum PositionCoordinateType { GRID_COL GRID_ROW LATITUDE @@ -3325,17 +3381,13 @@ enum TraitDataType { Text } -enum Type { - OBO - RDF - WEBPAGE -} - "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." input AdditionalInfoInput { + "A free space containing any additional information related to a particular object." additionalProperties: String } +"The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." input AlleleMatrixInput { "A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case." callSets: [CallSetInput] @@ -3357,6 +3409,7 @@ input AlleleMatrixInput { variants: [VariantInput] } +"An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used." input AnalysisInput { "Unique identifier for this analysis description" analysisDbId: String @@ -3376,6 +3429,7 @@ input AnalysisInput { variantSet: VariantSetInput } +"Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other." input AvailableFormatInput { "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)" dataFormat: DataFormat @@ -3395,6 +3449,7 @@ input AvailableFormatInput { variantSet: VariantSetInput } +"The techniques and protocol used to produce a Cross or Germplasm" input BreedingMethodInput { "A shortened version of the human readable name for a Breeding Method" abbreviation: String @@ -3410,6 +3465,11 @@ input BreedingMethodInput { pedigreeNodes: [PedigreeNodeInput] } +""" +A `Call` represents the determination of genotype with respect to a particular `Variant`. + +It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. +""" input CallInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -3434,6 +3494,7 @@ input CallInput { variantSet: VariantSetInput } +"A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" input CallSetInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -3521,6 +3582,7 @@ input CallsInput { variantSetDbIds: [String] } +"A persons contact information" input ContactInput { """ The ID which uniquely identifies this contact @@ -3560,6 +3622,11 @@ input ContactInput { type: String } +""" +The mixture of germplasm present in the seed lot. +
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 +
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100. +""" input ContentMixtureInput { "The cross for the germplasm using in this content mixture" cross: CrossInput @@ -3571,6 +3638,7 @@ input ContentMixtureInput { seedLot: SeedLotInput } +"A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'" input CrossAttributeInput { "a custom attributes associated with a cross" cross: CrossInput @@ -3580,6 +3648,7 @@ input CrossAttributeInput { crossAttributeValue: String } +"The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." input CrossInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -3601,12 +3670,13 @@ input CrossInput { parent1: CrossParentInput "the second parent used in the cross" parent2: CrossParentInput - "the unique identifier for a planned cross" + "The Cross that was used in the planning of this one." plannedCross: PlannedCrossInput - "The list of pollination events that occurred for this cross" + "The list of pollination events that occurred for this cross." pollinationEvents: [PollinationEventInput] } +"The identifying information gor the parent material of a cross." input CrossParentInput { "the germplasm of the cross parent" germplasm: GermplasmInput @@ -3649,6 +3719,7 @@ input CrossesInput { programNames: [String] } +"A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." input CrossingProjectInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -3708,6 +3779,7 @@ input CrossingProjectsInput { programNames: [String] } +"A link to extra data files associated with this study. Extra data could include notes, images, and reference data." input DataLinkInput { """ The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy) @@ -3751,6 +3823,7 @@ input DataLinkInput { version: String } +"A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." input DataMatrixInput { "Data matrices associated with an alleleMatrix" alleleMatrix: AlleleMatrixInput @@ -3770,6 +3843,7 @@ input DataMatrixInput { dataType: DataType } +"License and citation information for the data in this trial" input DatasetAuthorshipsInput { "The DOI or other permanent unique identifier for this published dataset" datasetPUI: String @@ -3783,13 +3857,17 @@ input DatasetAuthorshipsInput { trial: TrialInput } +"Links to various ontology documentation" input DocumentationLinkInput { + "The URL or URI to the documentation" URL: String "associated ontology reference" ontologyReference: OntologyReferenceInput - type: Type + "The type of documentation, which can be OBO Foundry, an RDF term or a webpage." + type: DocumentationLinkType } +"Identifier assigned to an accession by the material donor." input DonorInput { """ The accession number assigned by the donor @@ -3802,11 +3880,16 @@ input DonorInput {
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. """ donorInstituteCode: String - "donoers associated with a germplasm" + "donors associated with a germplasm" germplasm: GermplasmInput } -input EnvironmentParametersInput { +""" +Environmental parameters that were kept constant throughout the study and did not change between observation units. + +MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). +""" +input EnvironmentParameterInput { "Human-readable value of the environment parameter (defined above) constant within the experiment" description: String "Human-readable value of the environment parameter (defined above) constant within the experiment" @@ -3835,6 +3918,7 @@ input EnvironmentParametersInput { valuePUI: String } +"An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" input EventDateRangeInput { """ A list of dates when the event occurred @@ -3855,6 +3939,10 @@ input EventDateRangeInput { startDate: String } +""" +An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. +
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other +""" input EventInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -3887,6 +3975,7 @@ input EventInput { study: StudyInput } +"Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event." input EventParameterInput { """ The shortened code name of an event parameter @@ -3935,6 +4024,7 @@ input EventsInput { studyNames: [String] } +"The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" input ExperimentalDesignInput { "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology." PUI: String @@ -3951,6 +4041,7 @@ input ExternalReferenceInput { referenceSource: String } +"The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map." input GenomeMapInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -4023,6 +4114,7 @@ input GenomeMapsInput { types: [String] } +"Genotype Metadata are additional layers of metadata associated with each genotype." input GenotypeMetadataInput { "Genotype metadata associated with a call" call: CallInput @@ -4113,6 +4205,7 @@ input GeoJSONSearchAreaInput { type: String } +"The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" input GermplasmAttributeInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -4181,6 +4274,7 @@ input GermplasmAttributeInput { trait: TraitInput } +"The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." input GermplasmAttributeValueInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -4342,6 +4436,7 @@ input GermplasmAttributesInput { trialNames: [String] } +"A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes." input GermplasmChildInput { "The child germplasm" childGermplasm: GermplasmInput @@ -4360,6 +4455,7 @@ input GermplasmChildInput { pedigreeNode: PedigreeNodeInput } +"The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." input GermplasmInput { """ The unique identifier for a material or germplasm within a genebank @@ -4439,7 +4535,7 @@ input GermplasmInput { genus: String """ The ID which uniquely identifies a germplasm within the given database server -
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. +
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. """ germplasmDbId: String """ @@ -4453,7 +4549,7 @@ input GermplasmInput { """ The Permanent Unique Identifier which represents a germplasm - MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. MIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source @@ -4547,6 +4643,7 @@ input GermplasmInput { taxonIds: [TaxonIdInput] } +"Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." input GermplasmOriginInput { "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." coordinateUncertainty: String @@ -4563,6 +4660,7 @@ input GermplasmOriginInput { germplasm: GermplasmInput } +"A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." input GermplasmParentInput { "The parent germplasm" parentGermplasm: GermplasmInput @@ -4581,6 +4679,7 @@ input GermplasmParentInput { pedigreeNode: PedigreeNodeInput } +"Short description of the facility in which the study was carried out." input GrowthFacilityInput { "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology." PUI: String @@ -4590,6 +4689,7 @@ input GrowthFacilityInput { study: StudyInput } +"The metadata for an image file that is connected to some phenotypic observation data." input ImageInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -4690,15 +4790,19 @@ input ImagesInput { programNames: [String] } +"The date and time when this study was last modified" input LastUpdateInput { "The date and time when this study was last modified" lastUpdateDbId: String "Last update associated with a study" study: StudyInput + "The timestamp of the update." timestamp: String + "The version of the update." version: String } +"A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." input ListInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -4750,6 +4854,7 @@ input ListsInput { listType: ListType } +"A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." input LocationInput { "A shortened version of the human readable name for a Location" abbreviation: String @@ -4883,6 +4988,7 @@ input LocationsInput { programNames: [String] } +"A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." input MarkerPositionInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -4915,6 +5021,10 @@ input MarkerPositionsInput { variantDbIds: [String] } +""" +Indicates which types of genotyping data and metadata are available in the VariantSet. +
When possible, these field names and abbreviations should follow the VCF standard +""" input MetadataFieldInput { "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." dataType: DataType @@ -4926,6 +5036,10 @@ input MetadataFieldInput { variantSet: VariantSetInput } +""" +A description of the way an Observation should be collected. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". +""" input MethodInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -5003,6 +5117,7 @@ input MethodsInput { scaleDbIds: [String] } +"A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." input ObservationInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -5031,6 +5146,7 @@ input ObservationInput { observationUnit: ObservationUnitInput "The ID which uniquely identifies an observation variable" observationVariable: ObservationVariableInput + "The season for this Observation" season: SeasonInput "The ID which uniquely identifies a study within the given database server" study: StudyInput @@ -5040,6 +5156,24 @@ input ObservationInput { value: String } +"A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor." +input ObservationTreatmentInput { + """ + The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc + + MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor. + """ + factor: String + """ + The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc + + MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. + """ + modality: String + "associated observation Unit" + observationUnit: ObservationUnitInput +} + """ The exact level and level code of an observation unit. @@ -5067,6 +5201,7 @@ input ObservationUnitHierarchyLevelInput { levelOrder: Int } +"A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." input ObservationUnitInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -5119,7 +5254,7 @@ input ObservationUnitInput { MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. """ - treatments: [TreatmentInput] + treatments: [ObservationTreatmentInput] "The ID which uniquely identifies a trial" trial: TrialInput } @@ -5198,6 +5333,7 @@ input ObservationUnitLevelRelationshipInput { observationUnit: ObservationUnitInput } +"All positional and layout information related to this Observation Unit" input ObservationUnitPositionInput { "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"" entryType: EntryType @@ -5236,48 +5372,12 @@ input ObservationUnitPositionInput { observationUnit: ObservationUnitInput "The X position coordinate for an observation unit. Different systems may use different coordinate systems." positionCoordinateX: String - """ - The type of positional coordinate used. Must be one of the following values - - LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - - LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - - PLANTED_ROW - The physical planted row number - - PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row - - GRID_ROW - The row index number of a square grid overlay - - GRID_COL - The column index number of a square grid overlay - - MEASURED_ROW - The distance in meters from a defined 0-th row - - MEASURED_COL - The distance in meters from a defined 0-th column - """ - positionCoordinateXType: PositionCoordinateXType + "The type of positional coordinate used for the X coordinate of the position." + positionCoordinateXType: PositionCoordinateType "The Y position coordinate for an observation unit. Different systems may use different coordinate systems." positionCoordinateY: String - """ - The type of positional coordinate used. Must be one of the following values - - LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - - LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details - - PLANTED_ROW - The physical planted row number - - PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row - - GRID_ROW - The row index number of a square grid overlay - - GRID_COL - The column index number of a square grid overlay - - MEASURED_ROW - The distance in meters from a defined 0-th row - - MEASURED_COL - The distance in meters from a defined 0-th column - """ - positionCoordinateYType: PositionCoordinateYType + "The type of positional coordinate used for the Y coordinate of the position." + positionCoordinateYType: PositionCoordinateType } input ObservationUnitsInput { @@ -5579,6 +5679,7 @@ input OntologiesInput { ontologyNames: [String] } +"The identifier and metadata needed to reference an external controlled vocabulary" input OntologyInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -5600,6 +5701,12 @@ input OntologyInput { version: String } +""" +MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology +MIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). +MIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). +MIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). +""" input OntologyReferenceInput { "links to various ontology documentation" documentationLinks: [DocumentationLinkInput] @@ -5611,6 +5718,7 @@ input OntologyReferenceInput { version: String } +"A pointer to an ontology used by a genomic reference" input OntologyTermInput { "Species associated with a reference" reference: ReferenceInput @@ -5627,6 +5735,7 @@ input PageInput { pageSize: Int } +"Pagination info for the matrix" input PaginationInput { "Pagination associated with an alleleMatrix" alleleMatrix: AlleleMatrixInput @@ -5645,6 +5754,7 @@ input PaginationInput { totalPages: Int } +"A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances." input PedigreeNodeInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -5802,6 +5912,7 @@ input PeopleInput { userIDs: [String] } +"A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." input PersonInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -5829,6 +5940,7 @@ input PersonInput { userID: String } +"Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field." input PlannedCrossInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -5887,6 +5999,7 @@ input PlannedCrossesInput { statuses: [CrossStatus] } +"A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." input PlateInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -5963,8 +6076,9 @@ input PlatesInput { trialNames: [String] } +"A Pollination Event that was used or attempted for a Cross." input PollinationEventInput { - "Pollination events associated with a cross" + "The Cross associated with this Pollination Event" cross: CrossInput "The unique identifier for this pollination event" pollinationNumber: String @@ -5974,6 +6088,7 @@ input PollinationEventInput { pollinationTimeStamp: String } +"A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." input ProgramInput { "A shortened version of the human readable name for a Program" abbreviation: String @@ -6053,13 +6168,17 @@ input ProgramsInput { programTypes: [ProgramType] } +"MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." input PublicationInput { + "The permanent unique identifier of the publication." publicationPUI: String + "The publication reference." publicationReference: String "Publications associated with a trial" trial: TrialInput } +"A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." input ReferenceInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -6093,6 +6212,7 @@ input ReferenceInput { variants: [VariantInput] } +"A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." input ReferenceSetInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -6231,6 +6351,7 @@ input ReferencesInput { trialNames: [String] } +"The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." input SampleInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -6341,6 +6462,10 @@ input SamplesInput { trialNames: [String] } +""" +A Scale describes the units and acceptable values for an ObservationVariable. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". +""" input ScaleInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -6424,6 +6549,7 @@ input ScalesInput { scaleDbIds: [String] } +"A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"." input SeasonInput { "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'" seasonDbId: String @@ -6444,6 +6570,7 @@ input SeasonsInput { years: [String] } +"A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." input SeedLotInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -6491,6 +6618,7 @@ input SeedLotInput { units: String } +"The record of an event where material was moved in or out of a particular SeedLot" input SeedLotTransactionInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -6547,6 +6675,7 @@ input SeedLotsInput { seedLotDbIds: [String] } +"The type of storage this germplasm is kept in at a genebank." input StorageTypeInput { """ The 2 digit code representing the type of storage this germplasm is kept in at a genebank. @@ -6627,6 +6756,7 @@ input StudiesInput { trialNames: [String] } +"A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." input StudyInput { "A flag to indicate if a Study is currently active and ongoing" active: Boolean @@ -6654,7 +6784,7 @@ input StudyInput { MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). """ - environmentParameters: [EnvironmentParametersInput] + environmentParameters: [EnvironmentParameterInput] "events" events: [EventInput] "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" @@ -6734,6 +6864,7 @@ input StudyInput { variantSets: [VariantSetInput] } +"Alternative names or IDs used to reference this germplasm" input SynonymInput { "associated germplasm" germplasm: GermplasmInput @@ -6743,6 +6874,11 @@ input SynonymInput { type: String } +""" +The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. + +MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. +""" input TaxonIdInput { "associated germplasm" germplasm: GermplasmInput @@ -6752,6 +6888,10 @@ input TaxonIdInput { taxonId: String } +""" +A Trait describes what property is being observed. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". +""" input TraitInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -6844,23 +6984,7 @@ input TraitsInput { traitDbIds: [String] } -input TreatmentInput { - """ - The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc - - MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor. - """ - factor: String - """ - The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc - - MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. - """ - modality: String - "associated observation Unit" - observationUnit: ObservationUnitInput -} - +"A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." input TrialInput { "A flag to indicate if a Trial is currently active and ongoing" active: Boolean @@ -6990,6 +7114,7 @@ input TrialsInput { trialPUIs: [String] } +"If the Scale is a categorical type, these objects define the valid options" input ValidValuesCategoryInput { "A text label for a category" label: String @@ -6999,6 +7124,7 @@ input ValidValuesCategoryInput { value: String } +"Metadata describing the acceptable values for this Scale" input ValidValuesInput { "List of possible values with optional labels" categories: [ValidValuesCategoryInput] @@ -7010,6 +7136,7 @@ input ValidValuesInput { scale: ScaleInput } +"A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." input VariantInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput @@ -7077,6 +7204,7 @@ input VariantInput { variantType: String } +"A VariantSet is a collection of variants and variant calls intended to be analyzed together." input VariantSetInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index aa9ff676..f7370c40 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -1,15101 +1,16914 @@ { - "openapi" : "3.0.1", - "info" : { - "title" : "BrAPI", - "version" : "0.0.0" - }, - "paths" : { - "/breedingmethods" : { - "get" : { - "tags" : [ "Germplasm" ], - "summary" : "Get a filtered list of BreedingMethod", - "description" : "Get a list of BreedingMethod", - "parameters" : [ ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/BreedingMethodListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/calls" : { - "get" : { - "tags" : [ "Calls" ], - "summary" : "Get a filtered list of Call", - "description" : "Get a list of Call", - "parameters" : [ { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variant` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "expandHomozygote", - "in" : "query", - "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "sepPhased", - "in" : "query", - "description" : "The string used as a separator for phased allele calls.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sepUnphased", - "in" : "query", - "description" : "The string used as a separator for unphased allele calls.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "unknownString", - "in" : "query", - "description" : "The string used as a representation for missing data.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/callsets" : { - "get" : { - "tags" : [ "CallSets" ], - "summary" : "Get a filtered list of CallSet", - "description" : "Get a list of CallSet", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Samples` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleName", - "in" : "query", - "description" : "A list of human readable names associated with `Samples`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "callSetName", - "in" : "query", - "description" : "A list of human readable names associated with `CallSets`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallSetListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } + "openapi" : "3.0.1", + "info" : { + "title" : "BrAPI", + "version" : "2.1" }, - "/crosses" : { - "get" : { - "tags" : [ "Crosses" ], - "summary" : "Get a filtered list of Cross", - "description" : "Get a list of Cross", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossingProjectDbId", - "in" : "query", - "description" : "Search for Crossing Projects with this unique id", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossingProjectName", - "in" : "query", - "description" : "The human readable name for a crossing project", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossDbId", - "in" : "query", - "description" : "Search for Cross with this unique id", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossName", - "in" : "query", - "description" : "Search for Cross with this human readable name", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/CrossListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Crosses" ], - "summary" : "Update the details for an existing Cross", - "description" : "Update the details for an existing Cross", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/CrossNewRequest" - } + "paths" : { + "/breedingmethods" : { + "get" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Get a filtered list of BreedingMethod", + "description" : "Get a list of BreedingMethod", + "parameters" : [ ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/BreedingMethodListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/CrossListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Crosses" ], - "summary" : "Create new Cross", - "description" : "Add new Cross to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/CrossNewRequest" - } + "/calls" : { + "get" : { + "tags" : [ + "Calls" + ], + "summary" : "Get a filtered list of Call", + "description" : "Get a list of Call", + "parameters" : [ + { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "expandHomozygote", + "in" : "query", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "sepPhased", + "in" : "query", + "description" : "The string used as a separator for phased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sepUnphased", + "in" : "query", + "description" : "The string used as a separator for unphased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "unknownString", + "in" : "query", + "description" : "The string used as a representation for missing data.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/CrossListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/crossingprojects" : { - "get" : { - "tags" : [ "CrossingProjects" ], - "summary" : "Get a filtered list of CrossingProject", - "description" : "Get a list of CrossingProject", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossingProjectDbId", - "in" : "query", - "description" : "Search for Crossing Projects with this unique id", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossingProjectName", - "in" : "query", - "description" : "The human readable name for a crossing project", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "includePotentialParent", - "in" : "query", - "description" : "If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object.", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/CrossingProjectListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "CrossingProjects" ], - "summary" : "Create new CrossingProject", - "description" : "Add new CrossingProject to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/CrossingProjectNewRequest" - } + "/callsets" : { + "get" : { + "tags" : [ + "CallSets" + ], + "summary" : "Get a filtered list of CallSet", + "description" : "Get a list of CallSet", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleName", + "in" : "query", + "description" : "A list of human readable names associated with `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "callSetName", + "in" : "query", + "description" : "A list of human readable names associated with `CallSets`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/CrossingProjectListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/events" : { - "get" : { - "tags" : [ "Events" ], - "summary" : "Get a filtered list of Event", - "description" : "Get a list of Event", - "parameters" : [ { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationUnitDbId", - "in" : "query", - "description" : "The ID which uniquely identifies an observation unit.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "eventDbId", - "in" : "query", - "description" : "Filter based on an Event DbId.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "eventType", - "in" : "query", - "description" : "Filter based on an Event Type", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "dateRangeStart", - "in" : "query", - "description" : "Filter based on an Event start date.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "dateRangeEnd", - "in" : "query", - "description" : "Filter based on an Event start date.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/EventListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/maps" : { - "get" : { - "tags" : [ "GenomeMaps" ], - "summary" : "Get a filtered list of GenomeMap", - "description" : "Get a list of GenomeMap", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "mapDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a `GenomeMap`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "mapPUI", - "in" : "query", - "description" : "The DOI or other permanent identifier for a `GenomeMap`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scientificName", - "in" : "query", - "description" : "Full scientific binomial format name. This includes Genus, Species, and Sub-species", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "type", - "in" : "query", - "description" : "The type of map, usually \"Genetic\" or \"Physical\"", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/GenomeMapListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/germplasm" : { - "get" : { - "tags" : [ "Germplasm" ], - "summary" : "Get a filtered list of Germplasm", - "description" : "Get a list of Germplasm", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmPUI", - "in" : "query", - "description" : "List of Permanent Unique Identifiers to identify germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "accessionNumber", - "in" : "query", - "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "collection", - "in" : "query", - "description" : "A specific panel/collection/population name this germplasm belongs to.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "familyCode", - "in" : "query", - "description" : "A familyCode representing the family this germplasm belongs to.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "instituteCode", - "in" : "query", - "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "binomialName", - "in" : "query", - "description" : "List of the full binomial name (scientific name) to identify a germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "genu", - "in" : "query", - "description" : "List of Genus names to identify germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "specy", - "in" : "query", - "description" : "List of Species names to identify germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "synonym", - "in" : "query", - "description" : "List of alternative names or IDs used to reference this germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "parentDbId", - "in" : "query", - "description" : "Search for Germplasm with these parents", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "progenyDbId", - "in" : "query", - "description" : "Search for Germplasm with these children", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Germplasm" ], - "summary" : "Create new Germplasm", - "description" : "Add new Germplasm to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/GermplasmNewRequest" - } + "/crosses" : { + "get" : { + "tags" : [ + "Crosses" + ], + "summary" : "Get a filtered list of Cross", + "description" : "Get a list of Cross", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossingProjectDbId", + "in" : "query", + "description" : "Search for Crossing Projects with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossingProjectName", + "in" : "query", + "description" : "The human readable name for a crossing project", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossDbId", + "in" : "query", + "description" : "Search for Cross with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossName", + "in" : "query", + "description" : "Search for Cross with this human readable name", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Crosses" + ], + "summary" : "Update the details for an existing Cross", + "description" : "Update the details for an existing Cross", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Crosses" + ], + "summary" : "Create new Cross", + "description" : "Add new Cross to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/attributes" : { - "get" : { - "tags" : [ "GermplasmAttributes" ], - "summary" : "Get a filtered list of GermplasmAttribute", - "description" : "Get a list of GermplasmAttribute", - "parameters" : [ { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "methodDbId", - "in" : "query", - "description" : "List of methods to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "methodName", - "in" : "query", - "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "methodPUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scaleDbId", - "in" : "query", - "description" : "The unique identifier for a Scale", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scaleName", - "in" : "query", - "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scalePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitDbId", - "in" : "query", - "description" : "The unique identifier for a Trait", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitName", - "in" : "query", - "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitPUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "attributeDbId", - "in" : "query", - "description" : "List of Germplasm Attribute IDs to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "attributeName", - "in" : "query", - "description" : "List of human readable Germplasm Attribute names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "attributePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "attributeCategory", - "in" : "query", - "description" : "General category for the attribute. very similar to Trait class.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "GermplasmAttributes" ], - "summary" : "Create new GermplasmAttribute", - "description" : "Add new GermplasmAttribute to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/GermplasmAttributeNewRequest" - } + "/crossingprojects" : { + "get" : { + "tags" : [ + "CrossingProjects" + ], + "summary" : "Get a filtered list of CrossingProject", + "description" : "Get a list of CrossingProject", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossingProjectDbId", + "in" : "query", + "description" : "Search for Crossing Projects with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossingProjectName", + "in" : "query", + "description" : "The human readable name for a crossing project", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "includePotentialParent", + "in" : "query", + "description" : "If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object.", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "CrossingProjects" + ], + "summary" : "Create new CrossingProject", + "description" : "Add new CrossingProject to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossingProjectNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/attributevalues" : { - "get" : { - "tags" : [ "GermplasmAttributeValues" ], - "summary" : "Get a filtered list of GermplasmAttributeValue", - "description" : "Get a list of GermplasmAttributeValue", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "attributeValueDbId", - "in" : "query", - "description" : "List of Germplasm Attribute Value IDs to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "attributeDbId", - "in" : "query", - "description" : "List of Germplasm Attribute IDs to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "attributeName", - "in" : "query", - "description" : "List of human readable Germplasm Attribute names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "ontologyDbId", - "in" : "query", - "description" : "List of ontology IDs to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "methodDbId", - "in" : "query", - "description" : "List of methods to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scaleDbId", - "in" : "query", - "description" : "List of scales to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitDbId", - "in" : "query", - "description" : "List of trait unique ID to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitClass", - "in" : "query", - "description" : "List of trait classes to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "dataType", - "in" : "query", - "description" : "List of scale data types to filter search results", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/TraitDataType" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "GermplasmAttributeValues" ], - "summary" : "Create new GermplasmAttributeValue", - "description" : "Add new GermplasmAttributeValue to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/GermplasmAttributeValueNewRequest" - } + "/events" : { + "get" : { + "tags" : [ + "Events" + ], + "summary" : "Get a filtered list of Event", + "description" : "Get a list of Event", + "parameters" : [ + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The ID which uniquely identifies an observation unit.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "eventDbId", + "in" : "query", + "description" : "Filter based on an Event DbId.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "eventType", + "in" : "query", + "description" : "Filter based on an Event Type", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "dateRangeStart", + "in" : "query", + "description" : "Filter based on an Event start date.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "dateRangeEnd", + "in" : "query", + "description" : "Filter based on an Event start date.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/EventListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/images" : { - "get" : { - "tags" : [ "Images" ], - "summary" : "Get a filtered list of Image", - "description" : "Get a list of Image", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "descriptiveOntologyTerm", - "in" : "query", - "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "imageFileName", - "in" : "query", - "description" : "Image file names to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "imageFileSizeMax", - "in" : "query", - "description" : "A maximum image file size to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "imageFileSizeMin", - "in" : "query", - "description" : "A minimum image file size to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "imageHeightMax", - "in" : "query", - "description" : "A maximum image height to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "imageHeightMin", - "in" : "query", - "description" : "A minimum image height to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "imageLocation", - "in" : "query", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - } - }, { - "name" : "imageName", - "in" : "query", - "description" : "Human readable names to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "imageTimeStampRangeEnd", - "in" : "query", - "description" : "The latest timestamp to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "imageTimeStampRangeStart", - "in" : "query", - "description" : "The earliest timestamp to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "imageWidthMax", - "in" : "query", - "description" : "A maximum image width to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "imageWidthMin", - "in" : "query", - "description" : "A minimum image width to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "mimeType", - "in" : "query", - "description" : "A set of image file types to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationDbId", - "in" : "query", - "description" : "A list of observation Ids this image is associated with to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "imageDbId", - "in" : "query", - "description" : "A list of image Ids to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationUnitDbId", - "in" : "query", - "description" : "A set of observation unit identifiers to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ImageListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Images" ], - "summary" : "Create new Image", - "description" : "Add new Image to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ImageNewRequest" - } + "/maps" : { + "get" : { + "tags" : [ + "GenomeMaps" + ], + "summary" : "Get a filtered list of GenomeMap", + "description" : "Get a list of GenomeMap", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "mapDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a `GenomeMap`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "mapPUI", + "in" : "query", + "description" : "The DOI or other permanent identifier for a `GenomeMap`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scientificName", + "in" : "query", + "description" : "Full scientific binomial format name. This includes Genus, Species, and Sub-species", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "type", + "in" : "query", + "description" : "The type of map, usually \"Genetic\" or \"Physical\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GenomeMapListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ImageListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/lists" : { - "get" : { - "tags" : [ "Lists" ], - "summary" : "Get a filtered list of List", - "description" : "Get a list of List", - "parameters" : [ { - "name" : "dateCreatedRangeStart", - "in" : "query", - "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "dateCreatedRangeEnd", - "in" : "query", - "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "dateModifiedRangeStart", - "in" : "query", - "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "dateModifiedRangeEnd", - "in" : "query", - "description" : "Define the end for an interval of time and only include Lists that are modified within this interval.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "listDbId", - "in" : "query", - "description" : "An array of primary database identifiers to identify a set of Lists", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "listName", - "in" : "query", - "description" : "An array of human readable names to identify a set of Lists", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "listOwnerName", - "in" : "query", - "description" : "An array of names for the people or entities who are responsible for a set of Lists", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "listOwnerPersonDbId", - "in" : "query", - "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "listSource", - "in" : "query", - "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "listType", - "in" : "query", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/ListType" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ListListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Lists" ], - "summary" : "Create new List", - "description" : "Add new List to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ListNewRequest" - } + "/germplasm" : { + "get" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Get a filtered list of Germplasm", + "description" : "Get a list of Germplasm", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmPUI", + "in" : "query", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "accessionNumber", + "in" : "query", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "collection", + "in" : "query", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "familyCode", + "in" : "query", + "description" : "A familyCode representing the family this germplasm belongs to.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "instituteCode", + "in" : "query", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "binomialName", + "in" : "query", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "genu", + "in" : "query", + "description" : "List of Genus names to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "specy", + "in" : "query", + "description" : "List of Species names to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "synonym", + "in" : "query", + "description" : "List of alternative names or IDs used to reference this germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "parentDbId", + "in" : "query", + "description" : "Search for Germplasm with these parents", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "progenyDbId", + "in" : "query", + "description" : "Search for Germplasm with these children", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Create new Germplasm", + "description" : "Add new Germplasm to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ListListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/locations" : { - "get" : { - "tags" : [ "Locations" ], - "summary" : "Get a filtered list of Location", - "description" : "Get a list of Location", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationDbId", - "in" : "query", - "description" : "The location ids to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationName", - "in" : "query", - "description" : "A human readable names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "abbreviation", - "in" : "query", - "description" : "A list of shortened human readable names for a set of Locations", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "altitudeMin", - "in" : "query", - "description" : "The minimum altitude to search for", - "required" : false, - "schema" : { - "type" : "number" - } - }, { - "name" : "altitudeMax", - "in" : "query", - "description" : "The maximum altitude to search for", - "required" : false, - "schema" : { - "type" : "number" - } - }, { - "name" : "countryCode", - "in" : "query", - "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "countryName", - "in" : "query", - "description" : "The full name of the country to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "coordinate", - "in" : "query", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - } - }, { - "name" : "instituteAddress", - "in" : "query", - "description" : "The street address of the institute to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "instituteName", - "in" : "query", - "description" : "The name of the institute to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationType", - "in" : "query", - "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "parentLocationDbId", - "in" : "query", - "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "parentLocationName", - "in" : "query", - "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/LocationListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Locations" ], - "summary" : "Create new Location", - "description" : "Add new Location to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/LocationNewRequest" - } + "/attributes" : { + "get" : { + "tags" : [ + "GermplasmAttributes" + ], + "summary" : "Get a filtered list of GermplasmAttribute", + "description" : "Get a list of GermplasmAttribute", + "parameters" : [ + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "methodDbId", + "in" : "query", + "description" : "List of methods to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "methodName", + "in" : "query", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "methodPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scaleDbId", + "in" : "query", + "description" : "The unique identifier for a Scale", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scaleName", + "in" : "query", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scalePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitDbId", + "in" : "query", + "description" : "The unique identifier for a Trait", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitName", + "in" : "query", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "attributeDbId", + "in" : "query", + "description" : "List of Germplasm Attribute IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "attributeName", + "in" : "query", + "description" : "List of human readable Germplasm Attribute names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "attributePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "attributeCategory", + "in" : "query", + "description" : "General category for the attribute. very similar to Trait class.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "GermplasmAttributes" + ], + "summary" : "Create new GermplasmAttribute", + "description" : "Add new GermplasmAttribute to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/LocationListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/markerpositions" : { - "get" : { - "tags" : [ "MarkerPositions" ], - "summary" : "Get a filtered list of MarkerPosition", - "description" : "Get a list of MarkerPosition", - "parameters" : [ { - "name" : "mapDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `GenomeMaps` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "linkageGroupName", - "in" : "query", - "description" : "A list of Uniquely Identifiable linkage group names", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variants` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "minPosition", - "in" : "query", - "description" : "The minimum position of markers in a given map", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "maxPosition", - "in" : "query", - "description" : "The maximum position of markers in a given map", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/MarkerPositionListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/methods" : { - "get" : { - "tags" : [ "Methods" ], - "summary" : "Get a filtered list of Method", - "description" : "Get a list of Method", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "ontologyDbId", - "in" : "query", - "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scaleDbId", - "in" : "query", - "description" : "The unique identifier for a method.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableDbId", - "in" : "query", - "description" : "The unique identifier for an observation variable.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/MethodListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Methods" ], - "summary" : "Create new Method", - "description" : "Add new Method to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/MethodNewRequest" - } + "/attributevalues" : { + "get" : { + "tags" : [ + "GermplasmAttributeValues" + ], + "summary" : "Get a filtered list of GermplasmAttributeValue", + "description" : "Get a list of GermplasmAttributeValue", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "attributeValueDbId", + "in" : "query", + "description" : "List of Germplasm Attribute Value IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "attributeDbId", + "in" : "query", + "description" : "List of Germplasm Attribute IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "attributeName", + "in" : "query", + "description" : "List of human readable Germplasm Attribute names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "ontologyDbId", + "in" : "query", + "description" : "List of ontology IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "methodDbId", + "in" : "query", + "description" : "List of methods to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scaleDbId", + "in" : "query", + "description" : "List of scales to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitDbId", + "in" : "query", + "description" : "List of trait unique ID to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitClass", + "in" : "query", + "description" : "List of trait classes to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "dataType", + "in" : "query", + "description" : "List of scale data types to filter search results", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "GermplasmAttributeValues" + ], + "summary" : "Create new GermplasmAttributeValue", + "description" : "Add new GermplasmAttributeValue to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/MethodListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/observations" : { - "get" : { - "tags" : [ "Observations" ], - "summary" : "Get a filtered list of Observation", - "description" : "Get a list of Observation", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationDbId", - "in" : "query", - "description" : "The location ids to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationName", - "in" : "query", - "description" : "A human readable names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableDbId", - "in" : "query", - "description" : "The DbIds of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableName", - "in" : "query", - "description" : "The names of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariablePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationDbId", - "in" : "query", - "description" : "The unique id of an Observation", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationUnitDbId", - "in" : "query", - "description" : "The unique id of an Observation Unit", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationLevel", - "in" : "query", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" - } - }, { - "name" : "observationLevelRelationship", - "in" : "query", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" - } - }, { - "name" : "observationTimeStampRangeEnd", - "in" : "query", - "description" : "Timestamp range end", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationTimeStampRangeStart", - "in" : "query", - "description" : "Timestamp range start", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "seasonDbId", - "in" : "query", - "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Observations" ], - "summary" : "Update the details for an existing Observation", - "description" : "Update the details for an existing Observation", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ObservationNewRequest" - } + "/images" : { + "get" : { + "tags" : [ + "Images" + ], + "summary" : "Get a filtered list of Image", + "description" : "Get a list of Image", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "descriptiveOntologyTerm", + "in" : "query", + "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "imageFileName", + "in" : "query", + "description" : "Image file names to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "imageFileSizeMax", + "in" : "query", + "description" : "A maximum image file size to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "imageFileSizeMin", + "in" : "query", + "description" : "A minimum image file size to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "imageHeightMax", + "in" : "query", + "description" : "A maximum image height to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "imageHeightMin", + "in" : "query", + "description" : "A minimum image height to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "imageLocation", + "in" : "query", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + } + }, + { + "name" : "imageName", + "in" : "query", + "description" : "Human readable names to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "imageTimeStampRangeEnd", + "in" : "query", + "description" : "The latest timestamp to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "imageTimeStampRangeStart", + "in" : "query", + "description" : "The earliest timestamp to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "imageWidthMax", + "in" : "query", + "description" : "A maximum image width to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "imageWidthMin", + "in" : "query", + "description" : "A minimum image width to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "mimeType", + "in" : "query", + "description" : "A set of image file types to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationDbId", + "in" : "query", + "description" : "A list of observation Ids this image is associated with to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "imageDbId", + "in" : "query", + "description" : "A list of image Ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "A set of observation unit identifiers to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Images" + ], + "summary" : "Create new Image", + "description" : "Add new Image to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Observations" ], - "summary" : "Create new Observation", - "description" : "Add new Observation to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ObservationNewRequest" - } + "/lists" : { + "get" : { + "tags" : [ + "Lists" + ], + "summary" : "Get a filtered list of List", + "description" : "Get a list of List", + "parameters" : [ + { + "name" : "dateCreatedRangeStart", + "in" : "query", + "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "dateCreatedRangeEnd", + "in" : "query", + "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "dateModifiedRangeStart", + "in" : "query", + "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "dateModifiedRangeEnd", + "in" : "query", + "description" : "Define the end for an interval of time and only include Lists that are modified within this interval.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "listDbId", + "in" : "query", + "description" : "An array of primary database identifiers to identify a set of Lists", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "listName", + "in" : "query", + "description" : "An array of human readable names to identify a set of Lists", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "listOwnerName", + "in" : "query", + "description" : "An array of names for the people or entities who are responsible for a set of Lists", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "listOwnerPersonDbId", + "in" : "query", + "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "listSource", + "in" : "query", + "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "listType", + "in" : "query", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/ListType" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Lists" + ], + "summary" : "Create new List", + "description" : "Add new List to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/observationunits" : { - "get" : { - "tags" : [ "ObservationUnits" ], - "summary" : "Get a filtered list of ObservationUnit", - "description" : "Get a list of ObservationUnit", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationDbId", - "in" : "query", - "description" : "The location ids to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationName", - "in" : "query", - "description" : "A human readable names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableDbId", - "in" : "query", - "description" : "The DbIds of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableName", - "in" : "query", - "description" : "The names of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariablePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationUnitDbId", - "in" : "query", - "description" : "The unique id of an observation unit", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationUnitName", - "in" : "query", - "description" : "The human readable identifier for an Observation Unit", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationLevel", - "in" : "query", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" - } - }, { - "name" : "observationLevelRelationship", - "in" : "query", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" - } - }, { - "name" : "includeObservation", - "in" : "query", - "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "seasonDbId", - "in" : "query", - "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "ObservationUnits" ], - "summary" : "Update the details for an existing ObservationUnit", - "description" : "Update the details for an existing ObservationUnit", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ObservationUnitNewRequest" - } + "/locations" : { + "get" : { + "tags" : [ + "Locations" + ], + "summary" : "Get a filtered list of Location", + "description" : "Get a list of Location", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "abbreviation", + "in" : "query", + "description" : "A list of shortened human readable names for a set of Locations", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "altitudeMin", + "in" : "query", + "description" : "The minimum altitude to search for", + "required" : false, + "schema" : { + "type" : "number" + } + }, + { + "name" : "altitudeMax", + "in" : "query", + "description" : "The maximum altitude to search for", + "required" : false, + "schema" : { + "type" : "number" + } + }, + { + "name" : "countryCode", + "in" : "query", + "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "countryName", + "in" : "query", + "description" : "The full name of the country to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "coordinate", + "in" : "query", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + } + }, + { + "name" : "instituteAddress", + "in" : "query", + "description" : "The street address of the institute to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "instituteName", + "in" : "query", + "description" : "The name of the institute to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationType", + "in" : "query", + "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "parentLocationDbId", + "in" : "query", + "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "parentLocationName", + "in" : "query", + "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Locations" + ], + "summary" : "Create new Location", + "description" : "Add new Location to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "ObservationUnits" ], - "summary" : "Create new ObservationUnit", - "description" : "Add new ObservationUnit to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ObservationUnitNewRequest" - } + "/markerpositions" : { + "get" : { + "tags" : [ + "MarkerPositions" + ], + "summary" : "Get a filtered list of MarkerPosition", + "description" : "Get a list of MarkerPosition", + "parameters" : [ + { + "name" : "mapDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `GenomeMaps` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "linkageGroupName", + "in" : "query", + "description" : "A list of Uniquely Identifiable linkage group names", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "minPosition", + "in" : "query", + "description" : "The minimum position of markers in a given map", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "maxPosition", + "in" : "query", + "description" : "The maximum position of markers in a given map", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/MarkerPositionListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variables" : { - "get" : { - "tags" : [ "ObservationVariables" ], - "summary" : "Get a filtered list of ObservationVariable", - "description" : "Get a list of ObservationVariable", - "parameters" : [ { - "name" : "observationVariableDbId", - "in" : "query", - "description" : "The DbIds of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableName", - "in" : "query", - "description" : "The names of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariablePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "ontologyDbId", - "in" : "query", - "description" : "List of ontology IDs to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "methodDbId", - "in" : "query", - "description" : "List of methods to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "methodName", - "in" : "query", - "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "methodPUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scaleDbId", - "in" : "query", - "description" : "The unique identifier for a Scale", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scaleName", - "in" : "query", - "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scalePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "dataType", - "in" : "query", - "description" : "List of scale data types to filter search results", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/TraitDataType" - } - }, { - "name" : "traitClass", - "in" : "query", - "description" : "List of trait classes to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitDbId", - "in" : "query", - "description" : "The unique identifier for a Trait", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitName", - "in" : "query", - "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitPUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitAttribute", - "in" : "query", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitAttributePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitEntity", - "in" : "query", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitEntityPUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "ObservationVariables" ], - "summary" : "Create new ObservationVariable", - "description" : "Add new ObservationVariable to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ObservationVariableNewRequest" - } + "/methods" : { + "get" : { + "tags" : [ + "Methods" + ], + "summary" : "Get a filtered list of Method", + "description" : "Get a list of Method", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "ontologyDbId", + "in" : "query", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scaleDbId", + "in" : "query", + "description" : "The unique identifier for a method.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The unique identifier for an observation variable.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/MethodListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Methods" + ], + "summary" : "Create new Method", + "description" : "Add new Method to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MethodNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/MethodListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/ontologies" : { - "get" : { - "tags" : [ "Ontologies" ], - "summary" : "Get a filtered list of Ontology", - "description" : "Get a list of Ontology", - "parameters" : [ { - "name" : "ontologyDbId", - "in" : "query", - "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "ontologyName", - "in" : "query", - "description" : "The human readable identifier for an ontology definition.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/OntologyListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Ontologies" ], - "summary" : "Create new Ontology", - "description" : "Add new Ontology to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/OntologyNewRequest" - } + "/observations" : { + "get" : { + "tags" : [ + "Observations" + ], + "summary" : "Get a filtered list of Observation", + "description" : "Get a list of Observation", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationDbId", + "in" : "query", + "description" : "The unique id of an Observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The unique id of an Observation Unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationLevel", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, + { + "name" : "observationLevelRelationship", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + { + "name" : "observationTimeStampRangeEnd", + "in" : "query", + "description" : "Timestamp range end", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationTimeStampRangeStart", + "in" : "query", + "description" : "Timestamp range start", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "seasonDbId", + "in" : "query", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Observations" + ], + "summary" : "Update the details for an existing Observation", + "description" : "Update the details for an existing Observation", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Observations" + ], + "summary" : "Create new Observation", + "description" : "Add new Observation to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/OntologyListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/pedigree" : { - "get" : { - "tags" : [ "PedigreeNodes" ], - "summary" : "Get a filtered list of PedigreeNode", - "description" : "Get a list of PedigreeNode", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmPUI", - "in" : "query", - "description" : "List of Permanent Unique Identifiers to identify germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "accessionNumber", - "in" : "query", - "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "collection", - "in" : "query", - "description" : "A specific panel/collection/population name this germplasm belongs to.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "familyCode", - "in" : "query", - "description" : "A familyCode representing the family this germplasm belongs to.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "instituteCode", - "in" : "query", - "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "binomialName", - "in" : "query", - "description" : "List of the full binomial name (scientific name) to identify a germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "genu", - "in" : "query", - "description" : "List of Genus names to identify germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "specy", - "in" : "query", - "description" : "List of Species names to identify germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "synonym", - "in" : "query", - "description" : "List of alternative names or IDs used to reference this germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "includeParent", - "in" : "query", - "description" : "If this parameter is true, include the array of parents in the response", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "includeSibling", - "in" : "query", - "description" : "If this parameter is true, include the array of siblings in the response", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "includeProgeny", - "in" : "query", - "description" : "If this parameter is true, include the array of progeny in the response", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "includeFullTree", - "in" : "query", - "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "pedigreeDepth", - "in" : "query", - "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "progenyDepth", - "in" : "query", - "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/PedigreeNodeListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "PedigreeNodes" ], - "summary" : "Create new PedigreeNode", - "description" : "Add new PedigreeNode to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/PedigreeNode" - } + "/observationunits" : { + "get" : { + "tags" : [ + "ObservationUnits" + ], + "summary" : "Get a filtered list of ObservationUnit", + "description" : "Get a list of ObservationUnit", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The unique id of an observation unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitName", + "in" : "query", + "description" : "The human readable identifier for an Observation Unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationLevel", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, + { + "name" : "observationLevelRelationship", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + { + "name" : "includeObservation", + "in" : "query", + "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "seasonDbId", + "in" : "query", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "ObservationUnits" + ], + "summary" : "Update the details for an existing ObservationUnit", + "description" : "Update the details for an existing ObservationUnit", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "ObservationUnits" + ], + "summary" : "Create new ObservationUnit", + "description" : "Add new ObservationUnit to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/PedigreeNodeListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/people" : { - "get" : { - "tags" : [ "People" ], - "summary" : "Get a filtered list of Person", - "description" : "Get a list of Person", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "emailAddress", - "in" : "query", - "description" : "email address for this person", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "firstName", - "in" : "query", - "description" : "Persons first name", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "lastName", - "in" : "query", - "description" : "Persons last name", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "mailingAddress", - "in" : "query", - "description" : "physical address of this person", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "middleName", - "in" : "query", - "description" : "Persons middle name", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "personDbId", - "in" : "query", - "description" : "Unique ID for this person", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "phoneNumber", - "in" : "query", - "description" : "phone number of this person", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "userID", - "in" : "query", - "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/PersonListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "People" ], - "summary" : "Create new Person", - "description" : "Add new Person to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/PersonNewRequest" - } + "/variables" : { + "get" : { + "tags" : [ + "ObservationVariables" + ], + "summary" : "Get a filtered list of ObservationVariable", + "description" : "Get a list of ObservationVariable", + "parameters" : [ + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "ontologyDbId", + "in" : "query", + "description" : "List of ontology IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "methodDbId", + "in" : "query", + "description" : "List of methods to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "methodName", + "in" : "query", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "methodPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scaleDbId", + "in" : "query", + "description" : "The unique identifier for a Scale", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scaleName", + "in" : "query", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scalePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "dataType", + "in" : "query", + "description" : "List of scale data types to filter search results", + "required" : false, + "schema" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + { + "name" : "traitClass", + "in" : "query", + "description" : "List of trait classes to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitDbId", + "in" : "query", + "description" : "The unique identifier for a Trait", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitName", + "in" : "query", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitAttribute", + "in" : "query", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitAttributePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitEntity", + "in" : "query", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitEntityPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "ObservationVariables" + ], + "summary" : "Create new ObservationVariable", + "description" : "Add new ObservationVariable to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/PersonListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/plannedcrosses" : { - "get" : { - "tags" : [ "Crosses" ], - "summary" : "Get a filtered list of PlannedCross", - "description" : "Get a list of PlannedCross", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossingProjectDbId", - "in" : "query", - "description" : "Search for Crossing Projects with this unique id", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossingProjectName", - "in" : "query", - "description" : "The human readable name for a crossing project", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "plannedCrossDbId", - "in" : "query", - "description" : "Search for Planned Cross with this unique id", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "plannedCrossName", - "in" : "query", - "description" : "Search for Planned Cross with this human readable name", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "status", - "in" : "query", - "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", - "required" : false, - "schema" : { - "type" : "string", - "enum" : [ "TODO", "DONE", "SKIPPED" ] - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/PlannedCrossListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Crosses" ], - "summary" : "Update the details for an existing PlannedCross", - "description" : "Update the details for an existing PlannedCross", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/PlannedCross" - } + "/ontologies" : { + "get" : { + "tags" : [ + "Ontologies" + ], + "summary" : "Get a filtered list of Ontology", + "description" : "Get a list of Ontology", + "parameters" : [ + { + "name" : "ontologyDbId", + "in" : "query", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "ontologyName", + "in" : "query", + "description" : "The human readable identifier for an ontology definition.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Ontologies" + ], + "summary" : "Create new Ontology", + "description" : "Add new Ontology to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/OntologyNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/PlannedCrossListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Crosses" ], - "summary" : "Create new PlannedCross", - "description" : "Add new PlannedCross to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/PlannedCross" - } + "/pedigree" : { + "get" : { + "tags" : [ + "PedigreeNodes" + ], + "summary" : "Get a filtered list of PedigreeNode", + "description" : "Get a list of PedigreeNode", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmPUI", + "in" : "query", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "accessionNumber", + "in" : "query", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "collection", + "in" : "query", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "familyCode", + "in" : "query", + "description" : "A familyCode representing the family this germplasm belongs to.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "instituteCode", + "in" : "query", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "binomialName", + "in" : "query", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "genu", + "in" : "query", + "description" : "List of Genus names to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "specy", + "in" : "query", + "description" : "List of Species names to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "synonym", + "in" : "query", + "description" : "List of alternative names or IDs used to reference this germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "includeParent", + "in" : "query", + "description" : "If this parameter is true, include the array of parents in the response", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "includeSibling", + "in" : "query", + "description" : "If this parameter is true, include the array of siblings in the response", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "includeProgeny", + "in" : "query", + "description" : "If this parameter is true, include the array of progeny in the response", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "includeFullTree", + "in" : "query", + "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "pedigreeDepth", + "in" : "query", + "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "progenyDepth", + "in" : "query", + "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "PedigreeNodes" + ], + "summary" : "Create new PedigreeNode", + "description" : "Add new PedigreeNode to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PedigreeNode" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/PlannedCrossListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/plates" : { - "get" : { - "tags" : [ "Plates" ], - "summary" : "Get a filtered list of Plate", - "description" : "Get a list of Plate", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationUnitDbId", - "in" : "query", - "description" : "The ID which uniquely identifies an observation unit", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "plateDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a plate of samples", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "plateName", - "in" : "query", - "description" : "The human readable name of a plate of samples", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "plateBarcode", - "in" : "query", - "description" : "A unique identifier physically attached to the plate", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a sample", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleName", - "in" : "query", - "description" : "The human readable name of the sample", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleGroupDbId", - "in" : "query", - "description" : "The unique identifier for a group of related Samples", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/PlateListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Plates" ], - "summary" : "Create new Plate", - "description" : "Add new Plate to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/PlateNewRequest" - } + "/people" : { + "get" : { + "tags" : [ + "People" + ], + "summary" : "Get a filtered list of Person", + "description" : "Get a list of Person", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "emailAddress", + "in" : "query", + "description" : "email address for this person", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "firstName", + "in" : "query", + "description" : "Persons first name", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "lastName", + "in" : "query", + "description" : "Persons last name", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "mailingAddress", + "in" : "query", + "description" : "physical address of this person", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "middleName", + "in" : "query", + "description" : "Persons middle name", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "personDbId", + "in" : "query", + "description" : "Unique ID for this person", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "phoneNumber", + "in" : "query", + "description" : "phone number of this person", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "userID", + "in" : "query", + "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "People" + ], + "summary" : "Create new Person", + "description" : "Add new Person to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/PlateListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/programs" : { - "get" : { - "tags" : [ "Programs" ], - "summary" : "Get a filtered list of Program", - "description" : "Get a list of Program", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "abbreviation", - "in" : "query", - "description" : "A list of shortened human readable names for a set of Programs", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "leadPersonDbId", - "in" : "query", - "description" : "The person DbIds of the program leader to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "leadPersonName", - "in" : "query", - "description" : "The names of the program leader to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "objectife", - "in" : "query", - "description" : "A program objective to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programType", - "in" : "query", - "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", - "required" : false, - "schema" : { - "type" : "string", - "enum" : [ "STANDARD", "PROJECT" ] - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ProgramListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Programs" ], - "summary" : "Create new Program", - "description" : "Add new Program to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ProgramNewRequest" - } + "/plannedcrosses" : { + "get" : { + "tags" : [ + "Crosses" + ], + "summary" : "Get a filtered list of PlannedCross", + "description" : "Get a list of PlannedCross", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossingProjectDbId", + "in" : "query", + "description" : "Search for Crossing Projects with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossingProjectName", + "in" : "query", + "description" : "The human readable name for a crossing project", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "plannedCrossDbId", + "in" : "query", + "description" : "Search for Planned Cross with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "plannedCrossName", + "in" : "query", + "description" : "Search for Planned Cross with this human readable name", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "status", + "in" : "query", + "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", + "required" : false, + "schema" : { + "type" : "string", + "enum" : [ + "TODO", + "DONE", + "SKIPPED" + ] + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlannedCrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Crosses" + ], + "summary" : "Update the details for an existing PlannedCross", + "description" : "Update the details for an existing PlannedCross", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlannedCross" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlannedCrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Crosses" + ], + "summary" : "Create new PlannedCross", + "description" : "Add new PlannedCross to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlannedCross" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlannedCrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ProgramListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/references" : { - "get" : { - "tags" : [ "References" ], - "summary" : "Get a filtered list of Reference", - "description" : "Get a list of Reference", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "accession", - "in" : "query", - "description" : "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "md5checksum", - "in" : "query", - "description" : "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `References` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `ReferenceSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "isDerived", - "in" : "query", - "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "minLength", - "in" : "query", - "description" : "The minimum length of this `References` sequence.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "maxLength", - "in" : "query", - "description" : "The minimum length of this `References` sequence.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ReferenceListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/referencesets" : { - "get" : { - "tags" : [ "ReferenceSets" ], - "summary" : "Get a filtered list of ReferenceSet", - "description" : "Get a list of ReferenceSet", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "accession", - "in" : "query", - "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "assemblyPUI", - "in" : "query", - "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "md5checksum", - "in" : "query", - "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceSetDbId", - "in" : "query", - "description" : "The `ReferenceSets` to search.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ReferenceSetListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/samples" : { - "get" : { - "tags" : [ "Samples" ], - "summary" : "Get a filtered list of Sample", - "description" : "Get a list of Sample", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationUnitDbId", - "in" : "query", - "description" : "The ID which uniquely identifies an `ObservationUnit`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "plateDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a `Plate` of `Samples`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "plateName", - "in" : "query", - "description" : "The human readable name of a `Plate` of `Samples`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a `Sample`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleName", - "in" : "query", - "description" : "The human readable name of the `Sample`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleGroupDbId", - "in" : "query", - "description" : "The unique identifier for a group of related `Samples`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a `Germplasm`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/SampleListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Samples" ], - "summary" : "Update the details for an existing Sample", - "description" : "Update the details for an existing Sample", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/SampleNewRequest" - } + "/plates" : { + "get" : { + "tags" : [ + "Plates" + ], + "summary" : "Get a filtered list of Plate", + "description" : "Get a list of Plate", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The ID which uniquely identifies an observation unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "plateDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a plate of samples", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "plateName", + "in" : "query", + "description" : "The human readable name of a plate of samples", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "plateBarcode", + "in" : "query", + "description" : "A unique identifier physically attached to the plate", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a sample", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleName", + "in" : "query", + "description" : "The human readable name of the sample", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleGroupDbId", + "in" : "query", + "description" : "The unique identifier for a group of related Samples", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Plates" + ], + "summary" : "Create new Plate", + "description" : "Add new Plate to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlateNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/SampleListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Samples" ], - "summary" : "Create new Sample", - "description" : "Add new Sample to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/SampleNewRequest" - } + "/programs" : { + "get" : { + "tags" : [ + "Programs" + ], + "summary" : "Get a filtered list of Program", + "description" : "Get a list of Program", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "abbreviation", + "in" : "query", + "description" : "A list of shortened human readable names for a set of Programs", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "leadPersonDbId", + "in" : "query", + "description" : "The person DbIds of the program leader to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "leadPersonName", + "in" : "query", + "description" : "The names of the program leader to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "objectife", + "in" : "query", + "description" : "A program objective to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programType", + "in" : "query", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "required" : false, + "schema" : { + "type" : "string", + "enum" : [ + "STANDARD", + "PROJECT" + ] + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Programs" + ], + "summary" : "Create new Program", + "description" : "Add new Program to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/SampleListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/scales" : { - "get" : { - "tags" : [ "Scales" ], - "summary" : "Get a filtered list of Scale", - "description" : "Get a list of Scale", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "ontologyDbId", - "in" : "query", - "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "scaleDbId", - "in" : "query", - "description" : "The unique identifier for a scale.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableDbId", - "in" : "query", - "description" : "The unique identifier for an observation variable.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ScaleListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Scales" ], - "summary" : "Create new Scale", - "description" : "Add new Scale to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/ScaleNewRequest" - } + "/references" : { + "get" : { + "tags" : [ + "References" + ], + "summary" : "Get a filtered list of Reference", + "description" : "Get a list of Reference", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "accession", + "in" : "query", + "description" : "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "md5checksum", + "in" : "query", + "description" : "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `References` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `ReferenceSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "isDerived", + "in" : "query", + "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "minLength", + "in" : "query", + "description" : "The minimum length of this `References` sequence.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "maxLength", + "in" : "query", + "description" : "The minimum length of this `References` sequence.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ScaleListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/seasons" : { - "get" : { - "tags" : [ "Seasons" ], - "summary" : "Get a filtered list of Season", - "description" : "Get a list of Season", - "parameters" : [ { - "name" : "seasonDbId", - "in" : "query", - "description" : "The unique identifier for a season. For backward compatibility it can be a string like '2012', '1957-2004'.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "season", - "in" : "query", - "description" : "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\".", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "seasonName", - "in" : "query", - "description" : "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\".", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "year", - "in" : "query", - "description" : "The 4 digit year of a season. Example \"2017\"", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/SeasonListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Seasons" ], - "summary" : "Create new Season", - "description" : "Add new Season to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/Season" - } + "/referencesets" : { + "get" : { + "tags" : [ + "ReferenceSets" + ], + "summary" : "Get a filtered list of ReferenceSet", + "description" : "Get a list of ReferenceSet", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "accession", + "in" : "query", + "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "assemblyPUI", + "in" : "query", + "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "md5checksum", + "in" : "query", + "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "The `ReferenceSets` to search.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/SeasonListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/seedlots" : { - "get" : { - "tags" : [ "SeedLots" ], - "summary" : "Get a filtered list of SeedLot", - "description" : "Get a list of SeedLot", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "seedLotDbId", - "in" : "query", - "description" : "Unique id for a seed lot on this server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossDbId", - "in" : "query", - "description" : "Search for Cross with this unique id", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "crossName", - "in" : "query", - "description" : "Search for Cross with this human readable name", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/SeedLotListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "SeedLots" ], - "summary" : "Create new SeedLot", - "description" : "Add new SeedLot to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/SeedLotNewRequest" - } + "/samples" : { + "get" : { + "tags" : [ + "Samples" + ], + "summary" : "Get a filtered list of Sample", + "description" : "Get a list of Sample", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The ID which uniquely identifies an `ObservationUnit`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "plateDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a `Plate` of `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "plateName", + "in" : "query", + "description" : "The human readable name of a `Plate` of `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a `Sample`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleName", + "in" : "query", + "description" : "The human readable name of the `Sample`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleGroupDbId", + "in" : "query", + "description" : "The unique identifier for a group of related `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a `Germplasm`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Samples" + ], + "summary" : "Update the details for an existing Sample", + "description" : "Update the details for an existing Sample", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Samples" + ], + "summary" : "Create new Sample", + "description" : "Add new Sample to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/SeedLotListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/studies" : { - "get" : { - "tags" : [ "Studies" ], - "summary" : "Get a filtered list of Study", - "description" : "Get a list of Study", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationDbId", - "in" : "query", - "description" : "The location ids to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationName", - "in" : "query", - "description" : "A human readable names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableDbId", - "in" : "query", - "description" : "The DbIds of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableName", - "in" : "query", - "description" : "The names of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariablePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "actife", - "in" : "query", - "description" : "A flag to indicate if a Study is currently active and ongoing", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "seasonDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a season", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyType", - "in" : "query", - "description" : "The type of study being performed. ex. \"Yield Trial\", etc", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyCode", - "in" : "query", - "description" : "A short human readable code for a study", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyPUI", - "in" : "query", - "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/StudyListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Studies" ], - "summary" : "Create new Study", - "description" : "Add new Study to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/StudyNewRequest" - } + "/scales" : { + "get" : { + "tags" : [ + "Scales" + ], + "summary" : "Get a filtered list of Scale", + "description" : "Get a list of Scale", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "ontologyDbId", + "in" : "query", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "scaleDbId", + "in" : "query", + "description" : "The unique identifier for a scale.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The unique identifier for an observation variable.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ScaleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Scales" + ], + "summary" : "Create new Scale", + "description" : "Add new Scale to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ScaleNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ScaleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/StudyListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/traits" : { - "get" : { - "tags" : [ "Traits" ], - "summary" : "Get a filtered list of Trait", - "description" : "Get a list of Trait", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "ontologyDbId", - "in" : "query", - "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "traitDbId", - "in" : "query", - "description" : "The unique identifier for a trait.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableDbId", - "in" : "query", - "description" : "The unique identifier for an observation variable.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/TraitListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Traits" ], - "summary" : "Create new Trait", - "description" : "Add new Trait to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/TraitNewRequest" - } + "/seasons" : { + "get" : { + "tags" : [ + "Seasons" + ], + "summary" : "Get a filtered list of Season", + "description" : "Get a list of Season", + "parameters" : [ + { + "name" : "seasonDbId", + "in" : "query", + "description" : "The unique identifier for a season. For backward compatibility it can be a string like '2012', '1957-2004'.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "season", + "in" : "query", + "description" : "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\".", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "seasonName", + "in" : "query", + "description" : "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\".", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "year", + "in" : "query", + "description" : "The 4 digit year of a season. Example \"2017\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Seasons" + ], + "summary" : "Create new Season", + "description" : "Add new Season to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/Season" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/TraitListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/trials" : { - "get" : { - "tags" : [ "Trials" ], - "summary" : "Get a filtered list of Trial", - "description" : "Get a list of Trial", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationDbId", - "in" : "query", - "description" : "The location ids to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "locationName", - "in" : "query", - "description" : "A human readable names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableDbId", - "in" : "query", - "description" : "The DbIds of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariableName", - "in" : "query", - "description" : "The names of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "observationVariablePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "actife", - "in" : "query", - "description" : "A flag to indicate if a Trial is currently active and ongoing", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "contactDbId", - "in" : "query", - "description" : "List of contact entities associated with this trial", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "searchDateRangeStart", - "in" : "query", - "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "searchDateRangeEnd", - "in" : "query", - "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialPUI", - "in" : "query", - "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/TrialListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ "Trials" ], - "summary" : "Create new Trial", - "description" : "Add new Trial to database", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "$ref" : "#/components/schemas/TrialNewRequest" - } + "/seedlots" : { + "get" : { + "tags" : [ + "SeedLots" + ], + "summary" : "Get a filtered list of SeedLot", + "description" : "Get a list of SeedLot", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "seedLotDbId", + "in" : "query", + "description" : "Unique id for a seed lot on this server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossDbId", + "in" : "query", + "description" : "Search for Cross with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "crossName", + "in" : "query", + "description" : "Search for Cross with this human readable name", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "SeedLots" + ], + "summary" : "Create new SeedLot", + "description" : "Add new SeedLot to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/TrialListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variants" : { - "get" : { - "tags" : [ "Variants" ], - "summary" : "Get a filtered list of Variant", - "description" : "Get a list of Variant", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "callSetDbId", - "in" : "query", - "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "end", - "in" : "query", - "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "referenceDbId", - "in" : "query", - "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype `Reference`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceSetDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype `ReferenceSet`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "start", - "in" : "query", - "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variants`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variantsets" : { - "get" : { - "tags" : [ "VariantSets" ], - "summary" : "Get a filtered list of VariantSet", - "description" : "Get a list of VariantSet", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "callSetDbId", - "in" : "query", - "description" : "The unique identifier representing a CallSet", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantDbId", - "in" : "query", - "description" : "The unique identifier representing a Variant", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "The unique identifier representing a VariantSet", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype Reference", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceSetDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype ReferenceSet", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantSetListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/breedingmethods/{breedingMethodDbId}" : { - "get" : { - "tags" : [ "Germplasm" ], - "summary" : "Get the details of a specific BreedingMethod", - "description" : "Get details for a BreedingMethod", - "responses" : { - "200" : { - "$ref" : "#/components/responses/BreedingMethodSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/callsets/{callSetDbId}" : { - "get" : { - "tags" : [ "CallSets" ], - "summary" : "Get the details of a specific CallSet", - "description" : "Get details for a CallSet", - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallSetSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/callsets/{callSetDbId}/calls" : { - "get" : { - "tags" : [ "Calls" ], - "summary" : "Get a filtered list of Call", - "description" : "Get a list of Call", - "parameters" : [ { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variant` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "expandHomozygote", - "in" : "query", - "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "sepPhased", - "in" : "query", - "description" : "The string used as a separator for phased allele calls.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sepUnphased", - "in" : "query", - "description" : "The string used as a separator for unphased allele calls.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "unknownString", - "in" : "query", - "description" : "The string used as a representation for missing data.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/crossingprojects/{crossingProjectDbId}" : { - "get" : { - "tags" : [ "CrossingProjects" ], - "summary" : "Get the details of a specific CrossingProject", - "description" : "Get details for a CrossingProject", - "responses" : { - "200" : { - "$ref" : "#/components/responses/CrossingProjectSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "CrossingProjects" ], - "summary" : "Update the details for an existing CrossingProject", - "description" : "Update the details for an existing CrossingProject", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/CrossingProjectNewRequest" - } + "/studies" : { + "get" : { + "tags" : [ + "Studies" + ], + "summary" : "Get a filtered list of Study", + "description" : "Get a list of Study", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "actife", + "in" : "query", + "description" : "A flag to indicate if a Study is currently active and ongoing", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "seasonDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a season", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyType", + "in" : "query", + "description" : "The type of study being performed. ex. \"Yield Trial\", etc", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyCode", + "in" : "query", + "description" : "A short human readable code for a study", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyPUI", + "in" : "query", + "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Studies" + ], + "summary" : "Create new Study", + "description" : "Add new Study to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudyNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/CrossingProjectSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/maps/{mapDbId}" : { - "get" : { - "tags" : [ "GenomeMaps" ], - "summary" : "Get the details of a specific GenomeMap", - "description" : "Get details for a GenomeMap", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GenomeMapSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/germplasm/{germplasmDbId}" : { - "get" : { - "tags" : [ "Germplasm" ], - "summary" : "Get the details of a specific Germplasm", - "description" : "Get details for a Germplasm", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Germplasm" ], - "summary" : "Update the details for an existing Germplasm", - "description" : "Update the details for an existing Germplasm", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/GermplasmNewRequest" - } + "/traits" : { + "get" : { + "tags" : [ + "Traits" + ], + "summary" : "Get a filtered list of Trait", + "description" : "Get a list of Trait", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "ontologyDbId", + "in" : "query", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "traitDbId", + "in" : "query", + "description" : "The unique identifier for a trait.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The unique identifier for an observation variable.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/TraitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Traits" + ], + "summary" : "Create new Trait", + "description" : "Add new Trait to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TraitNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/TraitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/attributes/{attributeDbId}" : { - "get" : { - "tags" : [ "GermplasmAttributes" ], - "summary" : "Get the details of a specific GermplasmAttribute", - "description" : "Get details for a GermplasmAttribute", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "GermplasmAttributes" ], - "summary" : "Update the details for an existing GermplasmAttribute", - "description" : "Update the details for an existing GermplasmAttribute", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/GermplasmAttributeNewRequest" - } + "/trials" : { + "get" : { + "tags" : [ + "Trials" + ], + "summary" : "Get a filtered list of Trial", + "description" : "Get a list of Trial", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "actife", + "in" : "query", + "description" : "A flag to indicate if a Trial is currently active and ongoing", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "contactDbId", + "in" : "query", + "description" : "List of contact entities associated with this trial", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "searchDateRangeStart", + "in" : "query", + "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "searchDateRangeEnd", + "in" : "query", + "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialPUI", + "in" : "query", + "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Trials" + ], + "summary" : "Create new Trial", + "description" : "Add new Trial to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/attributevalues/{attributeValueDbId}" : { - "get" : { - "tags" : [ "GermplasmAttributeValues" ], - "summary" : "Get the details of a specific GermplasmAttributeValue", - "description" : "Get details for a GermplasmAttributeValue", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "GermplasmAttributeValues" ], - "summary" : "Update the details for an existing GermplasmAttributeValue", - "description" : "Update the details for an existing GermplasmAttributeValue", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/GermplasmAttributeValueNewRequest" - } + "/variants" : { + "get" : { + "tags" : [ + "Variants" + ], + "summary" : "Get a filtered list of Variant", + "description" : "Get a list of Variant", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "callSetDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "end", + "in" : "query", + "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "referenceDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype `Reference`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype `ReferenceSet`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "start", + "in" : "query", + "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variants`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/images/{imageDbId}" : { - "get" : { - "tags" : [ "Images" ], - "summary" : "Get the details of a specific Image", - "description" : "Get details for a Image", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ImageSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Images" ], - "summary" : "Update the details for an existing Image", - "description" : "Update the details for an existing Image", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/ImageNewRequest" - } + "/variantsets" : { + "get" : { + "tags" : [ + "VariantSets" + ], + "summary" : "Get a filtered list of VariantSet", + "description" : "Get a list of VariantSet", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "callSetDbId", + "in" : "query", + "description" : "The unique identifier representing a CallSet", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "The unique identifier representing a Variant", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "The unique identifier representing a VariantSet", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype Reference", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype ReferenceSet", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ImageSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/lists/{listDbId}" : { - "get" : { - "tags" : [ "Lists" ], - "summary" : "Get the details of a specific List", - "description" : "Get details for a List", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ListSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Lists" ], - "summary" : "Update the details for an existing List", - "description" : "Update the details for an existing List", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/ListNewRequest" - } + "/breedingmethods/{breedingMethodDbId}" : { + "get" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Get the details of a specific BreedingMethod", + "description" : "Get details for a BreedingMethod", + "responses" : { + "200" : { + "$ref" : "#/components/responses/BreedingMethodSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ListSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/locations/{locationDbId}" : { - "get" : { - "tags" : [ "Locations" ], - "summary" : "Get the details of a specific Location", - "description" : "Get details for a Location", - "responses" : { - "200" : { - "$ref" : "#/components/responses/LocationSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Locations" ], - "summary" : "Update the details for an existing Location", - "description" : "Update the details for an existing Location", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/LocationNewRequest" - } + "/callsets/{callSetDbId}" : { + "get" : { + "tags" : [ + "CallSets" + ], + "summary" : "Get the details of a specific CallSet", + "description" : "Get details for a CallSet", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/LocationSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/methods/{methodDbId}" : { - "get" : { - "tags" : [ "Methods" ], - "summary" : "Get the details of a specific Method", - "description" : "Get details for a Method", - "responses" : { - "200" : { - "$ref" : "#/components/responses/MethodSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Methods" ], - "summary" : "Update the details for an existing Method", - "description" : "Update the details for an existing Method", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/MethodNewRequest" - } + "/callsets/{callSetDbId}/calls" : { + "get" : { + "tags" : [ + "Calls" + ], + "summary" : "Get a filtered list of Call", + "description" : "Get a list of Call", + "parameters" : [ + { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "expandHomozygote", + "in" : "query", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "sepPhased", + "in" : "query", + "description" : "The string used as a separator for phased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sepUnphased", + "in" : "query", + "description" : "The string used as a separator for unphased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "unknownString", + "in" : "query", + "description" : "The string used as a representation for missing data.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/MethodSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/observations/{observationDbId}" : { - "get" : { - "tags" : [ "Observations" ], - "summary" : "Get the details of a specific Observation", - "description" : "Get details for a Observation", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/observationunits/{observationUnitDbId}" : { - "get" : { - "tags" : [ "ObservationUnits" ], - "summary" : "Get the details of a specific ObservationUnit", - "description" : "Get details for a ObservationUnit", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationUnitSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variables/{observationVariableDbId}" : { - "get" : { - "tags" : [ "ObservationVariables" ], - "summary" : "Get the details of a specific ObservationVariable", - "description" : "Get details for a ObservationVariable", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationVariableSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "ObservationVariables" ], - "summary" : "Update the details for an existing ObservationVariable", - "description" : "Update the details for an existing ObservationVariable", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/ObservationVariableNewRequest" - } + "/crossingprojects/{crossingProjectDbId}" : { + "get" : { + "tags" : [ + "CrossingProjects" + ], + "summary" : "Get the details of a specific CrossingProject", + "description" : "Get details for a CrossingProject", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "CrossingProjects" + ], + "summary" : "Update the details for an existing CrossingProject", + "description" : "Update the details for an existing CrossingProject", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossingProjectNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationVariableSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/ontologies/{ontologyDbId}" : { - "get" : { - "tags" : [ "Ontologies" ], - "summary" : "Get the details of a specific Ontology", - "description" : "Get details for a Ontology", - "responses" : { - "200" : { - "$ref" : "#/components/responses/OntologySingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Ontologies" ], - "summary" : "Update the details for an existing Ontology", - "description" : "Update the details for an existing Ontology", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/OntologyNewRequest" - } + "/maps/{mapDbId}" : { + "get" : { + "tags" : [ + "GenomeMaps" + ], + "summary" : "Get the details of a specific GenomeMap", + "description" : "Get details for a GenomeMap", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GenomeMapSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/OntologySingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/people/{personDbId}" : { - "get" : { - "tags" : [ "People" ], - "summary" : "Get the details of a specific Person", - "description" : "Get details for a Person", - "responses" : { - "200" : { - "$ref" : "#/components/responses/PersonSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "People" ], - "summary" : "Update the details for an existing Person", - "description" : "Update the details for an existing Person", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/PersonNewRequest" - } + "/germplasm/{germplasmDbId}" : { + "get" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Get the details of a specific Germplasm", + "description" : "Get details for a Germplasm", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Update the details for an existing Germplasm", + "description" : "Update the details for an existing Germplasm", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/PersonSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/plates/{plateDbId}" : { - "get" : { - "tags" : [ "Plates" ], - "summary" : "Get the details of a specific Plate", - "description" : "Get details for a Plate", - "responses" : { - "200" : { - "$ref" : "#/components/responses/PlateSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/programs/{programDbId}" : { - "get" : { - "tags" : [ "Programs" ], - "summary" : "Get the details of a specific Program", - "description" : "Get details for a Program", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ProgramSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Programs" ], - "summary" : "Update the details for an existing Program", - "description" : "Update the details for an existing Program", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/ProgramNewRequest" - } + "/attributes/{attributeDbId}" : { + "get" : { + "tags" : [ + "GermplasmAttributes" + ], + "summary" : "Get the details of a specific GermplasmAttribute", + "description" : "Get details for a GermplasmAttribute", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "GermplasmAttributes" + ], + "summary" : "Update the details for an existing GermplasmAttribute", + "description" : "Update the details for an existing GermplasmAttribute", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ProgramSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/references/{referenceDbId}" : { - "get" : { - "tags" : [ "References" ], - "summary" : "Get the details of a specific Reference", - "description" : "Get details for a Reference", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ReferenceSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/referencesets/{referenceSetDbId}" : { - "get" : { - "tags" : [ "ReferenceSets" ], - "summary" : "Get the details of a specific ReferenceSet", - "description" : "Get details for a ReferenceSet", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ReferenceSetSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/samples/{sampleDbId}" : { - "get" : { - "tags" : [ "Samples" ], - "summary" : "Get the details of a specific Sample", - "description" : "Get details for a Sample", - "responses" : { - "200" : { - "$ref" : "#/components/responses/SampleSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/scales/{scaleDbId}" : { - "get" : { - "tags" : [ "Scales" ], - "summary" : "Get the details of a specific Scale", - "description" : "Get details for a Scale", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ScaleSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Scales" ], - "summary" : "Update the details for an existing Scale", - "description" : "Update the details for an existing Scale", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/ScaleNewRequest" - } + "/attributevalues/{attributeValueDbId}" : { + "get" : { + "tags" : [ + "GermplasmAttributeValues" + ], + "summary" : "Get the details of a specific GermplasmAttributeValue", + "description" : "Get details for a GermplasmAttributeValue", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "GermplasmAttributeValues" + ], + "summary" : "Update the details for an existing GermplasmAttributeValue", + "description" : "Update the details for an existing GermplasmAttributeValue", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ScaleSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/seasons/{seasonDbId}" : { - "get" : { - "tags" : [ "Seasons" ], - "summary" : "Get the details of a specific Season", - "description" : "Get details for a Season", - "responses" : { - "200" : { - "$ref" : "#/components/responses/SeasonSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Seasons" ], - "summary" : "Update the details for an existing Season", - "description" : "Update the details for an existing Season", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/Season" - } + "/images/{imageDbId}" : { + "get" : { + "tags" : [ + "Images" + ], + "summary" : "Get the details of a specific Image", + "description" : "Get details for a Image", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Images" + ], + "summary" : "Update the details for an existing Image", + "description" : "Update the details for an existing Image", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/SeasonSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/seedlots/{seedLotDbId}" : { - "get" : { - "tags" : [ "SeedLots" ], - "summary" : "Get the details of a specific SeedLot", - "description" : "Get details for a SeedLot", - "responses" : { - "200" : { - "$ref" : "#/components/responses/SeedLotSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "SeedLots" ], - "summary" : "Update the details for an existing SeedLot", - "description" : "Update the details for an existing SeedLot", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/SeedLotNewRequest" - } + "/lists/{listDbId}" : { + "get" : { + "tags" : [ + "Lists" + ], + "summary" : "Get the details of a specific List", + "description" : "Get details for a List", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Lists" + ], + "summary" : "Update the details for an existing List", + "description" : "Update the details for an existing List", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/SeedLotSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/studies/{studyDbId}" : { - "get" : { - "tags" : [ "Studies" ], - "summary" : "Get the details of a specific Study", - "description" : "Get details for a Study", - "responses" : { - "200" : { - "$ref" : "#/components/responses/StudySingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Studies" ], - "summary" : "Update the details for an existing Study", - "description" : "Update the details for an existing Study", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/StudyNewRequest" - } + "/locations/{locationDbId}" : { + "get" : { + "tags" : [ + "Locations" + ], + "summary" : "Get the details of a specific Location", + "description" : "Get details for a Location", + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Locations" + ], + "summary" : "Update the details for an existing Location", + "description" : "Update the details for an existing Location", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/StudySingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/traits/{traitDbId}" : { - "get" : { - "tags" : [ "Traits" ], - "summary" : "Get the details of a specific Trait", - "description" : "Get details for a Trait", - "responses" : { - "200" : { - "$ref" : "#/components/responses/TraitSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Traits" ], - "summary" : "Update the details for an existing Trait", - "description" : "Update the details for an existing Trait", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/TraitNewRequest" - } + "/methods/{methodDbId}" : { + "get" : { + "tags" : [ + "Methods" + ], + "summary" : "Get the details of a specific Method", + "description" : "Get details for a Method", + "responses" : { + "200" : { + "$ref" : "#/components/responses/MethodSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Methods" + ], + "summary" : "Update the details for an existing Method", + "description" : "Update the details for an existing Method", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MethodNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/MethodSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/TraitSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/trials/{trialDbId}" : { - "get" : { - "tags" : [ "Trials" ], - "summary" : "Get the details of a specific Trial", - "description" : "Get details for a Trial", - "responses" : { - "200" : { - "$ref" : "#/components/responses/TrialSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "put" : { - "tags" : [ "Trials" ], - "summary" : "Update the details for an existing Trial", - "description" : "Update the details for an existing Trial", - "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/TrialNewRequest" - } + "/observations/{observationDbId}" : { + "get" : { + "tags" : [ + "Observations" + ], + "summary" : "Get the details of a specific Observation", + "description" : "Get details for a Observation", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/TrialSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variants/{variantDbId}" : { - "get" : { - "tags" : [ "Variants" ], - "summary" : "Get the details of a specific Variant", - "description" : "Get details for a Variant", - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variants/{variantDbId}/calls" : { - "get" : { - "tags" : [ "Calls" ], - "summary" : "Get a filtered list of Call", - "description" : "Get a list of Call", - "parameters" : [ { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variant` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "expandHomozygote", - "in" : "query", - "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "sepPhased", - "in" : "query", - "description" : "The string used as a separator for phased allele calls.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sepUnphased", - "in" : "query", - "description" : "The string used as a separator for unphased allele calls.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "unknownString", - "in" : "query", - "description" : "The string used as a representation for missing data.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variantsets/{variantSetDbId}" : { - "get" : { - "tags" : [ "VariantSets" ], - "summary" : "Get the details of a specific VariantSet", - "description" : "Get details for a VariantSet", - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantSetSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variantsets/{variantSetDbId}/calls" : { - "get" : { - "tags" : [ "Calls" ], - "summary" : "Get a filtered list of Call", - "description" : "Get a list of Call", - "parameters" : [ { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variant` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "expandHomozygote", - "in" : "query", - "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, { - "name" : "sepPhased", - "in" : "query", - "description" : "The string used as a separator for phased allele calls.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sepUnphased", - "in" : "query", - "description" : "The string used as a separator for unphased allele calls.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "unknownString", - "in" : "query", - "description" : "The string used as a representation for missing data.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variantsets/{variantSetDbId}/callsets" : { - "get" : { - "tags" : [ "CallSets" ], - "summary" : "Get a filtered list of CallSet", - "description" : "Get a list of CallSet", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Samples` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "sampleName", - "in" : "query", - "description" : "A list of human readable names associated with `Samples`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "callSetName", - "in" : "query", - "description" : "A list of human readable names associated with `CallSets`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallSetListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/variantsets/{variantSetDbId}/variants" : { - "get" : { - "tags" : [ "Variants" ], - "summary" : "Get a filtered list of Variant", - "description" : "Get a list of Variant", - "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "callSetDbId", - "in" : "query", - "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "end", - "in" : "query", - "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "referenceDbId", - "in" : "query", - "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype `Reference`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "referenceSetDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype `ReferenceSet`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "start", - "in" : "query", - "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variants`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { - "$ref" : "#/components/parameters/externalReferenceID" - }, { - "$ref" : "#/components/parameters/externalReferenceId" - }, { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { - "$ref" : "#/components/parameters/page" - }, { - "$ref" : "#/components/parameters/pageSize" - }, { - "$ref" : "#/components/parameters/authorizationHeader" - } ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/allelematrix" : { - "post" : { - "tags" : [ "AlleleMatrix" ], - "summary" : "Submit a search request for `AlleleMatrix`", - "description" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/AlleleMatrixListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/calls" : { - "post" : { - "tags" : [ "Calls" ], - "summary" : "Submit a search request for `Call`", - "description" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/callsets" : { - "post" : { - "tags" : [ "CallSets" ], - "summary" : "Submit a search request for `CallSet`", - "description" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallSetListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/germplasm" : { - "post" : { - "tags" : [ "Germplasm" ], - "summary" : "Submit a search request for `Germplasm`", - "description" : "Submit a search request for `Germplasm`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/attributes" : { - "post" : { - "tags" : [ "GermplasmAttributes" ], - "summary" : "Submit a search request for `GermplasmAttribute`", - "description" : "Submit a search request for `GermplasmAttribute`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/attributevalues" : { - "post" : { - "tags" : [ "GermplasmAttributeValues" ], - "summary" : "Submit a search request for `GermplasmAttributeValue`", - "description" : "Submit a search request for `GermplasmAttributeValue`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/images" : { - "post" : { - "tags" : [ "Images" ], - "summary" : "Submit a search request for `Image`", - "description" : "Submit a search request for `Image`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ImageListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/lists" : { - "post" : { - "tags" : [ "Lists" ], - "summary" : "Submit a search request for `List`", - "description" : "Submit a search request for `List`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ListListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/locations" : { - "post" : { - "tags" : [ "Locations" ], - "summary" : "Submit a search request for `Location`", - "description" : "Submit a search request for `Location`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/LocationListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/markerpositions" : { - "post" : { - "tags" : [ "MarkerPositions" ], - "summary" : "Submit a search request for `MarkerPosition`", - "description" : "Submit a search request for `MarkerPosition`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/MarkerPositionListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/observations" : { - "post" : { - "tags" : [ "Observations" ], - "summary" : "Submit a search request for `Observation`", - "description" : "Submit a search request for `Observation`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/observationunits" : { - "post" : { - "tags" : [ "ObservationUnits" ], - "summary" : "Submit a search request for `ObservationUnit`", - "description" : "Submit a search request for `ObservationUnit`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/variables" : { - "post" : { - "tags" : [ "ObservationVariables" ], - "summary" : "Submit a search request for `ObservationVariable`", - "description" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/pedigree" : { - "post" : { - "tags" : [ "PedigreeNodes" ], - "summary" : "Submit a search request for `PedigreeNode`", - "description" : "Submit a search request for `PedigreeNode`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/PedigreeNodeListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/people" : { - "post" : { - "tags" : [ "People" ], - "summary" : "Submit a search request for `Person`", - "description" : "Submit a search request for `Person`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/PersonListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/plates" : { - "post" : { - "tags" : [ "Plates" ], - "summary" : "Submit a search request for `Plate`", - "description" : "Submit a search request for `Plate`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/PlateListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/programs" : { - "post" : { - "tags" : [ "Programs" ], - "summary" : "Submit a search request for `Program`", - "description" : "Submit a search request for `Program`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ProgramListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/references" : { - "post" : { - "tags" : [ "References" ], - "summary" : "Submit a search request for `Reference`", - "description" : "Submit a search request for `Reference`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ReferenceListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/referencesets" : { - "post" : { - "tags" : [ "ReferenceSets" ], - "summary" : "Submit a search request for `ReferenceSet`", - "description" : "Submit a search request for `ReferenceSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ReferenceSetListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/samples" : { - "post" : { - "tags" : [ "Samples" ], - "summary" : "Submit a search request for `Sample`", - "description" : "Submit a search request for `Sample`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/SampleListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/studies" : { - "post" : { - "tags" : [ "Studies" ], - "summary" : "Submit a search request for `Study`", - "description" : "Submit a search request for `Study`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/StudyListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/trials" : { - "post" : { - "tags" : [ "Trials" ], - "summary" : "Submit a search request for `Trial`", - "description" : "Submit a search request for `Trial`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/TrialListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/variants" : { - "post" : { - "tags" : [ "Variants" ], - "summary" : "Submit a search request for `Variant`", - "description" : "Submit a search request for `Variant`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/variantsets" : { - "post" : { - "tags" : [ "VariantSets" ], - "summary" : "Submit a search request for `VariantSet`", - "description" : "Submit a search request for `VariantSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantSetListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/allelematrix/{searchResultsDbId}" : { - "get" : { - "tags" : [ "AlleleMatrix" ], - "summary" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `AlleleMatrix` search request
\nClients should submit a search request using the corresponding `POST /search/alleleMatrix` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/AlleleMatrixListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/calls/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Calls" ], - "summary" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Call` search request
\nClients should submit a search request using the corresponding `POST /search/call` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/callsets/{searchResultsDbId}" : { - "get" : { - "tags" : [ "CallSets" ], - "summary" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `CallSet` search request
\nClients should submit a search request using the corresponding `POST /search/callSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/CallSetListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/germplasm/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Germplasm" ], - "summary" : "Submit a search request for `Germplasm`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Germplasm` search request
\nClients should submit a search request using the corresponding `POST /search/germplasm` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/attributes/{searchResultsDbId}" : { - "get" : { - "tags" : [ "GermplasmAttributes" ], - "summary" : "Submit a search request for `GermplasmAttribute`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `GermplasmAttribute` search request
\nClients should submit a search request using the corresponding `POST /search/germplasmAttribute` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/attributevalues/{searchResultsDbId}" : { - "get" : { - "tags" : [ "GermplasmAttributeValues" ], - "summary" : "Submit a search request for `GermplasmAttributeValue`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `GermplasmAttributeValue` search request
\nClients should submit a search request using the corresponding `POST /search/germplasmAttributeValue` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/images/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Images" ], - "summary" : "Submit a search request for `Image`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Image` search request
\nClients should submit a search request using the corresponding `POST /search/image` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ImageListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/lists/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Lists" ], - "summary" : "Submit a search request for `List`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `List` search request
\nClients should submit a search request using the corresponding `POST /search/list` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ListListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/locations/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Locations" ], - "summary" : "Submit a search request for `Location`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Location` search request
\nClients should submit a search request using the corresponding `POST /search/location` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/LocationListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/markerpositions/{searchResultsDbId}" : { - "get" : { - "tags" : [ "MarkerPositions" ], - "summary" : "Submit a search request for `MarkerPosition`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `MarkerPosition` search request
\nClients should submit a search request using the corresponding `POST /search/markerPosition` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/MarkerPositionListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/observations/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Observations" ], - "summary" : "Submit a search request for `Observation`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Observation` search request
\nClients should submit a search request using the corresponding `POST /search/observation` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/observationunits/{searchResultsDbId}" : { - "get" : { - "tags" : [ "ObservationUnits" ], - "summary" : "Submit a search request for `ObservationUnit`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `ObservationUnit` search request
\nClients should submit a search request using the corresponding `POST /search/observationUnit` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/variables/{searchResultsDbId}" : { - "get" : { - "tags" : [ "ObservationVariables" ], - "summary" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `ObservationVariable` search request
\nClients should submit a search request using the corresponding `POST /search/observationVariable` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/pedigree/{searchResultsDbId}" : { - "get" : { - "tags" : [ "PedigreeNodes" ], - "summary" : "Submit a search request for `PedigreeNode`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `PedigreeNode` search request
\nClients should submit a search request using the corresponding `POST /search/pedigreeNode` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/PedigreeNodeListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/people/{searchResultsDbId}" : { - "get" : { - "tags" : [ "People" ], - "summary" : "Submit a search request for `Person`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Person` search request
\nClients should submit a search request using the corresponding `POST /search/person` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/PersonListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/plates/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Plates" ], - "summary" : "Submit a search request for `Plate`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Plate` search request
\nClients should submit a search request using the corresponding `POST /search/plate` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/PlateListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/programs/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Programs" ], - "summary" : "Submit a search request for `Program`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Program` search request
\nClients should submit a search request using the corresponding `POST /search/program` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ProgramListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/references/{searchResultsDbId}" : { - "get" : { - "tags" : [ "References" ], - "summary" : "Submit a search request for `Reference`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Reference` search request
\nClients should submit a search request using the corresponding `POST /search/reference` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ReferenceListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/referencesets/{searchResultsDbId}" : { - "get" : { - "tags" : [ "ReferenceSets" ], - "summary" : "Submit a search request for `ReferenceSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `ReferenceSet` search request
\nClients should submit a search request using the corresponding `POST /search/referenceSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ReferenceSetListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/samples/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Samples" ], - "summary" : "Submit a search request for `Sample`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Sample` search request
\nClients should submit a search request using the corresponding `POST /search/sample` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/SampleListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/studies/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Studies" ], - "summary" : "Submit a search request for `Study`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Study` search request
\nClients should submit a search request using the corresponding `POST /search/study` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/StudyListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/trials/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Trials" ], - "summary" : "Submit a search request for `Trial`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Trial` search request
\nClients should submit a search request using the corresponding `POST /search/trial` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/TrialListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/variants/{searchResultsDbId}" : { - "get" : { - "tags" : [ "Variants" ], - "summary" : "Submit a search request for `Variant`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `Variant` search request
\nClients should submit a search request using the corresponding `POST /search/variant` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/variantsets/{searchResultsDbId}" : { - "get" : { - "tags" : [ "VariantSets" ], - "summary" : "Submit a search request for `VariantSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `VariantSet` search request
\nClients should submit a search request using the corresponding `POST /search/variantSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantSetListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - } - }, - "components" : { - "schemas" : { - "AdditionalInfo" : { - "type" : "object", - "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "properties" : { - "additionalProperties" : { - "type" : "string" - } - } - }, - "AlleleMatrix" : { - "type" : "object", - "properties" : { - "callSetDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/observationunits/{observationUnitDbId}" : { + "get" : { + "tags" : [ + "ObservationUnits" + ], + "summary" : "Get the details of a specific ObservationUnit", + "description" : "Get details for a ObservationUnit", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "expandHomozygotes" : { - "type" : "boolean" - }, - "sepPhased" : { - "type" : "string" - }, - "sepUnphased" : { - "type" : "string" - }, - "unknownString" : { - "type" : "string" - }, - "variantDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + }, + "/variables/{observationVariableDbId}" : { + "get" : { + "tags" : [ + "ObservationVariables" + ], + "summary" : "Get the details of a specific ObservationVariable", + "description" : "Get details for a ObservationVariable", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "ObservationVariables" + ], + "summary" : "Update the details for an existing ObservationVariable", + "description" : "Update the details for an existing ObservationVariable", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "variantSetDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + }, + "/ontologies/{ontologyDbId}" : { + "get" : { + "tags" : [ + "Ontologies" + ], + "summary" : "Get the details of a specific Ontology", + "description" : "Get details for a Ontology", + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologySingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Ontologies" + ], + "summary" : "Update the details for an existing Ontology", + "description" : "Update the details for an existing Ontology", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/OntologyNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologySingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "required" : [ "callSetDbIds", "variantSetDbIds" ] - }, - "AlleleMatrixSearchRequest" : { - "type" : "object", - "properties" : { - "expandHomozygotes" : { - "type" : "boolean" - }, - "preview" : { - "type" : "boolean" - }, - "sepPhased" : { - "type" : "string" - }, - "sepUnphased" : { - "type" : "string" - }, - "unknownString" : { - "type" : "string" - } - } - }, - "Analysis" : { - "type" : "object", - "properties" : { - "analysisDbId" : { - "type" : "string" - }, - "analysisName" : { - "type" : "string" - }, - "created" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "software" : { - "type" : "array", - "items" : { - "type" : "string" + "/people/{personDbId}" : { + "get" : { + "tags" : [ + "People" + ], + "summary" : "Get the details of a specific Person", + "description" : "Get details for a Person", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "People" + ], + "summary" : "Update the details for an existing Person", + "description" : "Update the details for an existing Person", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "type" : { - "type" : "string" - }, - "updated" : { - "type" : "string" - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" - } }, - "required" : [ "analysisDbId" ] - }, - "Attribute" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attributeCategory" : { - "type" : "string" - }, - "attributeDbId" : { - "type" : "string" - }, - "attributeDescription" : { - "type" : "string" - }, - "attributeName" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "commonCropName" : { - "type" : "string" - }, - "contextOfUse" : { - "type" : "array", - "items" : { - "type" : "string" + "/plates/{plateDbId}" : { + "get" : { + "tags" : [ + "Plates" + ], + "summary" : "Get the details of a specific Plate", + "description" : "Get details for a Plate", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "method" : { - "$ref" : "#/components/schemas/Method" - }, - "ontologyReference" : { - "$ref" : "#/components/schemas/OntologyReference" - }, - "scale" : { - "$ref" : "#/components/schemas/Scale" - }, - "scientist" : { - "type" : "string" - }, - "status" : { - "type" : "string" - }, - "submissionTimestamp" : { - "type" : "string" - }, - "synonyms" : { - "type" : "array", - "items" : { - "type" : "string" + }, + "/programs/{programDbId}" : { + "get" : { + "tags" : [ + "Programs" + ], + "summary" : "Get the details of a specific Program", + "description" : "Get details for a Program", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Programs" + ], + "summary" : "Update the details for an existing Program", + "description" : "Update the details for an existing Program", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "trait" : { - "$ref" : "#/components/schemas/Trait" - } }, - "required" : [ "attributeName", "method", "scale", "trait" ] - }, - "AvailableFormat" : { - "type" : "object", - "properties" : { - "dataFormat" : { - "type" : "string", - "description" : "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)", - "enum" : [ "DartSeq", "VCF", "Hapmap", "tabular", "JSON" ] - }, - "expandHomozygotes" : { - "type" : "boolean" - }, - "fileFormat" : { - "type" : "string", - "description" : "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.", - "enum" : [ "text/csv", "text/tsv", "application/excel", "application/zip", "application/json" ] - }, - "fileURL" : { - "type" : "string" - }, - "sepPhased" : { - "type" : "string" - }, - "sepUnphased" : { - "type" : "string" - }, - "unknownString" : { - "type" : "string" - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" - } - } - }, - "BreedingMethod" : { - "type" : "object", - "properties" : { - "abbreviation" : { - "type" : "string" - }, - "breedingMethodDbId" : { - "type" : "string" - }, - "breedingMethodName" : { - "type" : "string" - }, - "description" : { - "type" : "string" - } + "/references/{referenceDbId}" : { + "get" : { + "tags" : [ + "References" + ], + "summary" : "Get the details of a specific Reference", + "description" : "Get details for a Reference", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "abbreviation", "breedingMethodDbId", "breedingMethodName", "description" ] - }, - "Call" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "callSetDbId" : { - "type" : "string" - }, - "callSetName" : { - "type" : "string" - }, - "genotypeValue" : { - "type" : "string" - }, - "phaseSet" : { - "type" : "string" - }, - "variantDbId" : { - "type" : "string" - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" - } + "/referencesets/{referenceSetDbId}" : { + "get" : { + "tags" : [ + "ReferenceSets" + ], + "summary" : "Get the details of a specific ReferenceSet", + "description" : "Get details for a ReferenceSet", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "callSetDbId", "variantDbId", "variantSetDbId" ] - }, - "CallSearchRequest" : { - "type" : "object", - "properties" : { - "expandHomozygotes" : { - "type" : "boolean" - }, - "sepPhased" : { - "type" : "string" - }, - "sepUnphased" : { - "type" : "string" - }, - "unknownString" : { - "type" : "string" - } - } - }, - "CallSet" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "callSetDbId" : { - "type" : "string" - }, - "callSetName" : { - "type" : "string" - }, - "created" : { - "type" : "string" - }, - "sampleDbId" : { - "type" : "string" - }, - "sampleName" : { - "type" : "string" - }, - "samplePUI" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "updated" : { - "type" : "string" - }, - "variantSetDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/samples/{sampleDbId}" : { + "get" : { + "tags" : [ + "Samples" + ], + "summary" : "Get the details of a specific Sample", + "description" : "Get details for a Sample", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "required" : [ "callSetDbId" ] - }, - "CallSetSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "Contact" : { - "type" : "object", - "properties" : { - "contactDbId" : { - "type" : "string" - }, - "email" : { - "type" : "string" - }, - "instituteName" : { - "type" : "string" - }, - "name" : { - "type" : "string" - }, - "orcid" : { - "type" : "string" - }, - "type" : { - "type" : "string" - } + "/scales/{scaleDbId}" : { + "get" : { + "tags" : [ + "Scales" + ], + "summary" : "Get the details of a specific Scale", + "description" : "Get details for a Scale", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ScaleSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Scales" + ], + "summary" : "Update the details for an existing Scale", + "description" : "Update the details for an existing Scale", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ScaleNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ScaleSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "contactDbId" ] - }, - "ContentMixture" : { - "type" : "object", - "properties" : { - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "mixturePercentage" : { - "type" : "integer", - "format" : "int32" - }, - "seedLotDbId" : { - "type" : "string" - }, - "seedLotName" : { - "type" : "string" - } - } - }, - "ContentTypes" : { - "type" : "string", - "enum" : [ "application/json", "text/csv", "text/tsv", "application/flapjack" ] - }, - "Context" : { - "type" : "array", - "description" : "The JSON-LD Context is used to provide JSON-LD definitions to each field in a JSON object. By providing an array of context file urls, a BrAPI response object becomes JSON-LD compatible. \n\nFor more information, see https://w3c.github.io/json-ld-syntax/#the-context", - "example" : [ "https://brapi.org/jsonld/context/metadata.jsonld" ], - "items" : { - "type" : "string", - "format" : "uri" + "/seasons/{seasonDbId}" : { + "get" : { + "tags" : [ + "Seasons" + ], + "summary" : "Get the details of a specific Season", + "description" : "Get details for a Season", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Seasons" + ], + "summary" : "Update the details for an existing Season", + "description" : "Update the details for an existing Season", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/Season" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "title" : "context" - }, - "Cross" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "crossName" : { - "type" : "string" - }, - "crossType" : { - "$ref" : "#/components/schemas/CrossType" - }, - "crossingProjectDbId" : { - "type" : "string" - }, - "crossingProjectName" : { - "type" : "string" - }, - "parent1" : { - "$ref" : "#/components/schemas/CrossParent" - }, - "parent2" : { - "$ref" : "#/components/schemas/CrossParent" - }, - "plannedCrossDbId" : { - "type" : "string" - }, - "plannedCrossName" : { - "type" : "string" - } + "/seedlots/{seedLotDbId}" : { + "get" : { + "tags" : [ + "SeedLots" + ], + "summary" : "Get the details of a specific SeedLot", + "description" : "Get details for a SeedLot", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "SeedLots" + ], + "summary" : "Update the details for an existing SeedLot", + "description" : "Update the details for an existing SeedLot", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "crossDbId" ] - }, - "CrossAttribute" : { - "type" : "object", - "properties" : { - "crossAttributeName" : { - "type" : "string" - }, - "crossAttributeValue" : { - "type" : "string" - }, - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" - } - } - }, - "CrossNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" - }, - "crossType" : { - "$ref" : "#/components/schemas/CrossType" - }, - "crossingProjectDbId" : { - "type" : "string" - }, - "crossingProjectName" : { - "type" : "string" - }, - "parent1" : { - "$ref" : "#/components/schemas/CrossParent" - }, - "parent2" : { - "$ref" : "#/components/schemas/CrossParent" - }, - "plannedCrossDbId" : { - "type" : "string" - }, - "plannedCrossName" : { - "type" : "string" - } + "/studies/{studyDbId}" : { + "get" : { + "tags" : [ + "Studies" + ], + "summary" : "Get the details of a specific Study", + "description" : "Get details for a Study", + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudySingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Studies" + ], + "summary" : "Update the details for an existing Study", + "description" : "Update the details for an existing Study", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudyNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudySingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "crossDbId", "crossDbId" ] - }, - "CrossParent" : { - "type" : "object", - "properties" : { - "germplasm" : { - "$ref" : "#/components/schemas/Germplasm" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "parentType" : { - "$ref" : "#/components/schemas/ParentType" - } - } - }, - "CrossType" : { - "type" : "string", - "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", - "enum" : [ "BIPARENTAL", "SELF", "OPEN_POLLINATED", "BULK", "BULK_SELFED", "BULK_OPEN_POLLINATED", "DOUBLE_HAPLOID" ] - }, - "CrossingProject" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "crossingProjectDescription" : { - "type" : "string" - }, - "crossingProjectName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - } + "/traits/{traitDbId}" : { + "get" : { + "tags" : [ + "Traits" + ], + "summary" : "Get the details of a specific Trait", + "description" : "Get details for a Trait", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TraitSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Traits" + ], + "summary" : "Update the details for an existing Trait", + "description" : "Update the details for an existing Trait", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TraitNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/TraitSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "crossingProjectDbId", "crossingProjectName" ] - }, - "CrossingProjectNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "crossingProjectDbId" : { - "type" : "string" - }, - "crossingProjectDescription" : { - "type" : "string" - }, - "crossingProjectName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - } + "/trials/{trialDbId}" : { + "get" : { + "tags" : [ + "Trials" + ], + "summary" : "Get the details of a specific Trial", + "description" : "Get details for a Trial", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ + "Trials" + ], + "summary" : "Update the details for an existing Trial", + "description" : "Update the details for an existing Trial", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "crossingProjectDbId", "crossingProjectDbId", "crossingProjectName" ] - }, - "DataLink" : { - "type" : "object", - "properties" : { - "dataFormat" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "fileFormat" : { - "type" : "string" - }, - "name" : { - "type" : "string" - }, - "provenance" : { - "type" : "string" - }, - "scientificType" : { - "type" : "string" - }, - "url" : { - "type" : "string" - }, - "version" : { - "type" : "string" - } - } - }, - "DataMatrix" : { - "type" : "object", - "properties" : { - "alleleMatrix" : { - "$ref" : "#/components/schemas/AlleleMatrix" - }, - "dataMatrix" : { - "type" : "array", - "items" : { - "type" : "array", - "items" : { - "type" : "string" - } + "/variants/{variantDbId}" : { + "get" : { + "tags" : [ + "Variants" + ], + "summary" : "Get the details of a specific Variant", + "description" : "Get details for a Variant", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "dataMatrixAbbreviation" : { - "type" : "string" - }, - "dataMatrixName" : { - "type" : "string" - }, - "dataType" : { - "type" : "string", - "description" : "The type of field represented in this data matrix. This is intended to help parse the data out of JSON.", - "enum" : [ "string", "integer", "float", "boolean" ] - } - } - }, - "DatasetAuthorships" : { - "type" : "object", - "properties" : { - "datasetPUI" : { - "type" : "string" - }, - "license" : { - "type" : "string" - }, - "publicReleaseDate" : { - "type" : "string" - }, - "submissionDate" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } - } - }, - "DocumentationLink" : { - "type" : "object", - "properties" : { - "URL" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "type" : { - "type" : "string", - "enum" : [ "OBO", "RDF", "WEBPAGE" ] - } - } - }, - "Donor" : { - "type" : "object", - "properties" : { - "donorAccessionNumber" : { - "type" : "string" - }, - "donorInstituteCode" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - } - } - }, - "EnvironmentParameters" : { - "type" : "object", - "properties" : { - "description" : { - "type" : "string" - }, - "environmentParametersDbId" : { - "type" : "string" - }, - "parameterName" : { - "type" : "string" - }, - "parameterPUI" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "unit" : { - "type" : "string" - }, - "unitPUI" : { - "type" : "string" - }, - "value" : { - "type" : "string" - }, - "valuePUI" : { - "type" : "string" - } }, - "required" : [ "description", "environmentParametersDbId", "parameterName" ] - }, - "Event" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "eventDbId" : { - "type" : "string" - }, - "eventDescription" : { - "type" : "string" - }, - "eventType" : { - "type" : "string" - }, - "eventTypeDbId" : { - "type" : "string" - }, - "observationUnitDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/variants/{variantDbId}/calls" : { + "get" : { + "tags" : [ + "Calls" + ], + "summary" : "Get a filtered list of Call", + "description" : "Get a list of Call", + "parameters" : [ + { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "expandHomozygote", + "in" : "query", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "sepPhased", + "in" : "query", + "description" : "The string used as a separator for phased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sepUnphased", + "in" : "query", + "description" : "The string used as a separator for unphased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "unknownString", + "in" : "query", + "description" : "The string used as a representation for missing data.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - } }, - "required" : [ "eventDbId", "eventType" ] - }, - "EventDateRange" : { - "type" : "object", - "properties" : { - "discreteDates" : { - "type" : "array", - "items" : { - "type" : "string" + "/variantsets/{variantSetDbId}" : { + "get" : { + "tags" : [ + "VariantSets" + ], + "summary" : "Get the details of a specific VariantSet", + "description" : "Get details for a VariantSet", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "endDate" : { - "type" : "string" - }, - "eventDbId" : { - "type" : "string" - }, - "startDate" : { - "type" : "string" - } - } - }, - "EventParameter" : { - "type" : "object", - "properties" : { - "code" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "eventDbId" : { - "type" : "string" - }, - "name" : { - "type" : "string" - }, - "units" : { - "type" : "string" - }, - "value" : { - "type" : "string" - }, - "valueDescription" : { - "type" : "string" - }, - "valuesByDate" : { - "type" : "array", - "items" : { - "type" : "string" + }, + "/variantsets/{variantSetDbId}/calls" : { + "get" : { + "tags" : [ + "Calls" + ], + "summary" : "Get a filtered list of Call", + "description" : "Get a list of Call", + "parameters" : [ + { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "expandHomozygote", + "in" : "query", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "sepPhased", + "in" : "query", + "description" : "The string used as a separator for phased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sepUnphased", + "in" : "query", + "description" : "The string used as a separator for unphased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "unknownString", + "in" : "query", + "description" : "The string used as a representation for missing data.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "ExperimentalDesign" : { - "type" : "object", - "properties" : { - "PUI" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - } - } - }, - "ExternalReference" : { - "type" : "object", - "properties" : { - "referenceId" : { - "type" : "string" - }, - "referenceSource" : { - "type" : "string" - } - } - }, - "GenomeMap" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "comments" : { - "type" : "string" - }, - "commonCropName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "linkageGroupCount" : { - "type" : "integer", - "format" : "int32" - }, - "mapDbId" : { - "type" : "string" - }, - "mapName" : { - "type" : "string" - }, - "mapPUI" : { - "type" : "string" - }, - "markerCount" : { - "type" : "integer", - "format" : "int32" - }, - "publishedDate" : { - "type" : "string" - }, - "scientificName" : { - "type" : "string" - }, - "type" : { - "type" : "string" - }, - "unit" : { - "type" : "string" - } }, - "required" : [ "commonCropName", "mapDbId", "type" ] - }, - "GenotypeMetadata" : { - "type" : "object", - "properties" : { - "call" : { - "$ref" : "#/components/schemas/Call" - }, - "dataType" : { - "type" : "string", - "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", - "enum" : [ "string", "integer", "float", "boolean" ] - }, - "fieldAbbreviation" : { - "type" : "string" - }, - "fieldName" : { - "type" : "string" - }, - "fieldValue" : { - "type" : "string" - } - } - }, - "GeoJSON" : { - "type" : "object", - "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "properties" : { - "geometry" : { - "$ref" : "#/components/schemas/GeoJSONGeometry" - }, - "type" : { - "type" : "string" - } - } - }, - "GeoJSONGeometry" : { - "oneOf" : [ { - "type" : "object", - "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "properties" : { - "coordinates" : { - "type" : "array", - "items" : { - "type" : "number" - } - }, - "type" : { - "type" : "string" + "/variantsets/{variantSetDbId}/callsets" : { + "get" : { + "tags" : [ + "CallSets" + ], + "summary" : "Get a filtered list of CallSet", + "description" : "Get a list of CallSet", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sampleName", + "in" : "query", + "description" : "A list of human readable names associated with `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "callSetName", + "in" : "query", + "description" : "A list of human readable names associated with `CallSets`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "required" : [ "coordinateDbIds", "type" ] - }, { - "type" : "object", - "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "properties" : { - "coordinates" : { - "type" : "array", - "items" : { - "type" : "array", - "items" : { - "type" : "array", - "items" : { - "type" : "number" - } + }, + "/variantsets/{variantSetDbId}/variants" : { + "get" : { + "tags" : [ + "Variants" + ], + "summary" : "Get a filtered list of Variant", + "description" : "Get a list of Variant", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "callSetDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "end", + "in" : "query", + "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "referenceDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype `Reference`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype `ReferenceSet`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "start", + "in" : "query", + "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variants`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, + { + "$ref" : "#/components/parameters/externalReferenceId" + }, + { + "$ref" : "#/components/parameters/externalReferenceSource" + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } } - } - }, - "type" : { - "type" : "string" } - }, - "required" : [ "coordinateDbIds", "type" ] - } ] - }, - "GeoJSONSearchArea" : { - "type" : "object", - "properties" : { - "geometry" : { - "$ref" : "#/components/schemas/GeoJSONGeometry" - }, - "germplasmOrigin" : { - "$ref" : "#/components/schemas/GermplasmOrigin" - }, - "imageDbId" : { - "type" : "string" - }, - "imageName" : { - "type" : "string" - }, - "observationDbId" : { - "type" : "string" - }, - "observationUnit" : { - "$ref" : "#/components/schemas/ObservationUnitPosition" - }, - "type" : { - "type" : "string" - } - } - }, - "Germplasm" : { - "type" : "object", - "properties" : { - "accessionNumber" : { - "type" : "string" - }, - "acquisitionDate" : { - "type" : "string" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "biologicalStatusOfAccessionCode" : { - "type" : "string", - "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", - "enum" : [ "100", "110", "120", "130", "200", "300", "400", "410", "411", "412", "413", "414", "415", "416", "420", "421", "422", "423", "500", "600", "999" ] - }, - "biologicalStatusOfAccessionDescription" : { - "type" : "string" - }, - "breedingMethodDbId" : { - "type" : "string" - }, - "breedingMethodName" : { - "type" : "string" - }, - "collection" : { - "type" : "string" - }, - "commonCropName" : { - "type" : "string" - }, - "countryOfOriginCode" : { - "type" : "string" - }, - "defaultDisplayName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "genus" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "germplasmPreprocessing" : { - "type" : "string" - }, - "instituteCode" : { - "type" : "string" - }, - "instituteName" : { - "type" : "string" - }, - "pedigree" : { - "type" : "string" - }, - "sampleDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + }, + "/search/allelematrix" : { + "post" : { + "tags" : [ + "AlleleMatrix" + ], + "summary" : "Submit a search request for `AlleleMatrix`", + "description" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/AlleleMatrixListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "seedSource" : { - "type" : "string" - }, - "seedSourceDescription" : { - "type" : "string" - }, - "species" : { - "type" : "string" - }, - "speciesAuthority" : { - "type" : "string" - }, - "subtaxa" : { - "type" : "string" - }, - "subtaxaAuthority" : { - "type" : "string" - } }, - "required" : [ "commonCropName", "germplasmDbId", "germplasmName", "germplasmPUI" ] - }, - "GermplasmAttribute" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attributeCategory" : { - "type" : "string" - }, - "attributeDescription" : { - "type" : "string" - }, - "attributeName" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "attributeValueDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/calls" : { + "post" : { + "tags" : [ + "Calls" + ], + "summary" : "Submit a search request for `Call`", + "description" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "commonCropName" : { - "type" : "string" - }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" - }, - "scientist" : { - "type" : "string" - }, - "status" : { - "type" : "string" - }, - "submissionTimestamp" : { - "type" : "string" - }, - "traitDbId" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" - } }, - "required" : [ "attributeDbId", "attributeName", "methodName", "scaleDbId", "scaleName", "traitName" ] - }, - "GermplasmAttributeNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attributeCategory" : { - "type" : "string" - }, - "attributeDbId" : { - "type" : "string" - }, - "attributeDescription" : { - "type" : "string" - }, - "attributeName" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "attributeValueDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/callsets" : { + "post" : { + "tags" : [ + "CallSets" + ], + "summary" : "Submit a search request for `CallSet`", + "description" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "commonCropName" : { - "type" : "string" - }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" - }, - "scientist" : { - "type" : "string" - }, - "status" : { - "type" : "string" - }, - "submissionTimestamp" : { - "type" : "string" - }, - "traitDbId" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" - } }, - "required" : [ "attributeDbId", "attributeName", "methodName", "scaleDbId", "scaleName", "traitName" ] - }, - "GermplasmAttributeSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "GermplasmAttributeValue" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attributeDbId" : { - "type" : "string" - }, - "attributeName" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "determinedDate" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "value" : { - "type" : "string" - } + "/search/germplasm" : { + "post" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Submit a search request for `Germplasm`", + "description" : "Submit a search request for `Germplasm`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "attributeName", "attributeValueDbId" ] - }, - "GermplasmAttributeValueNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attributeDbId" : { - "type" : "string" - }, - "attributeName" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "attributeValueDbId" : { - "type" : "string" - }, - "determinedDate" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "value" : { - "type" : "string" - } + "/search/attributes" : { + "post" : { + "tags" : [ + "GermplasmAttributes" + ], + "summary" : "Submit a search request for `GermplasmAttribute`", + "description" : "Submit a search request for `GermplasmAttribute`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "attributeName", "attributeValueDbId" ] - }, - "GermplasmAttributeValueSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "GermplasmChild" : { - "type" : "object", - "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "parentType" : { - "$ref" : "#/components/schemas/ParentType" - }, - "pedigreeNodeDbId" : { - "type" : "string" - } + "/search/attributevalues" : { + "post" : { + "tags" : [ + "GermplasmAttributeValues" + ], + "summary" : "Submit a search request for `GermplasmAttributeValue`", + "description" : "Submit a search request for `GermplasmAttributeValue`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "germplasmDbId", "germplasmName", "germplasmPUI", "parentType" ] - }, - "GermplasmNewRequest" : { - "type" : "object", - "properties" : { - "accessionNumber" : { - "type" : "string" - }, - "acquisitionDate" : { - "type" : "string" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "biologicalStatusOfAccessionCode" : { - "type" : "string", - "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", - "enum" : [ "100", "110", "120", "130", "200", "300", "400", "410", "411", "412", "413", "414", "415", "416", "420", "421", "422", "423", "500", "600", "999" ] - }, - "biologicalStatusOfAccessionDescription" : { - "type" : "string" - }, - "breedingMethodDbId" : { - "type" : "string" - }, - "breedingMethodName" : { - "type" : "string" - }, - "collection" : { - "type" : "string" - }, - "commonCropName" : { - "type" : "string" - }, - "countryOfOriginCode" : { - "type" : "string" - }, - "defaultDisplayName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "genus" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "germplasmPreprocessing" : { - "type" : "string" - }, - "instituteCode" : { - "type" : "string" - }, - "instituteName" : { - "type" : "string" - }, - "pedigree" : { - "type" : "string" - }, - "sampleDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/images" : { + "post" : { + "tags" : [ + "Images" + ], + "summary" : "Submit a search request for `Image`", + "description" : "Submit a search request for `Image`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "seedSource" : { - "type" : "string" - }, - "seedSourceDescription" : { - "type" : "string" - }, - "species" : { - "type" : "string" - }, - "speciesAuthority" : { - "type" : "string" - }, - "subtaxa" : { - "type" : "string" - }, - "subtaxaAuthority" : { - "type" : "string" - } }, - "required" : [ "commonCropName", "germplasmDbId", "germplasmDbId", "germplasmName", "germplasmPUI" ] - }, - "GermplasmOrigin" : { - "type" : "object", - "properties" : { - "coordinateUncertainty" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - } - } - }, - "GermplasmParent" : { - "type" : "object", - "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "parentType" : { - "$ref" : "#/components/schemas/ParentType" - }, - "pedigreeNodeDbId" : { - "type" : "string" - } + "/search/lists" : { + "post" : { + "tags" : [ + "Lists" + ], + "summary" : "Submit a search request for `List`", + "description" : "Submit a search request for `List`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "germplasmDbId", "germplasmName", "germplasmPUI", "parentType" ] - }, - "GermplasmSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "GrowthFacility" : { - "type" : "object", - "properties" : { - "PUI" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - } - } - }, - "Image" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "copyright" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "imageFileName" : { - "type" : "string" - }, - "imageFileSize" : { - "type" : "integer", - "format" : "int32" - }, - "imageHeight" : { - "type" : "integer", - "format" : "int32" - }, - "imageLocation" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "imageName" : { - "type" : "string" - }, - "imageTimeStamp" : { - "type" : "string" - }, - "imageURL" : { - "type" : "string" - }, - "imageWidth" : { - "type" : "integer", - "format" : "int32" - }, - "mimeType" : { - "type" : "string" - }, - "observationDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/locations" : { + "post" : { + "tags" : [ + "Locations" + ], + "summary" : "Submit a search request for `Location`", + "description" : "Submit a search request for `Location`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - } }, - "required" : [ "imageDbId" ] - }, - "ImageNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "copyright" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "imageDbId" : { - "type" : "string" - }, - "imageFileName" : { - "type" : "string" - }, - "imageFileSize" : { - "type" : "integer", - "format" : "int32" - }, - "imageHeight" : { - "type" : "integer", - "format" : "int32" - }, - "imageLocation" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "imageName" : { - "type" : "string" - }, - "imageTimeStamp" : { - "type" : "string" - }, - "imageURL" : { - "type" : "string" - }, - "imageWidth" : { - "type" : "integer", - "format" : "int32" - }, - "mimeType" : { - "type" : "string" - }, - "observationDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/markerpositions" : { + "post" : { + "tags" : [ + "MarkerPositions" + ], + "summary" : "Submit a search request for `MarkerPosition`", + "description" : "Submit a search request for `MarkerPosition`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/MarkerPositionListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - } }, - "required" : [ "imageDbId", "imageDbId" ] - }, - "ImageSearchRequest" : { - "type" : "object", - "properties" : { - "imageFileSizeMax" : { - "type" : "integer", - "format" : "int32" - }, - "imageFileSizeMin" : { - "type" : "integer", - "format" : "int32" - }, - "imageHeightMax" : { - "type" : "integer", - "format" : "int32" - }, - "imageHeightMin" : { - "type" : "integer", - "format" : "int32" - }, - "imageLocation" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - }, - "imageTimeStampRangeEnd" : { - "type" : "string" - }, - "imageTimeStampRangeStart" : { - "type" : "string" - }, - "imageWidthMax" : { - "type" : "integer", - "format" : "int32" - }, - "imageWidthMin" : { - "type" : "integer", - "format" : "int32" - } - } - }, - "LastUpdate" : { - "type" : "object", - "properties" : { - "lastUpdateDbId" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "timestamp" : { - "type" : "string" - }, - "version" : { - "type" : "string" - } + "/search/observations" : { + "post" : { + "tags" : [ + "Observations" + ], + "summary" : "Submit a search request for `Observation`", + "description" : "Submit a search request for `Observation`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "lastUpdateDbId" ] - }, - "List" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "dateCreated" : { - "type" : "string" - }, - "dateModified" : { - "type" : "string" - }, - "listDescription" : { - "type" : "string" - }, - "listName" : { - "type" : "string" - }, - "listOwnerName" : { - "type" : "string" - }, - "listSize" : { - "type" : "integer", - "format" : "int32" - }, - "listSource" : { - "type" : "string" - }, - "listType" : { - "$ref" : "#/components/schemas/ListType" - }, - "personDbId" : { - "type" : "string" - } + "/search/observationunits" : { + "post" : { + "tags" : [ + "ObservationUnits" + ], + "summary" : "Submit a search request for `ObservationUnit`", + "description" : "Submit a search request for `ObservationUnit`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "listDbId", "listName", "listType" ] - }, - "ListNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "dateCreated" : { - "type" : "string" - }, - "dateModified" : { - "type" : "string" - }, - "listDbId" : { - "type" : "string" - }, - "listDescription" : { - "type" : "string" - }, - "listName" : { - "type" : "string" - }, - "listOwnerName" : { - "type" : "string" - }, - "listSize" : { - "type" : "integer", - "format" : "int32" - }, - "listSource" : { - "type" : "string" - }, - "listType" : { - "$ref" : "#/components/schemas/ListType" - }, - "personDbId" : { - "type" : "string" - } + "/search/variables" : { + "post" : { + "tags" : [ + "ObservationVariables" + ], + "summary" : "Submit a search request for `ObservationVariable`", + "description" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "listDbId", "listDbId", "listName", "listType" ] - }, - "ListSearchRequest" : { - "type" : "object", - "properties" : { - "dateCreatedRangeEnd" : { - "type" : "string" - }, - "dateCreatedRangeStart" : { - "type" : "string" - }, - "dateModifiedRangeEnd" : { - "type" : "string" - }, - "dateModifiedRangeStart" : { - "type" : "string" - }, - "listType" : { - "$ref" : "#/components/schemas/ListType" - } - } - }, - "ListType" : { - "type" : "string", - "description" : "The type of objects that are referenced in a List", - "enum" : [ "germplasm", "markers", "variants", "programs", "trials", "studies", "observationUnits", "observations", "observationVariables", "samples" ] - }, - "Location" : { - "type" : "object", - "properties" : { - "abbreviation" : { - "type" : "string" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "childLocationDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/pedigree" : { + "post" : { + "tags" : [ + "PedigreeNodes" + ], + "summary" : "Submit a search request for `PedigreeNode`", + "description" : "Submit a search request for `PedigreeNode`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "coordinateDescription" : { - "type" : "string" - }, - "coordinateUncertainty" : { - "type" : "string" - }, - "coordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "countryCode" : { - "type" : "string" - }, - "countryName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "environmentType" : { - "type" : "string" - }, - "exposure" : { - "type" : "string" - }, - "instituteAddress" : { - "type" : "string" - }, - "instituteName" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "locationType" : { - "type" : "string" - }, - "siteStatus" : { - "type" : "string" - }, - "slope" : { - "type" : "string" - }, - "topography" : { - "type" : "string" - } }, - "required" : [ "locationDbId", "locationName" ] - }, - "LocationNewRequest" : { - "type" : "object", - "properties" : { - "abbreviation" : { - "type" : "string" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "childLocationDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/people" : { + "post" : { + "tags" : [ + "People" + ], + "summary" : "Submit a search request for `Person`", + "description" : "Submit a search request for `Person`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "coordinateDescription" : { - "type" : "string" - }, - "coordinateUncertainty" : { - "type" : "string" - }, - "coordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "countryCode" : { - "type" : "string" - }, - "countryName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "environmentType" : { - "type" : "string" - }, - "exposure" : { - "type" : "string" - }, - "instituteAddress" : { - "type" : "string" - }, - "instituteName" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "locationType" : { - "type" : "string" - }, - "siteStatus" : { - "type" : "string" - }, - "slope" : { - "type" : "string" - }, - "topography" : { - "type" : "string" - } }, - "required" : [ "locationDbId", "locationDbId", "locationName" ] - }, - "LocationSearchRequest" : { - "type" : "object", - "properties" : { - "altitudeMax" : { - "type" : "number" - }, - "altitudeMin" : { - "type" : "number" - }, - "coordinates" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - } - } - }, - "MarkerPosition" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "linkageGroupName" : { - "type" : "string" - }, - "mapDbId" : { - "type" : "string" - }, - "mapName" : { - "type" : "string" - }, - "mapPUI" : { - "type" : "string" - }, - "position" : { - "type" : "integer", - "format" : "int32" - }, - "variantDbId" : { - "type" : "string" - } - } - }, - "MarkerPositionSearchRequest" : { - "type" : "object", - "properties" : { - "maxPosition" : { - "type" : "integer", - "format" : "int32" - }, - "minPosition" : { - "type" : "integer", - "format" : "int32" - } - } - }, - "MetadataField" : { - "type" : "object", - "properties" : { - "dataType" : { - "type" : "string", - "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", - "enum" : [ "string", "integer", "float", "boolean" ] - }, - "fieldAbbreviation" : { - "type" : "string" - }, - "fieldName" : { - "type" : "string" - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" - } - } - }, - "Method" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "bibliographicalReference" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "formula" : { - "type" : "string" - }, - "methodClass" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - } + "/search/plates" : { + "post" : { + "tags" : [ + "Plates" + ], + "summary" : "Submit a search request for `Plate`", + "description" : "Submit a search request for `Plate`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } }, - "required" : [ "methodDbId", "methodName" ] - }, - "MethodNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "bibliographicalReference" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "formula" : { - "type" : "string" - }, - "methodClass" : { - "type" : "string" - }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - } - }, - "required" : [ "methodDbId", "methodName" ] - }, - "Observation" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "collector" : { - "type" : "string" - }, - "geoCoordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "observationTimeStamp" : { - "type" : "string" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "observationVariableDbId" : { - "type" : "string" - }, - "observationVariableName" : { - "type" : "string" - }, - "observationVariablePUI" : { - "type" : "string" - }, - "seasonDbId" : { - "type" : "string" - }, - "seasonName" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "uploadedBy" : { - "type" : "string" - }, - "value" : { - "type" : "string" - } - }, - "required" : [ "observationDbId" ] - }, - "ObservationNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "collector" : { - "type" : "string" - }, - "geoCoordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "observationDbId" : { - "type" : "string" - }, - "observationTimeStamp" : { - "type" : "string" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "observationVariableDbId" : { - "type" : "string" - }, - "observationVariableName" : { - "type" : "string" - }, - "observationVariablePUI" : { - "type" : "string" - }, - "seasonDbId" : { - "type" : "string" - }, - "seasonName" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "uploadedBy" : { - "type" : "string" - }, - "value" : { - "type" : "string" - } - }, - "required" : [ "observationDbId", "observationDbId" ] - }, - "ObservationSearchRequest" : { - "type" : "object", - "properties" : { - "observationTimeStampRangeEnd" : { - "type" : "string" - }, - "observationTimeStampRangeStart" : { - "type" : "string" - } - } - }, - "ObservationUnit" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "seedLotDbId" : { - "type" : "string" - }, - "seedLotName" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } - }, - "required" : [ "observationUnitDbId" ] - }, - "ObservationUnitHierarchyLevel" : { - "type" : "object", - "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", - "properties" : { - "levelName" : { - "type" : "string" - }, - "levelOrder" : { - "type" : "integer", - "format" : "int32" - } - } - }, - "ObservationUnitLevel" : { - "type" : "object", - "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", - "properties" : { - "levelCode" : { - "type" : "string" - }, - "levelName" : { - "type" : "string" - }, - "levelOrder" : { - "type" : "integer", - "format" : "int32" - } - } - }, - "ObservationUnitLevelRelationship" : { - "type" : "object", - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", - "properties" : { - "levelCode" : { - "type" : "string" - }, - "levelName" : { - "type" : "string" - }, - "levelOrder" : { - "type" : "integer", - "format" : "int32" - }, - "observationUnit" : { - "$ref" : "#/components/schemas/ObservationUnit" - } - } - }, - "ObservationUnitNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "seedLotDbId" : { - "type" : "string" - }, - "seedLotName" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } - }, - "required" : [ "observationUnitDbId", "observationUnitDbId" ] - }, - "ObservationUnitPosition" : { - "type" : "object", - "properties" : { - "entryType" : { - "type" : "string", - "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", - "enum" : [ "CHECK", "TEST", "FILLER" ] - }, - "observationLevel" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "positionCoordinateX" : { - "type" : "string" - }, - "positionCoordinateXType" : { - "type" : "string", - "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", - "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] - }, - "positionCoordinateY" : { - "type" : "string" - }, - "positionCoordinateYType" : { - "type" : "string", - "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", - "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] - } - } - }, - "ObservationUnitSearchRequest" : { - "type" : "object", - "properties" : { - "includeObservations" : { - "type" : "boolean" - } - } - }, - "ObservationVariable" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" - }, - "observationVariableName" : { - "type" : "string" - }, - "observationVariablePUI" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" - }, - "scientist" : { - "type" : "string" - }, - "status" : { - "type" : "string" - }, - "submissionTimestamp" : { - "type" : "string" - }, - "traitDbId" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" - } - }, - "required" : [ "methodName", "observationVariableDbId", "observationVariableName", "scaleDbId", "scaleName", "traitName" ] - }, - "ObservationVariableNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" - }, - "observationVariableDbId" : { - "type" : "string" - }, - "observationVariableName" : { - "type" : "string" - }, - "observationVariablePUI" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" - }, - "scientist" : { - "type" : "string" - }, - "status" : { - "type" : "string" - }, - "submissionTimestamp" : { - "type" : "string" - }, - "traitDbId" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" - } - }, - "required" : [ "methodName", "observationVariableDbId", "observationVariableDbId", "observationVariableName", "scaleDbId", "scaleName", "traitName" ] - }, - "ObservationVariableSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "Ontology" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "authors" : { - "type" : "string" - }, - "copyright" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "licence" : { - "type" : "string" - }, - "ontologyName" : { - "type" : "string" - }, - "version" : { - "type" : "string" - } - }, - "required" : [ "ontologyDbId", "ontologyName" ] - }, - "OntologyNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "authors" : { - "type" : "string" - }, - "copyright" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "licence" : { - "type" : "string" - }, - "ontologyDbId" : { - "type" : "string" - }, - "ontologyName" : { - "type" : "string" - }, - "version" : { - "type" : "string" - } - }, - "required" : [ "ontologyDbId", "ontologyDbId", "ontologyName" ] - }, - "OntologyReference" : { - "type" : "object", - "properties" : { - "ontology" : { - "$ref" : "#/components/schemas/Ontology" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "version" : { - "type" : "string" - } - }, - "required" : [ "ontology" ] - }, - "OntologyTerm" : { - "type" : "object", - "properties" : { - "term" : { - "type" : "string" - }, - "termURI" : { - "type" : "string" - } - } - }, - "Pagination" : { - "type" : "object", - "properties" : { - "alleleMatrix" : { - "$ref" : "#/components/schemas/AlleleMatrix" - }, - "dimension" : { - "type" : "string", - "description" : "The dimension of the matrix being paginated", - "enum" : [ "CALLSETS", "VARIANTS" ] - }, - "page" : { - "type" : "integer", - "format" : "int32" - }, - "pageSize" : { - "type" : "integer", - "format" : "int32" - }, - "totalCount" : { - "type" : "integer", - "format" : "int32" - }, - "totalPages" : { - "type" : "integer", - "format" : "int32" - } - } - }, - "ParentType" : { - "type" : "string", - "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", - "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] - }, - "PedigreeNode" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "breedingMethodDbId" : { - "type" : "string" - }, - "breedingMethodName" : { - "type" : "string" - }, - "crossingProjectDbId" : { - "type" : "string" - }, - "crossingProjectName" : { - "type" : "string" - }, - "crossingYear" : { - "type" : "integer", - "format" : "int32" - }, - "defaultDisplayName" : { - "type" : "string" - }, - "familyCode" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "pedigreeNodeDbId" : { - "type" : "string" - }, - "pedigreeString" : { - "type" : "string" - }, - "siblingDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/programs" : { + "post" : { + "tags" : [ + "Programs" + ], + "summary" : "Submit a search request for `Program`", + "description" : "Submit a search request for `Program`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - }, - "required" : [ "germplasmDbId", "germplasmName", "germplasmPUI" ] - }, - "PedigreeNodeSearchRequest" : { - "type" : "object", - "properties" : { - "includeFullTree" : { - "type" : "boolean" - }, - "includeParents" : { - "type" : "boolean" - }, - "includeProgeny" : { - "type" : "boolean" - }, - "includeSiblings" : { - "type" : "boolean" - }, - "pedigreeDepth" : { - "type" : "integer", - "format" : "int32" - }, - "progenyDepth" : { - "type" : "integer", - "format" : "int32" - } - } - }, - "Person" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "description" : { - "type" : "string" - }, - "emailAddress" : { - "type" : "string" - }, - "firstName" : { - "type" : "string" - }, - "lastName" : { - "type" : "string" - }, - "mailingAddress" : { - "type" : "string" - }, - "middleName" : { - "type" : "string" - }, - "phoneNumber" : { - "type" : "string" - }, - "userID" : { - "type" : "string" - } - }, - "required" : [ "personDbId" ] - }, - "PersonNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "description" : { - "type" : "string" - }, - "emailAddress" : { - "type" : "string" - }, - "firstName" : { - "type" : "string" - }, - "lastName" : { - "type" : "string" - }, - "mailingAddress" : { - "type" : "string" - }, - "middleName" : { - "type" : "string" - }, - "personDbId" : { - "type" : "string" - }, - "phoneNumber" : { - "type" : "string" - }, - "userID" : { - "type" : "string" - } - }, - "required" : [ "personDbId", "personDbId" ] - }, - "PersonSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "PlannedCross" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "crossType" : { - "$ref" : "#/components/schemas/CrossType" - }, - "crossingProjectDbId" : { - "type" : "string" - }, - "crossingProjectName" : { - "type" : "string" - }, - "parent1" : { - "$ref" : "#/components/schemas/CrossParent" - }, - "parent2" : { - "$ref" : "#/components/schemas/CrossParent" - }, - "plannedCrossDbId" : { - "type" : "string" - }, - "plannedCrossName" : { - "type" : "string" - }, - "status" : { - "type" : "string", - "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", - "enum" : [ "TODO", "DONE", "SKIPPED" ] - } }, - "required" : [ "plannedCrossDbId" ] - }, - "Plate" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "plateBarcode" : { - "type" : "string" - }, - "plateFormat" : { - "type" : "string", - "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", - "enum" : [ "PLATE_96", "TUBES" ] - }, - "plateName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "sampleType" : { - "type" : "string", - "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", - "enum" : [ "DNA", "RNA", "TISSUE", "MIXED" ] - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } - }, - "required" : [ "plateDbId", "plateName" ] - }, - "PlateNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "plateBarcode" : { - "type" : "string" - }, - "plateDbId" : { - "type" : "string" - }, - "plateFormat" : { - "type" : "string", - "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", - "enum" : [ "PLATE_96", "TUBES" ] - }, - "plateName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "sampleType" : { - "type" : "string", - "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", - "enum" : [ "DNA", "RNA", "TISSUE", "MIXED" ] - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } - }, - "required" : [ "plateDbId", "plateName" ] - }, - "PlateSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "PollinationEvent" : { - "type" : "object", - "properties" : { - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" - }, - "pollinationNumber" : { - "type" : "string" - }, - "pollinationSuccessful" : { - "type" : "boolean" - }, - "pollinationTimeStamp" : { - "type" : "string" - } - } - }, - "Program" : { - "type" : "object", - "properties" : { - "abbreviation" : { - "type" : "string" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "fundingInformation" : { - "type" : "string" - }, - "objective" : { - "type" : "string" - }, - "personDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "programType" : { - "type" : "string", - "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", - "enum" : [ "STANDARD", "PROJECT" ] - } - }, - "required" : [ "programDbId", "programName" ] - }, - "ProgramNewRequest" : { - "type" : "object", - "properties" : { - "abbreviation" : { - "type" : "string" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "fundingInformation" : { - "type" : "string" - }, - "objective" : { - "type" : "string" - }, - "personDbId" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "programType" : { - "type" : "string", - "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", - "enum" : [ "STANDARD", "PROJECT" ] - } - }, - "required" : [ "programDbId", "programDbId", "programName" ] - }, - "ProgramSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "Publication" : { - "type" : "object", - "properties" : { - "publicationPUI" : { - "type" : "string" - }, - "publicationReference" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } - } - }, - "Reference" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "isDerived" : { - "type" : "boolean" - }, - "length" : { - "type" : "integer", - "format" : "int32" - }, - "md5checksum" : { - "type" : "string" - }, - "referenceDbId" : { - "type" : "string" - }, - "referenceName" : { - "type" : "string" - }, - "referenceSetDbId" : { - "type" : "string" - }, - "referenceSetName" : { - "type" : "string" - }, - "sourceDivergence" : { - "type" : "number" - }, - "sourceGermplasmDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "sourceURI" : { - "type" : "string" - }, - "species" : { - "$ref" : "#/components/schemas/OntologyTerm" - }, - "variantDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/references" : { + "post" : { + "tags" : [ + "References" + ], + "summary" : "Submit a search request for `Reference`", + "description" : "Submit a search request for `Reference`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "required" : [ "referenceDbId", "referenceName" ] - }, - "ReferenceSearchRequest" : { - "type" : "object", - "properties" : { - "isDerived" : { - "type" : "boolean" - }, - "maxLength" : { - "type" : "integer", - "format" : "int32" - }, - "minLength" : { - "type" : "integer", - "format" : "int32" - } - } - }, - "ReferenceSet" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "assemblyPUI" : { - "type" : "string" - }, - "commonCropName" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "isDerived" : { - "type" : "boolean" - }, - "md5checksum" : { - "type" : "string" - }, - "referenceDbId" : { - "type" : "string" - }, - "referenceName" : { - "type" : "string" - }, - "referenceSetName" : { - "type" : "string" - }, - "sourceGermplasmDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "sourceURI" : { - "type" : "string" - }, - "species" : { - "$ref" : "#/components/schemas/OntologyTerm" - }, - "variantDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "variantSetDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/referencesets" : { + "post" : { + "tags" : [ + "ReferenceSets" + ], + "summary" : "Submit a search request for `ReferenceSet`", + "description" : "Submit a search request for `ReferenceSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "required" : [ "referenceSetDbId", "referenceSetName" ] - }, - "ReferenceSetNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "assemblyPUI" : { - "type" : "string" - }, - "commonCropName" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "isDerived" : { - "type" : "boolean" - }, - "md5checksum" : { - "type" : "string" - }, - "referenceDbId" : { - "type" : "string" - }, - "referenceName" : { - "type" : "string" - }, - "referenceSetDbId" : { - "type" : "string" - }, - "referenceSetName" : { - "type" : "string" - }, - "sourceGermplasmDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "sourceURI" : { - "type" : "string" - }, - "species" : { - "$ref" : "#/components/schemas/OntologyTerm" - }, - "variantDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "variantSetDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/samples" : { + "post" : { + "tags" : [ + "Samples" + ], + "summary" : "Submit a search request for `Sample`", + "description" : "Submit a search request for `Sample`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } }, - "required" : [ "referenceSetDbId", "referenceSetDbId", "referenceSetName" ] - }, - "ReferenceSetSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "Sample" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "callSetDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/studies" : { + "post" : { + "tags" : [ + "Studies" + ], + "summary" : "Submit a search request for `Study`", + "description" : "Submit a search request for `Study`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "column" : { - "type" : "integer", - "format" : "int32" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "plateDbId" : { - "type" : "string" - }, - "plateName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "row" : { - "type" : "string" - }, - "sampleBarcode" : { - "type" : "string" - }, - "sampleDescription" : { - "type" : "string" - }, - "sampleGroupId" : { - "type" : "string" - }, - "sampleName" : { - "type" : "string" - }, - "samplePUI" : { - "type" : "string" - }, - "sampleTimestamp" : { - "type" : "string" - }, - "sampleType" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "takenBy" : { - "type" : "string" - }, - "tissueType" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - }, - "well" : { - "type" : "string" - } }, - "required" : [ "sampleDbId", "sampleName" ] - }, - "SampleNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "callSetDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/trials" : { + "post" : { + "tags" : [ + "Trials" + ], + "summary" : "Submit a search request for `Trial`", + "description" : "Submit a search request for `Trial`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "column" : { - "type" : "integer", - "format" : "int32" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "plateDbId" : { - "type" : "string" - }, - "plateName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "row" : { - "type" : "string" - }, - "sampleBarcode" : { - "type" : "string" - }, - "sampleDbId" : { - "type" : "string" - }, - "sampleDescription" : { - "type" : "string" - }, - "sampleGroupId" : { - "type" : "string" - }, - "sampleName" : { - "type" : "string" - }, - "samplePUI" : { - "type" : "string" - }, - "sampleTimestamp" : { - "type" : "string" - }, - "sampleType" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "takenBy" : { - "type" : "string" - }, - "tissueType" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - }, - "well" : { - "type" : "string" - } - }, - "required" : [ "sampleDbId", "sampleName" ] - }, - "SampleSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "Scale" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "dataType" : { - "type" : "string", - "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", - "enum" : [ "Code", "Date", "Duration", "Nominal", "Numerical", "Ordinal", "Text" ] - }, - "decimalPlaces" : { - "type" : "integer", - "format" : "int32" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" - }, - "units" : { - "type" : "string" - }, - "validValues" : { - "$ref" : "#/components/schemas/ValidValues" - } - }, - "required" : [ "scaleDbId", "scaleName" ] - }, - "ScaleNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "dataType" : { - "type" : "string", - "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", - "enum" : [ "Code", "Date", "Duration", "Nominal", "Numerical", "Ordinal", "Text" ] - }, - "decimalPlaces" : { - "type" : "integer", - "format" : "int32" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" - }, - "units" : { - "type" : "string" - }, - "validValues" : { - "$ref" : "#/components/schemas/ValidValues" - } }, - "required" : [ "scaleDbId", "scaleDbId", "scaleName" ] - }, - "Season" : { - "type" : "object", - "properties" : { - "seasonDbId" : { - "type" : "string" - }, - "seasonName" : { - "type" : "string" - }, - "year" : { - "type" : "integer", - "format" : "int32" - } - }, - "required" : [ "seasonDbId" ] - }, - "SeedLot" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "amount" : { - "type" : "number" - }, - "createdDate" : { - "type" : "string" - }, - "lastUpdated" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "seedLotDescription" : { - "type" : "string" - }, - "seedLotName" : { - "type" : "string" - }, - "sourceCollection" : { - "type" : "string" - }, - "storageLocation" : { - "type" : "string" - }, - "units" : { - "type" : "string" - } - }, - "required" : [ "seedLotDbId", "seedLotName" ] - }, - "SeedLotNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "amount" : { - "type" : "number" - }, - "createdDate" : { - "type" : "string" - }, - "lastUpdated" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "seedLotDbId" : { - "type" : "string" - }, - "seedLotDescription" : { - "type" : "string" - }, - "seedLotName" : { - "type" : "string" - }, - "sourceCollection" : { - "type" : "string" - }, - "storageLocation" : { - "type" : "string" - }, - "units" : { - "type" : "string" - } - }, - "required" : [ "seedLotDbId", "seedLotDbId", "seedLotName" ] - }, - "SeedLotTransaction" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "amount" : { - "type" : "number" - }, - "seedLotDbId" : { - "type" : "string" - }, - "seedLotName" : { - "type" : "string" - }, - "transactionDbId" : { - "type" : "string" - }, - "transactionDescription" : { - "type" : "string" - }, - "transactionTimestamp" : { - "type" : "string" - }, - "units" : { - "type" : "string" - } - }, - "required" : [ "transactionDbId" ] - }, - "StorageType" : { - "type" : "object", - "properties" : { - "code" : { - "type" : "string", - "description" : "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", - "enum" : [ "10", "11", "12", "13", "20", "30", "40", "50", "99" ] - }, - "description" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - } - } - }, - "Study" : { - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "contactDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "culturalPractices" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "endDate" : { - "type" : "string" - }, - "environmentParameterDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "experimentalDesign" : { - "$ref" : "#/components/schemas/ExperimentalDesign" - }, - "growthFacility" : { - "$ref" : "#/components/schemas/GrowthFacility" - }, - "lastUpdateDbId" : { - "type" : "string" - }, - "license" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "observationUnitsDescription" : { - "type" : "string" - }, - "observationVariableDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/variants" : { + "post" : { + "tags" : [ + "Variants" + ], + "summary" : "Submit a search request for `Variant`", + "description" : "Submit a search request for `Variant`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "startDate" : { - "type" : "string" - }, - "studyCode" : { - "type" : "string" - }, - "studyDescription" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "studyType" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } }, - "required" : [ "studyDbId", "studyName" ] - }, - "StudyNewRequest" : { - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "contactDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "culturalPractices" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "endDate" : { - "type" : "string" - }, - "environmentParameterDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "experimentalDesign" : { - "$ref" : "#/components/schemas/ExperimentalDesign" - }, - "growthFacility" : { - "$ref" : "#/components/schemas/GrowthFacility" - }, - "lastUpdateDbId" : { - "type" : "string" - }, - "license" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "observationUnitsDescription" : { - "type" : "string" - }, - "observationVariableDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/variantsets" : { + "post" : { + "tags" : [ + "VariantSets" + ], + "summary" : "Submit a search request for `VariantSet`", + "description" : "Submit a search request for `VariantSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "startDate" : { - "type" : "string" - }, - "studyCode" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyDescription" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "studyType" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } - }, - "required" : [ "studyDbId", "studyDbId", "studyName" ] - }, - "StudySearchRequest" : { - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" - } - } - }, - "Synonym" : { - "type" : "object", - "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "synonym" : { - "type" : "string" - }, - "type" : { - "type" : "string" - } - } - }, - "TaxonId" : { - "type" : "object", - "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "sourceName" : { - "type" : "string" - }, - "taxonId" : { - "type" : "string" - } }, - "required" : [ "sourceName", "taxonId" ] - }, - "Trait" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attribute" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "entity" : { - "type" : "string" - }, - "entityPUI" : { - "type" : "string" - }, - "mainAbbreviation" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "status" : { - "type" : "string" - }, - "traitClass" : { - "type" : "string" - }, - "traitDescription" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" - } - }, - "required" : [ "traitDbId", "traitName" ] - }, - "TraitDataType" : { - "type" : "string", - "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", - "enum" : [ "Code", "Date", "Duration", "Nominal", "Numerical", "Ordinal", "Text" ] - }, - "TraitNewRequest" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attribute" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "entity" : { - "type" : "string" - }, - "entityPUI" : { - "type" : "string" - }, - "mainAbbreviation" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" - }, - "status" : { - "type" : "string" - }, - "traitClass" : { - "type" : "string" - }, - "traitDbId" : { - "type" : "string" - }, - "traitDescription" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" - } - }, - "required" : [ "traitDbId", "traitName" ] - }, - "Treatment" : { - "type" : "object", - "properties" : { - "factor" : { - "type" : "string" - }, - "modality" : { - "type" : "string" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - } - } - }, - "Trial" : { - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "contacts" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Contact" - } - }, - "documentationURL" : { - "type" : "string" - }, - "endDate" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "startDate" : { - "type" : "string" - }, - "studyDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/allelematrix/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "AlleleMatrix" + ], + "summary" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `AlleleMatrix` search request
\nClients should submit a search request using the corresponding `POST /search/alleleMatrix` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/AlleleMatrixListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "trialDescription" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } }, - "required" : [ "trialDbId", "trialName" ] - }, - "TrialNewRequest" : { - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "contacts" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Contact" - } - }, - "documentationURL" : { - "type" : "string" - }, - "endDate" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "startDate" : { - "type" : "string" - }, - "studyDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/calls/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Calls" + ], + "summary" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Call` search request
\nClients should submit a search request using the corresponding `POST /search/call` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "trialDbId" : { - "type" : "string" - }, - "trialDescription" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } }, - "required" : [ "trialDbId", "trialDbId", "trialName" ] - }, - "TrialSearchRequest" : { - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" - }, - "searchDateRangeEnd" : { - "type" : "string" - }, - "searchDateRangeStart" : { - "type" : "string" - } - } - }, - "ValidValues" : { - "type" : "object", - "properties" : { - "maximumValue" : { - "type" : "string" - }, - "minimumValue" : { - "type" : "string" - }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" - } - } - }, - "ValidValuesCategory" : { - "type" : "object", - "properties" : { - "label" : { - "type" : "string" - }, - "validValues" : { - "$ref" : "#/components/schemas/ValidValues" - }, - "value" : { - "type" : "string" - } - } - }, - "Variable" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "contextOfUse" : { - "type" : "array", - "items" : { - "type" : "string" - } - }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "method" : { - "$ref" : "#/components/schemas/Method" - }, - "ontologyReference" : { - "$ref" : "#/components/schemas/OntologyReference" - }, - "scale" : { - "$ref" : "#/components/schemas/Scale" - }, - "scientist" : { - "type" : "string" - }, - "status" : { - "type" : "string" - }, - "submissionTimestamp" : { - "type" : "string" - }, - "synonyms" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/callsets/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "CallSets" + ], + "summary" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `CallSet` search request
\nClients should submit a search request using the corresponding `POST /search/callSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "trait" : { - "$ref" : "#/components/schemas/Trait" - } - }, - "required" : [ "method", "scale", "trait" ] - }, - "Variant" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "created" : { - "type" : "string" - }, - "end" : { - "type" : "integer", - "format" : "int32" - }, - "filtersApplied" : { - "type" : "boolean" - }, - "filtersPassed" : { - "type" : "boolean" - }, - "referenceBases" : { - "type" : "string" - }, - "referenceDbId" : { - "type" : "string" - }, - "referenceName" : { - "type" : "string" - }, - "referenceSetDbId" : { - "type" : "string" - }, - "referenceSetName" : { - "type" : "string" - }, - "start" : { - "type" : "integer", - "format" : "int32" - }, - "svlen" : { - "type" : "integer", - "format" : "int32" - }, - "updated" : { - "type" : "string" - }, - "variantDbId" : { - "type" : "string" - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" - }, - "variantType" : { - "type" : "string" - } }, - "required" : [ "variantDbId" ] - }, - "VariantSearchRequest" : { - "type" : "object", - "properties" : { - "end" : { - "type" : "integer", - "format" : "int32" - }, - "referenceDbId" : { - "type" : "string" - }, - "start" : { - "type" : "integer", - "format" : "int32" - } - } - }, - "VariantSet" : { - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "analysiDbIds" : { - "type" : "array", - "items" : { - "type" : "string" + "/search/germplasm/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Submit a search request for `Germplasm`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Germplasm` search request
\nClients should submit a search request using the corresponding `POST /search/germplasm` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - }, - "callSetCount" : { - "type" : "integer", - "format" : "int32" - }, - "referenceSetDbId" : { - "type" : "string" - }, - "referenceSetName" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "variantCount" : { - "type" : "integer", - "format" : "int32" - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" - } - }, - "required" : [ "variantSetDbId" ] - }, - "VariantSetSearchRequest" : { - "type" : "object", - "properties" : { } - }, - "basePagination" : { - "type" : "object", - "description" : "The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Pages are zero indexed, so the first page will be page 0 (zero).", - "properties" : { - "currentPage" : { - "type" : "integer", - "default" : 0, - "description" : "The index number for the returned page of data. This should always match the requested page number or the default page (0).", - "example" : 0 - }, - "pageSize" : { - "type" : "integer", - "default" : 1000, - "description" : "The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned.", - "example" : 1000 - }, - "totalCount" : { - "type" : "integer", - "description" : "The total number of elements that are available on the server and match the requested query parameters.", - "example" : 10 - }, - "totalPages" : { - "type" : "integer", - "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", - "example" : 1 - } }, - "required" : [ "currentPage", "pageSize" ] - }, - "dataFile" : { - "type" : "object", - "description" : "A dataFile contains a URL and the relevant file metadata to represent a file", - "properties" : { - "fileURL" : { - "type" : "string", - "format" : "uri", - "description" : "The absolute URL where the file is located", - "example" : "https://wiki.brapi.org/examples/datafile.xlsx" - }, - "fileName" : { - "type" : "string", - "description" : "The name of the file", - "example" : "datafile.xlsx" - }, - "fileSize" : { - "type" : "integer", - "description" : "The size of the file in bytes", - "example" : 4398 - }, - "fileDescription" : { - "type" : "string", - "description" : "A human readable description of the file contents", - "example" : "This is an Excel data file" - }, - "fileType" : { - "type" : "string", - "description" : "The type or format of the file. Preferably MIME Type.", - "example" : "application/vnd.ms-excel" - }, - "fileMD5Hash" : { - "type" : "string", - "description" : "The MD5 Hash of the file contents to be used as a check sum", - "example" : "c2365e900c81a89cf74d83dab60df146" - } - }, - "required" : [ "fileURL" ] - }, - "metadata" : { - "allOf" : [ { - "$ref" : "#/components/schemas/metadataBase" - }, { - "type" : "object", - "properties" : { - "pagination" : { - "$ref" : "#/components/schemas/basePagination" - } - } - } ] - }, - "metadataBase" : { - "type" : "object", - "description" : "An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information.", - "properties" : { - "datafiles" : { - "type" : "array", - "description" : "The datafiles contains a list of file URLs and metadata. \nThese files contain additional information related to the returned object and can be retrieved by a subsequent call. \nThis could be a supplementary data file, an informational file, the uploaded file where the data originated from, a generated file representing the whole dataset in a particular format, or any other related file. ", - "example" : [ ], - "items" : { - "$ref" : "#/components/schemas/dataFile" - } - }, - "status" : { - "type" : "array", - "description" : "The status field contains a list of informational status messages from the server. \nIf no status is reported, an empty list should be returned. See Error Reporting for more information.", - "items" : { - "$ref" : "#/components/schemas/status" - } - } - } - }, - "metadataTokenPagination" : { - "allOf" : [ { - "$ref" : "#/components/schemas/metadataBase" - }, { - "type" : "object", - "properties" : { - "pagination" : { - "$ref" : "#/components/schemas/tokenPagination" + "/search/attributes/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "GermplasmAttributes" + ], + "summary" : "Submit a search request for `GermplasmAttribute`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `GermplasmAttribute` search request
\nClients should submit a search request using the corresponding `POST /search/germplasmAttribute` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } ] - }, - "status" : { - "type" : "object", - "description" : "An array of status messages to convey technical logging information from the server to the client.", - "properties" : { - "message" : { - "type" : "string", - "description" : "A short message concerning the status of this request/response", - "example" : "Request accepted, response successful" - }, - "messageType" : { - "type" : "string", - "description" : "The logging level for the attached message", - "enum" : [ "DEBUG", "ERROR", "WARNING", "INFO" ], - "example" : "INFO" - } }, - "required" : [ "message", "messageType" ] - }, - "tokenPagination" : { - "allOf" : [ { - "$ref" : "#/components/schemas/basePagination" - }, { - "type" : "object", - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken to construct an additional query and move to the next or previous page respectively. ", - "example" : { - "currentPage" : 0, - "pageSize" : 1000, - "totalCount" : 10, - "totalPages" : 1 - }, - "properties" : { - "nextPageToken" : { - "type" : "string", - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the next page of data.", - "example" : "cb668f63" - }, - "currentPageToken" : { - "type" : "string", - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the current page of data.", - "example" : "48bc6ac1" - }, - "prevPageToken" : { - "type" : "string", - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the previous page of data.", - "example" : "9659857e" - } - }, - "required" : [ "nextPageToken" ] - } ] - } - }, - "responses" : { - "ObservationVariableSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/ObservationVariable" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ObservationVariableSingleResponse" - } - } - } - }, - "SeedLotSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/SeedLot" - } - }, - "required" : [ "metadata", "result" ], - "title" : "SeedLotSingleResponse" - } - } - } - }, - "VariantSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Variant" - } - }, - "required" : [ "metadata", "result" ], - "title" : "VariantSingleResponse" - } - } - } - }, - "202AcceptedSearchResponse" : { - "description" : "Accepted", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "searchResultsDbId" : { - "type" : "string", - "example" : "551ae08c" - } - } - } - }, - "title" : "202AcceptedSearchResponse" - } - } - } - }, - "StudySingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Study" - } - }, - "required" : [ "metadata", "result" ], - "title" : "StudySingleResponse" - } - } - } - }, - "MarkerPositionListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/MarkerPosition" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "MarkerPositionListResponse" - } - } - } - }, - "TrialListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Trial" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "TrialListResponse" - } - } - } - }, - "MethodSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Method" - } - }, - "required" : [ "metadata", "result" ], - "title" : "MethodSingleResponse" - } - } - } - }, - "SeedLotListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/SeedLot" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "SeedLotListResponse" - } - } - } - }, - "VariantSetListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/VariantSet" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "VariantSetListResponse" - } - } - } - }, - "SampleSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Sample" - } - }, - "required" : [ "metadata", "result" ], - "title" : "SampleSingleResponse" - } - } - } - }, - "CallSetListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/CallSet" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "CallSetListResponse" - } - } - } - }, - "CallSetSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/CallSet" - } - }, - "required" : [ "metadata", "result" ], - "title" : "CallSetSingleResponse" - } - } - } - }, - "VariantSetSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/VariantSet" - } - }, - "required" : [ "metadata", "result" ], - "title" : "VariantSetSingleResponse" - } - } - } - }, - "ObservationVariableListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/ObservationVariable" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "ObservationVariableListResponse" - } - } - } - }, - "ReferenceSetSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/ReferenceSet" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ReferenceSetSingleResponse" - } - } - } - }, - "CrossListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Cross" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "CrossListResponse" - } - } - } - }, - "ImageSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Image" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ImageSingleResponse" - } - } - } - }, - "PlateListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Plate" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "PlateListResponse" - } - } - } - }, - "SeasonListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Season" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "SeasonListResponse" - } - } - } - }, - "ObservationUnitListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/ObservationUnit" - } + "/search/attributevalues/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "GermplasmAttributeValues" + ], + "summary" : "Submit a search request for `GermplasmAttributeValue`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `GermplasmAttributeValue` search request
\nClients should submit a search request using the corresponding `POST /search/germplasmAttributeValue` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" } - }, - "required" : [ "data" ] } - }, - "required" : [ "metadata", "result" ], - "title" : "ObservationUnitListResponse" - } - } - } - }, - "ReferenceListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Reference" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "ReferenceListResponse" } - } - } - }, - "ObservationListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Observation" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "ObservationListResponse" - } - } - } - }, - "AlleleMatrixListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/AlleleMatrix" - } + }, + "/search/images/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Images" + ], + "summary" : "Submit a search request for `Image`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Image` search request
\nClients should submit a search request using the corresponding `POST /search/image` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" } - }, - "required" : [ "data" ] } - }, - "required" : [ "metadata", "result" ], - "title" : "AlleleMatrixListResponse" - } - } - } - }, - "GenomeMapSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/GenomeMap" - } - }, - "required" : [ "metadata", "result" ], - "title" : "GenomeMapSingleResponse" - } - } - } - }, - "PersonListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Person" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "PersonListResponse" - } - } - } - }, - "PlannedCrossListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/PlannedCross" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "PlannedCrossListResponse" - } - } - } - }, - "LocationListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Location" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "LocationListResponse" - } - } - } - }, - "403Forbidden" : { - "description" : "Forbidden", - "content" : { - "application/json" : { - "schema" : { - "type" : "string" - }, - "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action" - } - } - }, - "OntologySingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Ontology" - } - }, - "required" : [ "metadata", "result" ], - "title" : "OntologySingleResponse" } - } - } - }, - "ProgramListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Program" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "ProgramListResponse" - } - } - } - }, - "ObservationUnitSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/ObservationUnit" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ObservationUnitSingleResponse" - } - } - } - }, - "ScaleListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Scale" - } + }, + "/search/lists/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Lists" + ], + "summary" : "Submit a search request for `List`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `List` search request
\nClients should submit a search request using the corresponding `POST /search/list` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" } - }, - "required" : [ "data" ] } - }, - "required" : [ "metadata", "result" ], - "title" : "ScaleListResponse" - } - } - } - }, - "ListListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/List" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "ListListResponse" } - } - } - }, - "400BadRequest" : { - "description" : "Bad Request", - "content" : { - "application/json" : { - "schema" : { - "type" : "string" - }, - "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing" - } - } - }, - "MethodListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Method" - } + }, + "/search/locations/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Locations" + ], + "summary" : "Submit a search request for `Location`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Location` search request
\nClients should submit a search request using the corresponding `POST /search/location` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" } - }, - "required" : [ "data" ] } - }, - "required" : [ "metadata", "result" ], - "title" : "MethodListResponse" - } - } - } - }, - "CrossingProjectListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/CrossingProject" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "CrossingProjectListResponse" - } - } - } - }, - "GermplasmAttributeSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/GermplasmAttribute" - } - }, - "required" : [ "metadata", "result" ], - "title" : "GermplasmAttributeSingleResponse" - } - } - } - }, - "TraitSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Trait" - } - }, - "required" : [ "metadata", "result" ], - "title" : "TraitSingleResponse" - } - } - } - }, - "401Unauthorized" : { - "description" : "Unauthorized", - "content" : { - "application/json" : { - "schema" : { - "type" : "string" - }, - "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token" - } - } - }, - "GermplasmAttributeListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/GermplasmAttribute" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "GermplasmAttributeListResponse" } - } - } - }, - "GermplasmListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Germplasm" - } + }, + "/search/markerpositions/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "MarkerPositions" + ], + "summary" : "Submit a search request for `MarkerPosition`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `MarkerPosition` search request
\nClients should submit a search request using the corresponding `POST /search/markerPosition` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/MarkerPositionListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" } - }, - "required" : [ "data" ] } - }, - "required" : [ "metadata", "result" ], - "title" : "GermplasmListResponse" - } - } - } - }, - "EventListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Event" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "EventListResponse" - } - } - } - }, - "CrossingProjectSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/CrossingProject" - } - }, - "required" : [ "metadata", "result" ], - "title" : "CrossingProjectSingleResponse" } - } - } - }, - "TraitListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Trait" - } + }, + "/search/observations/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Observations" + ], + "summary" : "Submit a search request for `Observation`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Observation` search request
\nClients should submit a search request using the corresponding `POST /search/observation` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" } - }, - "required" : [ "data" ] } - }, - "required" : [ "metadata", "result" ], - "title" : "TraitListResponse" - } - } - } - }, - "SampleListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Sample" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "SampleListResponse" - } - } - } - }, - "ReferenceSetListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/ReferenceSet" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "ReferenceSetListResponse" - } - } - } - }, - "TrialSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Trial" - } - }, - "required" : [ "metadata", "result" ], - "title" : "TrialSingleResponse" - } - } - } - }, - "GermplasmSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Germplasm" - } - }, - "required" : [ "metadata", "result" ], - "title" : "GermplasmSingleResponse" } - } - } - }, - "OntologyListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Ontology" - } + }, + "/search/observationunits/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "ObservationUnits" + ], + "summary" : "Submit a search request for `ObservationUnit`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `ObservationUnit` search request
\nClients should submit a search request using the corresponding `POST /search/observationUnit` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" } - }, - "required" : [ "data" ] } - }, - "required" : [ "metadata", "result" ], - "title" : "OntologyListResponse" - } - } - } - }, - "ReferenceSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Reference" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ReferenceSingleResponse" - } - } - } - }, - "SeasonSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Season" - } - }, - "required" : [ "metadata", "result" ], - "title" : "SeasonSingleResponse" - } - } - } - }, - "404NotFound" : { - "description" : "Not Found", - "content" : { - "application/json" : { - "schema" : { - "type" : "string" - }, - "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found" - } - } - }, - "StudyListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Study" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "StudyListResponse" - } - } - } - }, - "ScaleSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Scale" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ScaleSingleResponse" } - } - } - }, - "CallListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Call" - } + }, + "/search/variables/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "ObservationVariables" + ], + "summary" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `ObservationVariable` search request
\nClients should submit a search request using the corresponding `POST /search/observationVariable` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" } - }, - "required" : [ "data" ] } - }, - "required" : [ "metadata", "result" ], - "title" : "CallListResponse" - } - } - } - }, - "BreedingMethodSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/BreedingMethod" - } - }, - "required" : [ "metadata", "result" ], - "title" : "BreedingMethodSingleResponse" - } - } - } - }, - "LocationSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Location" - } - }, - "required" : [ "metadata", "result" ], - "title" : "LocationSingleResponse" } - } - } - }, - "PersonSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Person" - } - }, - "required" : [ "metadata", "result" ], - "title" : "PersonSingleResponse" + }, + "/search/pedigree/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "PedigreeNodes" + ], + "summary" : "Submit a search request for `PedigreeNode`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `PedigreeNode` search request
\nClients should submit a search request using the corresponding `POST /search/pedigreeNode` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "ImageListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Image" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "ImageListResponse" + }, + "/search/people/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "People" + ], + "summary" : "Submit a search request for `Person`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Person` search request
\nClients should submit a search request using the corresponding `POST /search/person` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "VariantListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Variant" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "VariantListResponse" + }, + "/search/plates/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Plates" + ], + "summary" : "Submit a search request for `Plate`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Plate` search request
\nClients should submit a search request using the corresponding `POST /search/plate` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "PlateSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Plate" - } - }, - "required" : [ "metadata", "result" ], - "title" : "PlateSingleResponse" + }, + "/search/programs/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Programs" + ], + "summary" : "Submit a search request for `Program`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Program` search request
\nClients should submit a search request using the corresponding `POST /search/program` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "GermplasmAttributeValueListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/GermplasmAttributeValue" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "GermplasmAttributeValueListResponse" + }, + "/search/references/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "References" + ], + "summary" : "Submit a search request for `Reference`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Reference` search request
\nClients should submit a search request using the corresponding `POST /search/reference` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "BreedingMethodListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/BreedingMethod" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "BreedingMethodListResponse" + }, + "/search/referencesets/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "ReferenceSets" + ], + "summary" : "Submit a search request for `ReferenceSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `ReferenceSet` search request
\nClients should submit a search request using the corresponding `POST /search/referenceSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "GermplasmAttributeValueSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/GermplasmAttributeValue" - } - }, - "required" : [ "metadata", "result" ], - "title" : "GermplasmAttributeValueSingleResponse" + }, + "/search/samples/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Samples" + ], + "summary" : "Submit a search request for `Sample`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Sample` search request
\nClients should submit a search request using the corresponding `POST /search/sample` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "GenomeMapListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/GenomeMap" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "GenomeMapListResponse" + }, + "/search/studies/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Studies" + ], + "summary" : "Submit a search request for `Study`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Study` search request
\nClients should submit a search request using the corresponding `POST /search/study` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "PedigreeNodeListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/PedigreeNode" - } - } - }, - "required" : [ "data" ] - } - }, - "required" : [ "metadata", "result" ], - "title" : "PedigreeNodeListResponse" + }, + "/search/trials/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Trials" + ], + "summary" : "Submit a search request for `Trial`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Trial` search request
\nClients should submit a search request using the corresponding `POST /search/trial` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "ObservationSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Observation" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ObservationSingleResponse" + }, + "/search/variants/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "Variants" + ], + "summary" : "Submit a search request for `Variant`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Variant` search request
\nClients should submit a search request using the corresponding `POST /search/variant` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } - } - }, - "ListSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/List" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ListSingleResponse" + }, + "/search/variantsets/{searchResultsDbId}" : { + "get" : { + "tags" : [ + "VariantSets" + ], + "summary" : "Submit a search request for `VariantSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `VariantSet` search request
\nClients should submit a search request using the corresponding `POST /search/variantSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } - } } - }, - "ProgramSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "type" : "object", - "properties" : { - "@context" : { - "type" : "object", - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "type" : "object", - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "type" : "object", - "$ref" : "#/components/schemas/Program" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ProgramSingleResponse" - } - } - } - } }, - "parameters" : { - "externalReferenceID" : { - "name" : "externalReferenceID", - "in" : "query", - "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", - "required" : false, - "deprecated" : true, - "style" : "form", - "explode" : true, - "schema" : { - "type" : "string" - } - }, - "externalReferenceId" : { - "name" : "externalReferenceId", - "in" : "query", - "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", - "required" : false, - "style" : "form", - "explode" : true, - "schema" : { - "type" : "string" - } - }, - "externalReferenceSource" : { - "name" : "externalReferenceSource", - "in" : "query", - "description" : "An identifier for the source system or database of an external reference (use with `externalReferenceId` parameter)", - "required" : false, - "style" : "form", - "explode" : true, - "schema" : { - "type" : "string" - } - }, - "acceptHeader" : { - "name" : "Accept", - "in" : "header", - "description" : "A standard HTTP request header that is used to request a specific content type (JSON, CSV, etc) which is \"acceptable\" to the client and should be returned by the server", - "required" : true, - "style" : "simple", - "explode" : false, - "schema" : { - "$ref" : "#/components/schemas/ContentTypes" - }, - "example" : "application/json" - }, - "searchResultsDbId" : { - "name" : "searchResultsDbId", - "in" : "path", - "description" : "Unique identifier which references the search results", - "required" : true, - "style" : "simple", - "explode" : false, - "schema" : { - "type" : "string" - } - }, - "pageSize" : { - "name" : "pageSize", - "in" : "query", - "description" : "The size of the pages to be returned. Default is `1000`.", - "required" : false, - "style" : "form", - "explode" : true, - "schema" : { - "type" : "integer" - }, - "example" : 1000 - }, - "authorizationHeader" : { - "name" : "Authorization", - "in" : "header", - "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", - "required" : false, - "style" : "simple", - "explode" : false, - "schema" : { - "type" : "string", - "pattern" : "^Bearer .*$" + "components" : { + "schemas" : { + "AdditionalInfo" : { + "type" : "object", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + }, + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + }, + "AlleleMatrix" : { + "required" : [ + "callSetDbIds", + "variantSetDbIds" + ], + "type" : "object", + "properties" : { + "callSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "expandHomozygotes" : { + "type" : "boolean" + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + }, + "variantDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "description" : "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." + }, + "AlleleMatrixSearchRequest" : { + "type" : "object", + "properties" : { + "expandHomozygotes" : { + "type" : "boolean" + }, + "preview" : { + "type" : "boolean" + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + } + }, + "description" : "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." + }, + "Analysis" : { + "required" : [ + "analysisDbId" + ], + "type" : "object", + "properties" : { + "analysisDbId" : { + "type" : "string" + }, + "analysisName" : { + "type" : "string" + }, + "created" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "software" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "type" : { + "type" : "string" + }, + "updated" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "description" : "An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used." + }, + "Attribute" : { + "required" : [ + "attributeName", + "method", + "scale", + "trait" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "attributeCategory" : { + "type" : "string" + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeDescription" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "contextOfUse" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "method" : { + "$ref" : "#/components/schemas/Method" + }, + "ontologyReference" : { + "$ref" : "#/components/schemas/OntologyReference" + }, + "scale" : { + "$ref" : "#/components/schemas/Scale" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trait" : { + "$ref" : "#/components/schemas/Trait" + } + } + }, + "AvailableFormat" : { + "type" : "object", + "properties" : { + "dataFormat" : { + "type" : "string", + "description" : "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)", + "enum" : [ + "DartSeq", + "VCF", + "Hapmap", + "tabular", + "JSON" + ] + }, + "expandHomozygotes" : { + "type" : "boolean" + }, + "fileFormat" : { + "type" : "string", + "description" : "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.", + "enum" : [ + "text/csv", + "text/tsv", + "application/excel", + "application/zip", + "application/json" + ] + }, + "fileURL" : { + "type" : "string" + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "description" : "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other." + }, + "BreedingMethod" : { + "required" : [ + "abbreviation", + "breedingMethodDbId", + "breedingMethodName", + "description" + ], + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "description" : { + "type" : "string" + } + }, + "description" : "The techniques and protocol used to produce a Cross or Germplasm" + }, + "Call" : { + "required" : [ + "callSetDbId", + "variantDbId", + "variantSetDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "callSetDbId" : { + "type" : "string" + }, + "callSetName" : { + "type" : "string" + }, + "genotypeValue" : { + "type" : "string" + }, + "phaseSet" : { + "type" : "string" + }, + "variantDbId" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "description" : "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345." + }, + "CallSearchRequest" : { + "type" : "object", + "properties" : { + "expandHomozygotes" : { + "type" : "boolean" + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + } + }, + "description" : "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345." + }, + "CallSet" : { + "required" : [ + "callSetDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "callSetDbId" : { + "type" : "string" + }, + "callSetName" : { + "type" : "string" + }, + "created" : { + "type" : "string" + }, + "sampleDbId" : { + "type" : "string" + }, + "sampleName" : { + "type" : "string" + }, + "samplePUI" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "updated" : { + "type" : "string" + }, + "variantSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "description" : "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" + }, + "CallSetSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" + }, + "Contact" : { + "required" : [ + "contactDbId" + ], + "type" : "object", + "properties" : { + "contactDbId" : { + "type" : "string" + }, + "email" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "name" : { + "type" : "string" + }, + "orcid" : { + "type" : "string" + }, + "type" : { + "type" : "string" + } + }, + "description" : "A persons contact information" + }, + "ContentMixture" : { + "type" : "object", + "properties" : { + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "mixturePercentage" : { + "type" : "integer", + "format" : "int32" + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + } + }, + "description" : "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100." + }, + "ContentTypes" : { + "type" : "string", + "enum" : [ + "application/json", + "text/csv", + "text/tsv", + "application/flapjack" + ] + }, + "Context" : { + "title" : "context", + "type" : "array", + "description" : "The JSON-LD Context is used to provide JSON-LD definitions to each field in a JSON object. By providing an array of context file urls, a BrAPI response object becomes JSON-LD compatible. \n\nFor more information, see https://w3c.github.io/json-ld-syntax/#the-context", + "example" : [ + "https://brapi.org/jsonld/context/metadata.jsonld" + ], + "items" : { + "type" : "string", + "format" : "uri" + } + }, + "Cross" : { + "required" : [ + "crossDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "crossName" : { + "type" : "string" + }, + "crossType" : { + "$ref" : "#/components/schemas/CrossType" + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "parent1" : { + "$ref" : "#/components/schemas/CrossParent" + }, + "parent2" : { + "$ref" : "#/components/schemas/CrossParent" + }, + "plannedCrossDbId" : { + "type" : "string" + }, + "plannedCrossName" : { + "type" : "string" + } + }, + "description" : "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." + }, + "CrossAttribute" : { + "type" : "object", + "properties" : { + "crossAttributeName" : { + "type" : "string" + }, + "crossAttributeValue" : { + "type" : "string" + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + } + }, + "description" : "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'" + }, + "CrossNewRequest" : { + "required" : [ + "crossDbId", + "crossDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "crossType" : { + "$ref" : "#/components/schemas/CrossType" + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "parent1" : { + "$ref" : "#/components/schemas/CrossParent" + }, + "parent2" : { + "$ref" : "#/components/schemas/CrossParent" + }, + "plannedCrossDbId" : { + "type" : "string" + }, + "plannedCrossName" : { + "type" : "string" + } + }, + "description" : "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." + }, + "CrossParent" : { + "type" : "object", + "properties" : { + "germplasm" : { + "$ref" : "#/components/schemas/Germplasm" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "parentType" : { + "$ref" : "#/components/schemas/ParentType" + } + }, + "description" : "The identifying information gor the parent material of a cross." + }, + "CrossType" : { + "type" : "string", + "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", + "enum" : [ + "BIPARENTAL", + "SELF", + "OPEN_POLLINATED", + "BULK", + "BULK_SELFED", + "BULK_OPEN_POLLINATED", + "DOUBLE_HAPLOID" + ] + }, + "CrossingProject" : { + "required" : [ + "crossingProjectDbId", + "crossingProjectName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "crossingProjectDescription" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + } + }, + "description" : "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." + }, + "CrossingProjectNewRequest" : { + "required" : [ + "crossingProjectDbId", + "crossingProjectDbId", + "crossingProjectName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectDescription" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + } + }, + "description" : "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." + }, + "DataLink" : { + "type" : "object", + "properties" : { + "dataFormat" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "fileFormat" : { + "type" : "string" + }, + "name" : { + "type" : "string" + }, + "provenance" : { + "type" : "string" + }, + "scientificType" : { + "type" : "string" + }, + "url" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "description" : "A link to extra data files associated with this study. Extra data could include notes, images, and reference data." + }, + "DataMatrix" : { + "type" : "object", + "properties" : { + "alleleMatrix" : { + "$ref" : "#/components/schemas/AlleleMatrix" + }, + "dataMatrix" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "dataMatrixAbbreviation" : { + "type" : "string" + }, + "dataMatrixName" : { + "type" : "string" + }, + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this data matrix. This is intended to help parse the data out of JSON.", + "enum" : [ + "string", + "integer", + "float", + "boolean" + ] + } + }, + "description" : "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." + }, + "DatasetAuthorships" : { + "type" : "object", + "properties" : { + "datasetPUI" : { + "type" : "string" + }, + "license" : { + "type" : "string" + }, + "publicReleaseDate" : { + "type" : "string" + }, + "submissionDate" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "License and citation information for the data in this trial" + }, + "DocumentationLink" : { + "type" : "object", + "properties" : { + "URL" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "type" : { + "type" : "string", + "description" : "The type of documentation, which can be OBO Foundry, an RDF term or a webpage.", + "enum" : [ + "OBO", + "RDF", + "WEBPAGE" + ] + } + }, + "description" : "Links to various ontology documentation" + }, + "Donor" : { + "type" : "object", + "properties" : { + "donorAccessionNumber" : { + "type" : "string" + }, + "donorInstituteCode" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + }, + "description" : "Identifier assigned to an accession by the material donor." + }, + "EnvironmentParameter" : { + "required" : [ + "description", + "environmentParametersDbId", + "parameterName" + ], + "type" : "object", + "properties" : { + "description" : { + "type" : "string" + }, + "environmentParametersDbId" : { + "type" : "string" + }, + "parameterName" : { + "type" : "string" + }, + "parameterPUI" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "unit" : { + "type" : "string" + }, + "unitPUI" : { + "type" : "string" + }, + "value" : { + "type" : "string" + }, + "valuePUI" : { + "type" : "string" + } + }, + "description" : "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)." + }, + "Event" : { + "required" : [ + "eventDbId", + "eventType" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "eventDbId" : { + "type" : "string" + }, + "eventDescription" : { + "type" : "string" + }, + "eventType" : { + "type" : "string" + }, + "eventTypeDbId" : { + "type" : "string" + }, + "observationUnitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + }, + "description" : "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other" + }, + "EventDateRange" : { + "type" : "object", + "properties" : { + "discreteDates" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "endDate" : { + "type" : "string" + }, + "eventDbId" : { + "type" : "string" + }, + "startDate" : { + "type" : "string" + } + }, + "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" + }, + "EventParameter" : { + "type" : "object", + "properties" : { + "code" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "eventDbId" : { + "type" : "string" + }, + "name" : { + "type" : "string" + }, + "units" : { + "type" : "string" + }, + "value" : { + "type" : "string" + }, + "valueDescription" : { + "type" : "string" + }, + "valuesByDate" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "description" : "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event." + }, + "ExperimentalDesign" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + }, + "description" : "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" + }, + "ExternalReference" : { + "type" : "object", + "properties" : { + "referenceId" : { + "type" : "string" + }, + "referenceSource" : { + "type" : "string" + } + } + }, + "GenomeMap" : { + "required" : [ + "commonCropName", + "mapDbId", + "type" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "comments" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "linkageGroupCount" : { + "type" : "integer", + "format" : "int32" + }, + "mapDbId" : { + "type" : "string" + }, + "mapName" : { + "type" : "string" + }, + "mapPUI" : { + "type" : "string" + }, + "markerCount" : { + "type" : "integer", + "format" : "int32" + }, + "publishedDate" : { + "type" : "string" + }, + "scientificName" : { + "type" : "string" + }, + "type" : { + "type" : "string" + }, + "unit" : { + "type" : "string" + } + }, + "description" : "The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map." + }, + "GenotypeMetadata" : { + "type" : "object", + "properties" : { + "call" : { + "$ref" : "#/components/schemas/Call" + }, + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "enum" : [ + "string", + "integer", + "float", + "boolean" + ] + }, + "fieldAbbreviation" : { + "type" : "string" + }, + "fieldName" : { + "type" : "string" + }, + "fieldValue" : { + "type" : "string" + } + }, + "description" : "Genotype Metadata are additional layers of metadata associated with each genotype." + }, + "GeoJSON" : { + "type" : "object", + "properties" : { + "geometry" : { + "$ref" : "#/components/schemas/GeoJSONGeometry" + }, + "type" : { + "type" : "string" + } + }, + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." + }, + "GeoJSONGeometry" : { + "oneOf" : [ + { + "required" : [ + "coordinateDbIds", + "type" + ], + "type" : "object", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." + }, + { + "required" : [ + "coordinateDbIds", + "type" + ], + "type" : "object", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." + } + ] + }, + "GeoJSONSearchArea" : { + "type" : "object", + "properties" : { + "geometry" : { + "$ref" : "#/components/schemas/GeoJSONGeometry" + }, + "germplasmOrigin" : { + "$ref" : "#/components/schemas/GermplasmOrigin" + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "$ref" : "#/components/schemas/ObservationUnitPosition" + }, + "type" : { + "type" : "string" + } + } + }, + "Germplasm" : { + "required" : [ + "commonCropName", + "germplasmDbId", + "germplasmName", + "germplasmPUI" + ], + "type" : "object", + "properties" : { + "accessionNumber" : { + "type" : "string" + }, + "acquisitionDate" : { + "type" : "string" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "biologicalStatusOfAccessionCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum" : [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999" + ] + }, + "biologicalStatusOfAccessionDescription" : { + "type" : "string" + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "collection" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "countryOfOriginCode" : { + "type" : "string" + }, + "defaultDisplayName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "genus" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "germplasmPreprocessing" : { + "type" : "string" + }, + "instituteCode" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "pedigree" : { + "type" : "string" + }, + "sampleDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "seedSource" : { + "type" : "string" + }, + "seedSourceDescription" : { + "type" : "string" + }, + "species" : { + "type" : "string" + }, + "speciesAuthority" : { + "type" : "string" + }, + "subtaxa" : { + "type" : "string" + }, + "subtaxaAuthority" : { + "type" : "string" + } + }, + "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." + }, + "GermplasmAttribute" : { + "required" : [ + "attributeDbId", + "attributeName", + "methodDbId", + "methodName", + "scaleDbId", + "scaleName", + "traitName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "attributeCategory" : { + "type" : "string" + }, + "attributeDescription" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "attributeValueDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropName" : { + "type" : "string" + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" + }, + "GermplasmAttributeNewRequest" : { + "required" : [ + "attributeDbId", + "attributeName", + "methodDbId", + "methodName", + "scaleDbId", + "scaleName", + "traitName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "attributeCategory" : { + "type" : "string" + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeDescription" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "attributeValueDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropName" : { + "type" : "string" + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" + }, + "GermplasmAttributeSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" + }, + "GermplasmAttributeValue" : { + "required" : [ + "attributeName", + "attributeValueDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "determinedDate" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "value" : { + "type" : "string" + } + }, + "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." + }, + "GermplasmAttributeValueNewRequest" : { + "required" : [ + "attributeName", + "attributeValueDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "attributeValueDbId" : { + "type" : "string" + }, + "determinedDate" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "value" : { + "type" : "string" + } + }, + "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." + }, + "GermplasmAttributeValueSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." + }, + "GermplasmChild" : { + "required" : [ + "germplasmDbId", + "germplasmName", + "germplasmPUI", + "parentType" + ], + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "parentType" : { + "$ref" : "#/components/schemas/ParentType" + }, + "pedigreeNodeDbId" : { + "type" : "string" + } + }, + "description" : "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes." + }, + "GermplasmNewRequest" : { + "required" : [ + "commonCropName", + "germplasmDbId", + "germplasmDbId", + "germplasmName", + "germplasmPUI" + ], + "type" : "object", + "properties" : { + "accessionNumber" : { + "type" : "string" + }, + "acquisitionDate" : { + "type" : "string" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "biologicalStatusOfAccessionCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum" : [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999" + ] + }, + "biologicalStatusOfAccessionDescription" : { + "type" : "string" + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "collection" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "countryOfOriginCode" : { + "type" : "string" + }, + "defaultDisplayName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "genus" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "germplasmPreprocessing" : { + "type" : "string" + }, + "instituteCode" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "pedigree" : { + "type" : "string" + }, + "sampleDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "seedSource" : { + "type" : "string" + }, + "seedSourceDescription" : { + "type" : "string" + }, + "species" : { + "type" : "string" + }, + "speciesAuthority" : { + "type" : "string" + }, + "subtaxa" : { + "type" : "string" + }, + "subtaxaAuthority" : { + "type" : "string" + } + }, + "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." + }, + "GermplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + }, + "description" : "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." + }, + "GermplasmParent" : { + "required" : [ + "germplasmDbId", + "germplasmName", + "germplasmPUI", + "parentType" + ], + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "parentType" : { + "$ref" : "#/components/schemas/ParentType" + }, + "pedigreeNodeDbId" : { + "type" : "string" + } + }, + "description" : "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." + }, + "GermplasmSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." + }, + "GrowthFacility" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + }, + "description" : "Short description of the facility in which the study was carried out." + }, + "Image" : { + "required" : [ + "imageDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "copyright" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "imageFileName" : { + "type" : "string" + }, + "imageFileSize" : { + "type" : "integer", + "format" : "int32" + }, + "imageHeight" : { + "type" : "integer", + "format" : "int32" + }, + "imageLocation" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "imageName" : { + "type" : "string" + }, + "imageTimeStamp" : { + "type" : "string" + }, + "imageURL" : { + "type" : "string" + }, + "imageWidth" : { + "type" : "integer", + "format" : "int32" + }, + "mimeType" : { + "type" : "string" + }, + "observationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + } + }, + "description" : "The metadata for an image file that is connected to some phenotypic observation data." + }, + "ImageNewRequest" : { + "required" : [ + "imageDbId", + "imageDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "copyright" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "imageDbId" : { + "type" : "string" + }, + "imageFileName" : { + "type" : "string" + }, + "imageFileSize" : { + "type" : "integer", + "format" : "int32" + }, + "imageHeight" : { + "type" : "integer", + "format" : "int32" + }, + "imageLocation" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "imageName" : { + "type" : "string" + }, + "imageTimeStamp" : { + "type" : "string" + }, + "imageURL" : { + "type" : "string" + }, + "imageWidth" : { + "type" : "integer", + "format" : "int32" + }, + "mimeType" : { + "type" : "string" + }, + "observationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + } + }, + "description" : "The metadata for an image file that is connected to some phenotypic observation data." + }, + "ImageSearchRequest" : { + "type" : "object", + "properties" : { + "imageFileSizeMax" : { + "type" : "integer", + "format" : "int32" + }, + "imageFileSizeMin" : { + "type" : "integer", + "format" : "int32" + }, + "imageHeightMax" : { + "type" : "integer", + "format" : "int32" + }, + "imageHeightMin" : { + "type" : "integer", + "format" : "int32" + }, + "imageLocation" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + }, + "imageTimeStampRangeEnd" : { + "type" : "string" + }, + "imageTimeStampRangeStart" : { + "type" : "string" + }, + "imageWidthMax" : { + "type" : "integer", + "format" : "int32" + }, + "imageWidthMin" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "The metadata for an image file that is connected to some phenotypic observation data." + }, + "LastUpdate" : { + "required" : [ + "lastUpdateDbId" + ], + "type" : "object", + "properties" : { + "lastUpdateDbId" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "timestamp" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "description" : "The date and time when this study was last modified" + }, + "List" : { + "required" : [ + "listDbId", + "listName", + "listType" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "dateCreated" : { + "type" : "string" + }, + "dateModified" : { + "type" : "string" + }, + "listDescription" : { + "type" : "string" + }, + "listName" : { + "type" : "string" + }, + "listOwnerName" : { + "type" : "string" + }, + "listSize" : { + "type" : "integer", + "format" : "int32" + }, + "listSource" : { + "type" : "string" + }, + "listType" : { + "$ref" : "#/components/schemas/ListType" + }, + "personDbId" : { + "type" : "string" + } + }, + "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." + }, + "ListNewRequest" : { + "required" : [ + "listDbId", + "listDbId", + "listName", + "listType" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "dateCreated" : { + "type" : "string" + }, + "dateModified" : { + "type" : "string" + }, + "listDbId" : { + "type" : "string" + }, + "listDescription" : { + "type" : "string" + }, + "listName" : { + "type" : "string" + }, + "listOwnerName" : { + "type" : "string" + }, + "listSize" : { + "type" : "integer", + "format" : "int32" + }, + "listSource" : { + "type" : "string" + }, + "listType" : { + "$ref" : "#/components/schemas/ListType" + }, + "personDbId" : { + "type" : "string" + } + }, + "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." + }, + "ListSearchRequest" : { + "type" : "object", + "properties" : { + "dateCreatedRangeEnd" : { + "type" : "string" + }, + "dateCreatedRangeStart" : { + "type" : "string" + }, + "dateModifiedRangeEnd" : { + "type" : "string" + }, + "dateModifiedRangeStart" : { + "type" : "string" + }, + "listType" : { + "$ref" : "#/components/schemas/ListType" + } + }, + "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." + }, + "ListType" : { + "type" : "string", + "description" : "The type of objects that are referenced in a List", + "enum" : [ + "germplasm", + "markers", + "variants", + "programs", + "trials", + "studies", + "observationUnits", + "observations", + "observationVariables", + "samples" + ] + }, + "Location" : { + "required" : [ + "locationDbId", + "locationName" + ], + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "childLocationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "coordinateDescription" : { + "type" : "string" + }, + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "countryCode" : { + "type" : "string" + }, + "countryName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "environmentType" : { + "type" : "string" + }, + "exposure" : { + "type" : "string" + }, + "instituteAddress" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "locationType" : { + "type" : "string" + }, + "siteStatus" : { + "type" : "string" + }, + "slope" : { + "type" : "string" + }, + "topography" : { + "type" : "string" + } + }, + "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." + }, + "LocationNewRequest" : { + "required" : [ + "locationDbId", + "locationDbId", + "locationName" + ], + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "childLocationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "coordinateDescription" : { + "type" : "string" + }, + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "countryCode" : { + "type" : "string" + }, + "countryName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "environmentType" : { + "type" : "string" + }, + "exposure" : { + "type" : "string" + }, + "instituteAddress" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "locationType" : { + "type" : "string" + }, + "siteStatus" : { + "type" : "string" + }, + "slope" : { + "type" : "string" + }, + "topography" : { + "type" : "string" + } + }, + "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." + }, + "LocationSearchRequest" : { + "type" : "object", + "properties" : { + "altitudeMax" : { + "type" : "number" + }, + "altitudeMin" : { + "type" : "number" + }, + "coordinates" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + } + }, + "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." + }, + "MarkerPosition" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "linkageGroupName" : { + "type" : "string" + }, + "mapDbId" : { + "type" : "string" + }, + "mapName" : { + "type" : "string" + }, + "mapPUI" : { + "type" : "string" + }, + "position" : { + "type" : "integer", + "format" : "int32" + }, + "variantDbId" : { + "type" : "string" + } + }, + "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." + }, + "MarkerPositionSearchRequest" : { + "type" : "object", + "properties" : { + "maxPosition" : { + "type" : "integer", + "format" : "int32" + }, + "minPosition" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." + }, + "MetadataField" : { + "type" : "object", + "properties" : { + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "enum" : [ + "string", + "integer", + "float", + "boolean" + ] + }, + "fieldAbbreviation" : { + "type" : "string" + }, + "fieldName" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "description" : "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard " + }, + "Method" : { + "required" : [ + "methodDbId", + "methodName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "bibliographicalReference" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "formula" : { + "type" : "string" + }, + "methodClass" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + } + }, + "description" : "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". " + }, + "MethodNewRequest" : { + "required" : [ + "methodDbId", + "methodDbId", + "methodName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "bibliographicalReference" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "formula" : { + "type" : "string" + }, + "methodClass" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + } + }, + "description" : "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". " + }, + "Observation" : { + "required" : [ + "observationDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "collector" : { + "type" : "string" + }, + "geoCoordinates" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationTimeStamp" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observationVariableDbId" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "seasonDbId" : { + "type" : "string" + }, + "seasonName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "uploadedBy" : { + "type" : "string" + }, + "value" : { + "type" : "string" + } + }, + "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + }, + "ObservationNewRequest" : { + "required" : [ + "observationDbId", + "observationDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "collector" : { + "type" : "string" + }, + "geoCoordinates" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationTimeStamp" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observationVariableDbId" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "seasonDbId" : { + "type" : "string" + }, + "seasonName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "uploadedBy" : { + "type" : "string" + }, + "value" : { + "type" : "string" + } + }, + "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + }, + "ObservationSearchRequest" : { + "type" : "object", + "properties" : { + "observationTimeStampRangeEnd" : { + "type" : "string" + }, + "observationTimeStampRangeStart" : { + "type" : "string" + } + }, + "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + }, + "ObservationTreatment" : { + "type" : "object", + "properties" : { + "factor" : { + "type" : "string" + }, + "modality" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + } + }, + "description" : "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor." + }, + "ObservationUnit" : { + "required" : [ + "observationUnitDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + }, + "ObservationUnitHierarchyLevel" : { + "type" : "object", + "properties" : { + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" " + }, + "ObservationUnitLevel" : { + "type" : "object", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" " + }, + "ObservationUnitLevelRelationship" : { + "type" : "object", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + }, + "observationUnit" : { + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** " + }, + "ObservationUnitNewRequest" : { + "required" : [ + "observationUnitDbId", + "observationUnitDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + }, + "ObservationUnitPosition" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ + "CHECK", + "TEST", + "FILLER" + ] + }, + "observationLevel" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "$ref" : "#/components/schemas/PositionCoordinateType" + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "$ref" : "#/components/schemas/PositionCoordinateType" + } + }, + "description" : "All positional and layout information related to this Observation Unit" + }, + "ObservationUnitSearchRequest" : { + "type" : "object", + "properties" : { + "includeObservations" : { + "type" : "boolean" + } + }, + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + }, + "ObservationVariable" : { + "required" : [ + "methodDbId", + "methodName", + "observationVariableDbId", + "observationVariableName", + "scaleDbId", + "scaleName", + "traitName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + } + }, + "ObservationVariableNewRequest" : { + "required" : [ + "methodDbId", + "methodName", + "observationVariableDbId", + "observationVariableDbId", + "observationVariableName", + "scaleDbId", + "scaleName", + "traitName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "observationVariableDbId" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + } + }, + "ObservationVariableSearchRequest" : { + "type" : "object", + "properties" : { } + }, + "Ontology" : { + "required" : [ + "ontologyDbId", + "ontologyName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "authors" : { + "type" : "string" + }, + "copyright" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "licence" : { + "type" : "string" + }, + "ontologyName" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "description" : "The identifier and metadata needed to reference an external controlled vocabulary" + }, + "OntologyNewRequest" : { + "required" : [ + "ontologyDbId", + "ontologyDbId", + "ontologyName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "authors" : { + "type" : "string" + }, + "copyright" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "licence" : { + "type" : "string" + }, + "ontologyDbId" : { + "type" : "string" + }, + "ontologyName" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "description" : "The identifier and metadata needed to reference an external controlled vocabulary" + }, + "OntologyReference" : { + "required" : [ + "ontology" + ], + "type" : "object", + "properties" : { + "ontology" : { + "$ref" : "#/components/schemas/Ontology" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "description" : "MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)." + }, + "OntologyTerm" : { + "type" : "object", + "properties" : { + "term" : { + "type" : "string" + }, + "termURI" : { + "type" : "string" + } + }, + "description" : "A pointer to an ontology used by a genomic reference" + }, + "Pagination" : { + "type" : "object", + "properties" : { + "alleleMatrix" : { + "$ref" : "#/components/schemas/AlleleMatrix" + }, + "dimension" : { + "type" : "string", + "description" : "The dimension of the matrix being paginated", + "enum" : [ + "CALLSETS", + "VARIANTS" + ] + }, + "page" : { + "type" : "integer", + "format" : "int32" + }, + "pageSize" : { + "type" : "integer", + "format" : "int32" + }, + "totalCount" : { + "type" : "integer", + "format" : "int32" + }, + "totalPages" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "Pagination info for the matrix" + }, + "ParentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ + "MALE", + "FEMALE", + "SELF", + "POPULATION", + "CLONAL" + ] + }, + "PedigreeNode" : { + "required" : [ + "germplasmDbId", + "germplasmName", + "germplasmPUI" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "crossingYear" : { + "type" : "integer", + "format" : "int32" + }, + "defaultDisplayName" : { + "type" : "string" + }, + "familyCode" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "pedigreeNodeDbId" : { + "type" : "string" + }, + "pedigreeString" : { + "type" : "string" + }, + "siblingDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "description" : "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances." + }, + "PedigreeNodeSearchRequest" : { + "type" : "object", + "properties" : { + "includeFullTree" : { + "type" : "boolean" + }, + "includeParents" : { + "type" : "boolean" + }, + "includeProgeny" : { + "type" : "boolean" + }, + "includeSiblings" : { + "type" : "boolean" + }, + "pedigreeDepth" : { + "type" : "integer", + "format" : "int32" + }, + "progenyDepth" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances." + }, + "Person" : { + "required" : [ + "personDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "description" : { + "type" : "string" + }, + "emailAddress" : { + "type" : "string" + }, + "firstName" : { + "type" : "string" + }, + "lastName" : { + "type" : "string" + }, + "mailingAddress" : { + "type" : "string" + }, + "middleName" : { + "type" : "string" + }, + "phoneNumber" : { + "type" : "string" + }, + "userID" : { + "type" : "string" + } + }, + "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." + }, + "PersonNewRequest" : { + "required" : [ + "personDbId", + "personDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "description" : { + "type" : "string" + }, + "emailAddress" : { + "type" : "string" + }, + "firstName" : { + "type" : "string" + }, + "lastName" : { + "type" : "string" + }, + "mailingAddress" : { + "type" : "string" + }, + "middleName" : { + "type" : "string" + }, + "personDbId" : { + "type" : "string" + }, + "phoneNumber" : { + "type" : "string" + }, + "userID" : { + "type" : "string" + } + }, + "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." + }, + "PersonSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." + }, + "PlannedCross" : { + "required" : [ + "plannedCrossDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "crossType" : { + "$ref" : "#/components/schemas/CrossType" + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "parent1" : { + "$ref" : "#/components/schemas/CrossParent" + }, + "parent2" : { + "$ref" : "#/components/schemas/CrossParent" + }, + "plannedCrossDbId" : { + "type" : "string" + }, + "plannedCrossName" : { + "type" : "string" + }, + "status" : { + "type" : "string", + "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", + "enum" : [ + "TODO", + "DONE", + "SKIPPED" + ] + } + }, + "description" : "Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field." + }, + "Plate" : { + "required" : [ + "plateDbId", + "plateName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "plateBarcode" : { + "type" : "string" + }, + "plateFormat" : { + "type" : "string", + "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", + "enum" : [ + "PLATE_96", + "TUBES" + ] + }, + "plateName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "sampleType" : { + "type" : "string", + "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", + "enum" : [ + "DNA", + "RNA", + "TISSUE", + "MIXED" + ] + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." + }, + "PlateNewRequest" : { + "required" : [ + "plateDbId", + "plateName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "plateBarcode" : { + "type" : "string" + }, + "plateDbId" : { + "type" : "string" + }, + "plateFormat" : { + "type" : "string", + "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", + "enum" : [ + "PLATE_96", + "TUBES" + ] + }, + "plateName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "sampleType" : { + "type" : "string", + "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", + "enum" : [ + "DNA", + "RNA", + "TISSUE", + "MIXED" + ] + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." + }, + "PlateSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." + }, + "PollinationEvent" : { + "type" : "object", + "properties" : { + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "pollinationNumber" : { + "type" : "string" + }, + "pollinationSuccessful" : { + "type" : "boolean" + }, + "pollinationTimeStamp" : { + "type" : "string" + } + }, + "description" : "A Pollination Event that was used or attempted for a Cross." + }, + "PositionCoordinateType" : { + "type" : "string", + "description" : "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ + "LONGITUDE", + "LATITUDE", + "PLANTED_ROW", + "PLANTED_INDIVIDUAL", + "GRID_ROW", + "GRID_COL", + "MEASURED_ROW", + "MEASURED_COL" + ] + }, + "Program" : { + "required" : [ + "programDbId", + "programName" + ], + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "fundingInformation" : { + "type" : "string" + }, + "objective" : { + "type" : "string" + }, + "personDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "programType" : { + "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "enum" : [ + "STANDARD", + "PROJECT" + ] + } + }, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." + }, + "ProgramNewRequest" : { + "required" : [ + "programDbId", + "programDbId", + "programName" + ], + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "fundingInformation" : { + "type" : "string" + }, + "objective" : { + "type" : "string" + }, + "personDbId" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "programType" : { + "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "enum" : [ + "STANDARD", + "PROJECT" + ] + } + }, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." + }, + "ProgramSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." + }, + "Publication" : { + "type" : "object", + "properties" : { + "publicationPUI" : { + "type" : "string" + }, + "publicationReference" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." + }, + "Reference" : { + "required" : [ + "referenceDbId", + "referenceName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "isDerived" : { + "type" : "boolean" + }, + "length" : { + "type" : "integer", + "format" : "int32" + }, + "md5checksum" : { + "type" : "string" + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "sourceDivergence" : { + "type" : "number" + }, + "sourceGermplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sourceURI" : { + "type" : "string" + }, + "species" : { + "$ref" : "#/components/schemas/OntologyTerm" + }, + "variantDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "description" : "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." + }, + "ReferenceSearchRequest" : { + "type" : "object", + "properties" : { + "isDerived" : { + "type" : "boolean" + }, + "maxLength" : { + "type" : "integer", + "format" : "int32" + }, + "minLength" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." + }, + "ReferenceSet" : { + "required" : [ + "referenceSetDbId", + "referenceSetName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "assemblyPUI" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "isDerived" : { + "type" : "boolean" + }, + "md5checksum" : { + "type" : "string" + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "sourceGermplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sourceURI" : { + "type" : "string" + }, + "species" : { + "$ref" : "#/components/schemas/OntologyTerm" + }, + "variantDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." + }, + "ReferenceSetNewRequest" : { + "required" : [ + "referenceSetDbId", + "referenceSetDbId", + "referenceSetName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "assemblyPUI" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "isDerived" : { + "type" : "boolean" + }, + "md5checksum" : { + "type" : "string" + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "sourceGermplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sourceURI" : { + "type" : "string" + }, + "species" : { + "$ref" : "#/components/schemas/OntologyTerm" + }, + "variantDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." + }, + "ReferenceSetSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." + }, + "Sample" : { + "required" : [ + "sampleDbId", + "sampleName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "callSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "column" : { + "type" : "integer", + "format" : "int32" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "plateDbId" : { + "type" : "string" + }, + "plateName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "row" : { + "type" : "string" + }, + "sampleBarcode" : { + "type" : "string" + }, + "sampleDescription" : { + "type" : "string" + }, + "sampleGroupId" : { + "type" : "string" + }, + "sampleName" : { + "type" : "string" + }, + "samplePUI" : { + "type" : "string" + }, + "sampleTimestamp" : { + "type" : "string" + }, + "sampleType" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "takenBy" : { + "type" : "string" + }, + "tissueType" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + }, + "well" : { + "type" : "string" + } + }, + "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." + }, + "SampleNewRequest" : { + "required" : [ + "sampleDbId", + "sampleName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "callSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "column" : { + "type" : "integer", + "format" : "int32" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "plateDbId" : { + "type" : "string" + }, + "plateName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "row" : { + "type" : "string" + }, + "sampleBarcode" : { + "type" : "string" + }, + "sampleDbId" : { + "type" : "string" + }, + "sampleDescription" : { + "type" : "string" + }, + "sampleGroupId" : { + "type" : "string" + }, + "sampleName" : { + "type" : "string" + }, + "samplePUI" : { + "type" : "string" + }, + "sampleTimestamp" : { + "type" : "string" + }, + "sampleType" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "takenBy" : { + "type" : "string" + }, + "tissueType" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + }, + "well" : { + "type" : "string" + } + }, + "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." + }, + "SampleSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." + }, + "Scale" : { + "required" : [ + "scaleDbId", + "scaleName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "dataType" : { + "type" : "string", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "enum" : [ + "Code", + "Date", + "Duration", + "Nominal", + "Numerical", + "Ordinal", + "Text" + ] + }, + "decimalPlaces" : { + "type" : "integer", + "format" : "int32" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "units" : { + "type" : "string" + }, + "validValues" : { + "$ref" : "#/components/schemas/ValidValues" + } + }, + "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"." + }, + "ScaleNewRequest" : { + "required" : [ + "scaleDbId", + "scaleDbId", + "scaleName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "dataType" : { + "type" : "string", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "enum" : [ + "Code", + "Date", + "Duration", + "Nominal", + "Numerical", + "Ordinal", + "Text" + ] + }, + "decimalPlaces" : { + "type" : "integer", + "format" : "int32" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "units" : { + "type" : "string" + }, + "validValues" : { + "$ref" : "#/components/schemas/ValidValues" + } + }, + "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"." + }, + "Season" : { + "required" : [ + "seasonDbId" + ], + "type" : "object", + "properties" : { + "seasonDbId" : { + "type" : "string" + }, + "seasonName" : { + "type" : "string" + }, + "year" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"." + }, + "SeedLot" : { + "required" : [ + "seedLotDbId", + "seedLotName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "amount" : { + "type" : "number" + }, + "createdDate" : { + "type" : "string" + }, + "lastUpdated" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "seedLotDescription" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "sourceCollection" : { + "type" : "string" + }, + "storageLocation" : { + "type" : "string" + }, + "units" : { + "type" : "string" + } + }, + "description" : "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." + }, + "SeedLotNewRequest" : { + "required" : [ + "seedLotDbId", + "seedLotDbId", + "seedLotName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "amount" : { + "type" : "number" + }, + "createdDate" : { + "type" : "string" + }, + "lastUpdated" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotDescription" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "sourceCollection" : { + "type" : "string" + }, + "storageLocation" : { + "type" : "string" + }, + "units" : { + "type" : "string" + } + }, + "description" : "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." + }, + "SeedLotTransaction" : { + "required" : [ + "transactionDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "amount" : { + "type" : "number" + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "transactionDbId" : { + "type" : "string" + }, + "transactionDescription" : { + "type" : "string" + }, + "transactionTimestamp" : { + "type" : "string" + }, + "units" : { + "type" : "string" + } + }, + "description" : "The record of an event where material was moved in or out of a particular SeedLot" + }, + "StorageType" : { + "type" : "object", + "properties" : { + "code" : { + "type" : "string", + "description" : "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", + "enum" : [ + "10", + "11", + "12", + "13", + "20", + "30", + "40", + "50", + "99" + ] + }, + "description" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + }, + "description" : "The type of storage this germplasm is kept in at a genebank." + }, + "Study" : { + "required" : [ + "studyDbId", + "studyName" + ], + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "contactDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "culturalPractices" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "endDate" : { + "type" : "string" + }, + "experimentalDesign" : { + "$ref" : "#/components/schemas/ExperimentalDesign" + }, + "growthFacility" : { + "$ref" : "#/components/schemas/GrowthFacility" + }, + "lastUpdateDbId" : { + "type" : "string" + }, + "license" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationLevelDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitsDescription" : { + "type" : "string" + }, + "observationVariableDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "startDate" : { + "type" : "string" + }, + "studyCode" : { + "type" : "string" + }, + "studyDescription" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "studyType" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." + }, + "StudyNewRequest" : { + "required" : [ + "studyDbId", + "studyDbId", + "studyName" + ], + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "contactDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "culturalPractices" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "endDate" : { + "type" : "string" + }, + "experimentalDesign" : { + "$ref" : "#/components/schemas/ExperimentalDesign" + }, + "growthFacility" : { + "$ref" : "#/components/schemas/GrowthFacility" + }, + "lastUpdateDbId" : { + "type" : "string" + }, + "license" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationLevelDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitsDescription" : { + "type" : "string" + }, + "observationVariableDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "startDate" : { + "type" : "string" + }, + "studyCode" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyDescription" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "studyType" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." + }, + "StudySearchRequest" : { + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + } + }, + "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." + }, + "Synonym" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "synonym" : { + "type" : "string" + }, + "type" : { + "type" : "string" + } + }, + "description" : "Alternative names or IDs used to reference this germplasm" + }, + "TaxonId" : { + "required" : [ + "sourceName", + "taxonId" + ], + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "sourceName" : { + "type" : "string" + }, + "taxonId" : { + "type" : "string" + } + }, + "description" : "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended." + }, + "Trait" : { + "required" : [ + "traitDbId", + "traitName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "attribute" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "entity" : { + "type" : "string" + }, + "entityPUI" : { + "type" : "string" + }, + "mainAbbreviation" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "traitClass" : { + "type" : "string" + }, + "traitDescription" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "description" : "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". " + }, + "TraitDataType" : { + "type" : "string", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "enum" : [ + "Code", + "Date", + "Duration", + "Nominal", + "Numerical", + "Ordinal", + "Text" + ] + }, + "TraitNewRequest" : { + "required" : [ + "traitDbId", + "traitName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "attribute" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "entity" : { + "type" : "string" + }, + "entityPUI" : { + "type" : "string" + }, + "mainAbbreviation" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "traitClass" : { + "type" : "string" + }, + "traitDbId" : { + "type" : "string" + }, + "traitDescription" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "description" : "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". " + }, + "Trial" : { + "required" : [ + "trialDbId", + "trialName" + ], + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "contacts" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Contact" + } + }, + "documentationURL" : { + "type" : "string" + }, + "endDate" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "startDate" : { + "type" : "string" + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDescription" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." + }, + "TrialNewRequest" : { + "required" : [ + "trialDbId", + "trialDbId", + "trialName" + ], + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "contacts" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Contact" + } + }, + "documentationURL" : { + "type" : "string" + }, + "endDate" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "startDate" : { + "type" : "string" + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbId" : { + "type" : "string" + }, + "trialDescription" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." + }, + "TrialSearchRequest" : { + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "searchDateRangeEnd" : { + "type" : "string" + }, + "searchDateRangeStart" : { + "type" : "string" + } + }, + "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." + }, + "ValidValues" : { + "type" : "object", + "properties" : { + "maximumValue" : { + "type" : "string" + }, + "minimumValue" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + } + }, + "description" : "Metadata describing the acceptable values for this Scale" + }, + "ValidValuesCategory" : { + "type" : "object", + "properties" : { + "label" : { + "type" : "string" + }, + "validValues" : { + "$ref" : "#/components/schemas/ValidValues" + }, + "value" : { + "type" : "string" + } + }, + "description" : "If the Scale is a categorical type, these objects define the valid options" + }, + "Variable" : { + "required" : [ + "method", + "scale", + "trait" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string" + }, + "contextOfUse" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "method" : { + "$ref" : "#/components/schemas/Method" + }, + "ontologyReference" : { + "$ref" : "#/components/schemas/OntologyReference" + }, + "scale" : { + "$ref" : "#/components/schemas/Scale" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trait" : { + "$ref" : "#/components/schemas/Trait" + } + }, + "description" : "A unique combination of Trait, Method, and Scale to define a clear context for an Observation." + }, + "Variant" : { + "required" : [ + "variantDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "created" : { + "type" : "string" + }, + "end" : { + "type" : "integer", + "format" : "int32" + }, + "filtersApplied" : { + "type" : "boolean" + }, + "filtersPassed" : { + "type" : "boolean" + }, + "referenceBases" : { + "type" : "string" + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "start" : { + "type" : "integer", + "format" : "int32" + }, + "svlen" : { + "type" : "integer", + "format" : "int32" + }, + "updated" : { + "type" : "string" + }, + "variantDbId" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + }, + "variantType" : { + "type" : "string" + } + }, + "description" : "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." + }, + "VariantSearchRequest" : { + "type" : "object", + "properties" : { + "end" : { + "type" : "integer", + "format" : "int32" + }, + "referenceDbId" : { + "type" : "string" + }, + "start" : { + "type" : "integer", + "format" : "int32" + } + }, + "description" : "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." + }, + "VariantSet" : { + "required" : [ + "variantSetDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "analysiDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "callSetCount" : { + "type" : "integer", + "format" : "int32" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "variantCount" : { + "type" : "integer", + "format" : "int32" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "description" : "A VariantSet is a collection of variants and variant calls intended to be analyzed together." + }, + "VariantSetSearchRequest" : { + "type" : "object", + "properties" : { }, + "description" : "A VariantSet is a collection of variants and variant calls intended to be analyzed together." + }, + "basePagination" : { + "required" : [ + "currentPage", + "pageSize" + ], + "type" : "object", + "properties" : { + "currentPage" : { + "type" : "integer", + "description" : "The index number for the returned page of data. This should always match the requested page number or the default page (0).", + "example" : 0, + "default" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned.", + "example" : 1000, + "default" : 1000 + }, + "totalCount" : { + "type" : "integer", + "description" : "The total number of elements that are available on the server and match the requested query parameters.", + "example" : 10 + }, + "totalPages" : { + "type" : "integer", + "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", + "example" : 1 + } + }, + "description" : "The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Pages are zero indexed, so the first page will be page 0 (zero)." + }, + "dataFile" : { + "required" : [ + "fileURL" + ], + "type" : "object", + "properties" : { + "fileURL" : { + "type" : "string", + "description" : "The absolute URL where the file is located", + "format" : "uri", + "example" : "https://wiki.brapi.org/examples/datafile.xlsx" + }, + "fileName" : { + "type" : "string", + "description" : "The name of the file", + "example" : "datafile.xlsx" + }, + "fileSize" : { + "type" : "integer", + "description" : "The size of the file in bytes", + "example" : 4398 + }, + "fileDescription" : { + "type" : "string", + "description" : "A human readable description of the file contents", + "example" : "This is an Excel data file" + }, + "fileType" : { + "type" : "string", + "description" : "The type or format of the file. Preferably MIME Type.", + "example" : "application/vnd.ms-excel" + }, + "fileMD5Hash" : { + "type" : "string", + "description" : "The MD5 Hash of the file contents to be used as a check sum", + "example" : "c2365e900c81a89cf74d83dab60df146" + } + }, + "description" : "A dataFile contains a URL and the relevant file metadata to represent a file" + }, + "metadata" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/metadataBase" + }, + { + "type" : "object", + "properties" : { + "pagination" : { + "$ref" : "#/components/schemas/basePagination" + } + } + } + ] + }, + "metadataBase" : { + "type" : "object", + "properties" : { + "datafiles" : { + "type" : "array", + "description" : "The datafiles contains a list of file URLs and metadata. \nThese files contain additional information related to the returned object and can be retrieved by a subsequent call. \nThis could be a supplementary data file, an informational file, the uploaded file where the data originated from, a generated file representing the whole dataset in a particular format, or any other related file. ", + "example" : [ ], + "items" : { + "$ref" : "#/components/schemas/dataFile" + } + }, + "status" : { + "type" : "array", + "description" : "The status field contains a list of informational status messages from the server. \nIf no status is reported, an empty list should be returned. See Error Reporting for more information.", + "items" : { + "$ref" : "#/components/schemas/status" + } + } + }, + "description" : "An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information." + }, + "metadataTokenPagination" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/metadataBase" + }, + { + "type" : "object", + "properties" : { + "pagination" : { + "$ref" : "#/components/schemas/tokenPagination" + } + } + } + ] + }, + "status" : { + "required" : [ + "message", + "messageType" + ], + "type" : "object", + "properties" : { + "message" : { + "type" : "string", + "description" : "A short message concerning the status of this request/response", + "example" : "Request accepted, response successful" + }, + "messageType" : { + "type" : "string", + "description" : "The logging level for the attached message", + "example" : "INFO", + "enum" : [ + "DEBUG", + "ERROR", + "WARNING", + "INFO" + ] + } + }, + "description" : "An array of status messages to convey technical logging information from the server to the client." + }, + "tokenPagination" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/basePagination" + }, + { + "required" : [ + "nextPageToken" + ], + "type" : "object", + "properties" : { + "nextPageToken" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the next page of data.", + "example" : "cb668f63", + "deprecated" : true + }, + "currentPageToken" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the current page of data.", + "example" : "48bc6ac1", + "deprecated" : true + }, + "prevPageToken" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the previous page of data.", + "example" : "9659857e", + "deprecated" : true + } + }, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken to construct an additional query and move to the next or previous page respectively. ", + "example" : { + "currentPage" : 0, + "pageSize" : 1000, + "totalCount" : 10, + "totalPages" : 1 + } + } + ] + } }, - "example" : "Bearer XXXX" - }, - "pageToken" : { - "name" : "pageToken", - "in" : "query", - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", - "required" : false, - "deprecated" : true, - "style" : "form", - "explode" : true, - "schema" : { - "type" : "string" + "responses" : { + "ObservationVariableSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationVariableSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ObservationVariable" + } + } + } + } + } + }, + "SeedLotSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "SeedLotSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/SeedLot" + } + } + } + } + } + }, + "VariantSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "VariantSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Variant" + } + } + } + } + } + }, + "202AcceptedSearchResponse" : { + "description" : "Accepted", + "content" : { + "application/json" : { + "schema" : { + "title" : "202AcceptedSearchResponse", + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "properties" : { + "searchResultsDbId" : { + "type" : "string", + "example" : "551ae08c" + } + } + } + } + } + } + } + }, + "StudySingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "StudySingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Study" + } + } + } + } + } + }, + "MarkerPositionListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "MarkerPositionListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/MarkerPosition" + } + } + } + } + } + } + } + } + }, + "TrialListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "TrialListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Trial" + } + } + } + } + } + } + } + } + }, + "MethodSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "MethodSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Method" + } + } + } + } + } + }, + "SeedLotListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "SeedLotListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/SeedLot" + } + } + } + } + } + } + } + } + }, + "VariantSetListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "VariantSetListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/VariantSet" + } + } + } + } + } + } + } + } + }, + "SampleSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "SampleSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Sample" + } + } + } + } + } + }, + "CallSetListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "CallSetListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/CallSet" + } + } + } + } + } + } + } + } + }, + "CallSetSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "CallSetSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/CallSet" + } + } + } + } + } + }, + "VariantSetSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "VariantSetSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/VariantSet" + } + } + } + } + } + }, + "ObservationVariableListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationVariableListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ObservationVariable" + } + } + } + } + } + } + } + } + }, + "ReferenceSetSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ReferenceSetSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ReferenceSet" + } + } + } + } + } + }, + "CrossListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "CrossListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Cross" + } + } + } + } + } + } + } + } + }, + "ImageSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ImageSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Image" + } + } + } + } + } + }, + "PlateListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "PlateListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Plate" + } + } + } + } + } + } + } + } + }, + "SeasonListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "SeasonListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Season" + } + } + } + } + } + } + } + } + }, + "ObservationUnitListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationUnitListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ObservationUnit" + } + } + } + } + } + } + } + } + }, + "ReferenceListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ReferenceListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Reference" + } + } + } + } + } + } + } + } + }, + "ObservationListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Observation" + } + } + } + } + } + } + } + } + }, + "AlleleMatrixListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "AlleleMatrixListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/AlleleMatrix" + } + } + } + } + } + } + } + } + }, + "GenomeMapSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GenomeMapSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GenomeMap" + } + } + } + } + } + }, + "PersonListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "PersonListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Person" + } + } + } + } + } + } + } + } + }, + "PlannedCrossListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "PlannedCrossListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/PlannedCross" + } + } + } + } + } + } + } + } + }, + "LocationListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "LocationListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Location" + } + } + } + } + } + } + } + } + }, + "403Forbidden" : { + "description" : "Forbidden", + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + }, + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action" + } + } + }, + "OntologySingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "OntologySingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Ontology" + } + } + } + } + } + }, + "ProgramListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ProgramListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Program" + } + } + } + } + } + } + } + } + }, + "ObservationUnitSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationUnitSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ObservationUnit" + } + } + } + } + } + }, + "ScaleListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ScaleListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Scale" + } + } + } + } + } + } + } + } + }, + "ListListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ListListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/List" + } + } + } + } + } + } + } + } + }, + "400BadRequest" : { + "description" : "Bad Request", + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + }, + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing" + } + } + }, + "MethodListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "MethodListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Method" + } + } + } + } + } + } + } + } + }, + "CrossingProjectListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "CrossingProjectListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/CrossingProject" + } + } + } + } + } + } + } + } + }, + "GermplasmAttributeSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GermplasmAttributeSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GermplasmAttribute" + } + } + } + } + } + }, + "TraitSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "TraitSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Trait" + } + } + } + } + } + }, + "401Unauthorized" : { + "description" : "Unauthorized", + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + }, + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token" + } + } + }, + "GermplasmAttributeListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GermplasmAttributeListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/GermplasmAttribute" + } + } + } + } + } + } + } + } + }, + "GermplasmListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GermplasmListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Germplasm" + } + } + } + } + } + } + } + } + }, + "EventListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "EventListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Event" + } + } + } + } + } + } + } + } + }, + "CrossingProjectSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "CrossingProjectSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/CrossingProject" + } + } + } + } + } + }, + "TraitListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "TraitListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Trait" + } + } + } + } + } + } + } + } + }, + "SampleListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "SampleListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Sample" + } + } + } + } + } + } + } + } + }, + "ReferenceSetListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ReferenceSetListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ReferenceSet" + } + } + } + } + } + } + } + } + }, + "TrialSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "TrialSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Trial" + } + } + } + } + } + }, + "GermplasmSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GermplasmSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Germplasm" + } + } + } + } + } + }, + "OntologyListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "OntologyListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Ontology" + } + } + } + } + } + } + } + } + }, + "ReferenceSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ReferenceSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Reference" + } + } + } + } + } + }, + "SeasonSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "SeasonSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Season" + } + } + } + } + } + }, + "404NotFound" : { + "description" : "Not Found", + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + }, + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found" + } + } + }, + "StudyListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "StudyListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Study" + } + } + } + } + } + } + } + } + }, + "ScaleSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ScaleSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Scale" + } + } + } + } + } + }, + "CallListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "CallListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Call" + } + } + } + } + } + } + } + } + }, + "BreedingMethodSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "BreedingMethodSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/BreedingMethod" + } + } + } + } + } + }, + "LocationSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "LocationSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Location" + } + } + } + } + } + }, + "PersonSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "PersonSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Person" + } + } + } + } + } + }, + "ImageListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ImageListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Image" + } + } + } + } + } + } + } + } + }, + "VariantListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "VariantListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Variant" + } + } + } + } + } + } + } + } + }, + "PlateSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "PlateSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Plate" + } + } + } + } + } + }, + "GermplasmAttributeValueListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GermplasmAttributeValueListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + } + } + } + } + } + } + } + }, + "BreedingMethodListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "BreedingMethodListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/BreedingMethod" + } + } + } + } + } + } + } + } + }, + "GermplasmAttributeValueSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GermplasmAttributeValueSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + } + } + } + } + }, + "GenomeMapListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GenomeMapListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/GenomeMap" + } + } + } + } + } + } + } + } + }, + "PedigreeNodeListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "PedigreeNodeListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/PedigreeNode" + } + } + } + } + } + } + } + } + }, + "ObservationSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Observation" + } + } + } + } + } + }, + "ListSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ListSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/List" + } + } + } + } + } + }, + "ProgramSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ProgramSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Program" + } + } + } + } + } + } }, - "example" : "33c27874" - }, - "page" : { - "name" : "page", - "in" : "query", - "description" : "Used to request a specific page of data to be returned.\n\nThe page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "required" : false, - "style" : "form", - "explode" : true, - "schema" : { - "type" : "integer" + "parameters" : { + "externalReferenceID" : { + "name" : "externalReferenceID", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "required" : false, + "deprecated" : true, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "string" + } + }, + "externalReferenceId" : { + "name" : "externalReferenceId", + "in" : "query", + "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "string" + } + }, + "externalReferenceSource" : { + "name" : "externalReferenceSource", + "in" : "query", + "description" : "An identifier for the source system or database of an external reference (use with `externalReferenceId` parameter)", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "string" + } + }, + "acceptHeader" : { + "name" : "Accept", + "in" : "header", + "description" : "A standard HTTP request header that is used to request a specific content type (JSON, CSV, etc) which is \"acceptable\" to the client and should be returned by the server", + "required" : true, + "style" : "simple", + "explode" : false, + "schema" : { + "$ref" : "#/components/schemas/ContentTypes" + }, + "example" : "application/json" + }, + "searchResultsDbId" : { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "Unique identifier which references the search results", + "required" : true, + "style" : "simple", + "explode" : false, + "schema" : { + "type" : "string" + } + }, + "pageSize" : { + "name" : "pageSize", + "in" : "query", + "description" : "The size of the pages to be returned. Default is `1000`.", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "integer" + }, + "example" : 1000 + }, + "page" : { + "name" : "page", + "in" : "query", + "description" : "Used to request a specific page of data to be returned.\n\nThe page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "integer" + }, + "example" : "0" + }, + "pageToken" : { + "name" : "pageToken", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", + "required" : false, + "deprecated" : true, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "string" + }, + "example" : "33c27874" + }, + "authorizationHeader" : { + "name" : "Authorization", + "in" : "header", + "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", + "required" : false, + "style" : "simple", + "explode" : false, + "schema" : { + "pattern" : "^Bearer .*$", + "type" : "string" + }, + "example" : "Bearer XXXX" + } }, - "example" : "0" - } - }, - "securitySchemes" : { - "AuthorizationToken" : { - "type" : "http", - "description" : "OAuth Bearer Token - A valid Bearer token to prove authorization", - "scheme" : "bearer", - "bearerFormat" : "nonce token or JWT" - } + "securitySchemes" : { + "AuthorizationToken" : { + "type" : "http", + "description" : "OAuth Bearer Token - A valid Bearer token to prove authorization", + "scheme" : "bearer", + "bearerFormat" : "nonce token or JWT" + } + } } - } } \ No newline at end of file diff --git a/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl index 52ef746e..2342ca0d 100644 --- a/Specification/Generated/brapi_generated.ttl +++ b/Specification/Generated/brapi_generated.ttl @@ -18,8 +18,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "GermplasmChild"@en . + rdf:type owl:Class; + rdfs:comment "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes."@en; + rdfs:label "GermplasmChild"@en . rdf:type owl:NamedIndividual , . @@ -74,8 +75,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "ValidValues"@en . + rdf:type owl:Class; + rdfs:comment "Metadata describing the acceptable values for this Scale"@en; + rdfs:label "ValidValues"@en . rdf:type owl:DatatypeProperty; @@ -84,10 +86,6 @@ PREFIX xsd: rdfs:label "synonyms"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -104,7 +102,7 @@ PREFIX xsd: rdf:type owl:ObjectProperty; - rdfs:comment "donoers associated with a germplasm"@en; + rdfs:comment "donors associated with a germplasm"@en; rdfs:domain ; rdfs:label "germplasm"@en; rdfs:range . @@ -116,11 +114,6 @@ PREFIX xsd: rdfs:label "defaultValue"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; - rdfs:label "PositionCoordinateYType"@en . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a `GenomeMap`"@en; @@ -142,12 +135,9 @@ PREFIX xsd: rdfs:label "analysis"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -156,6 +146,13 @@ PREFIX xsd: rdfs:label "seedLot"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The unique DbId of the breeding program this Seed Lot belongs to"@en; @@ -236,10 +233,6 @@ PREFIX xsd: rdfs:label "crossName"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)"@en; @@ -247,8 +240,12 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -257,12 +254,8 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The child germplasm"@en; - rdfs:domain ; - rdfs:label "childGermplasm"@en; - rdfs:range . + + rdf:type owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -272,15 +265,16 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "DocumentationLink"@en . + rdf:type owl:Class; + rdfs:comment "Links to various ontology documentation"@en; + rdfs:label "DocumentationLink"@en . - + rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . + rdfs:comment "The child germplasm"@en; + rdfs:domain ; + rdfs:label "childGermplasm"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -289,10 +283,6 @@ PREFIX xsd: rdfs:label "takenBy"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; @@ -308,18 +298,19 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Publication"@en . + rdf:type owl:Class; + rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; + rdfs:label "Publication"@en . - rdf:type owl:Class; - rdfs:label "Season"@en . + rdf:type owl:Class; + rdfs:comment "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"."@en; + rdfs:label "Season"@en . - - rdf:type owl:DatatypeProperty; - rdfs:domain ; - rdfs:label "version"@en; - rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; + rdfs:label "DocumentationLinkType"@en . rdf:type owl:DatatypeProperty; @@ -328,6 +319,13 @@ PREFIX xsd: rdfs:label "transactionDescription"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The version of the update."@en; + rdfs:domain ; + rdfs:label "version"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -366,6 +364,13 @@ PREFIX xsd: rdfs:label "attributePUI"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "URI pointing to an ontology class for the unit"@en; + rdfs:domain ; + rdfs:label "unitPUI"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The total number of elements that are available on the server and match the requested query parameters."@en; @@ -419,8 +424,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "GermplasmOrigin"@en . + rdf:type owl:Class; + rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; + rdfs:label "GermplasmOrigin"@en . rdf:type owl:ObjectProperty; @@ -479,13 +485,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; - rdfs:domain ; - rdfs:label "positionCoordinateYType"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "A program identifier to search for"@en; @@ -493,6 +492,13 @@ PREFIX xsd: rdfs:label "program"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of positional coordinate used for the Y coordinate of the position."@en; + rdfs:domain ; + rdfs:label "positionCoordinateYType"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study"@en; @@ -507,13 +513,6 @@ PREFIX xsd: rdfs:label "crossAttributeValue"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "the unique identifier for a program"@en; @@ -521,6 +520,13 @@ PREFIX xsd: rdfs:label "program"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; @@ -550,8 +556,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "CallSet"@en . + rdf:type owl:Class; + rdfs:comment "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample"@en; + rdfs:label "CallSet"@en . rdf:type owl:NamedIndividual , . @@ -591,8 +598,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "SeedLotTransaction"@en . + rdf:type owl:Class; + rdfs:comment "The record of an event where material was moved in or out of a particular SeedLot"@en; + rdfs:label "SeedLotTransaction"@en . rdf:type owl:DatatypeProperty; @@ -643,17 +651,19 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "AlleleMatrix"@en . + rdf:type owl:Class; + rdfs:comment "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier."@en; + rdfs:label "AlleleMatrix"@en . rdf:type , owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; - rdfs:domain ; - rdfs:label "additionalProperties"@en; - rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; + rdfs:comment "A free space containing any additional information related to a particular object."@en; + rdfs:domain ; + rdfs:label "additionalProperties"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -676,6 +686,13 @@ PREFIX xsd: rdfs:label "programType"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "Environment parameters associated with a study"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -717,13 +734,6 @@ PREFIX xsd: rdfs:label "crossType"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "variants"@en; - rdfs:domain ; - rdfs:label "variants"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "the type of cross"@en; @@ -731,6 +741,13 @@ PREFIX xsd: rdfs:label "crossType"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "variants"@en; + rdfs:domain ; + rdfs:label "variants"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -756,8 +773,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "BreedingMethod"@en . + rdf:type owl:Class; + rdfs:comment "The techniques and protocol used to produce a Cross or Germplasm"@en; + rdfs:label "BreedingMethod"@en . rdf:type owl:ObjectProperty; @@ -767,8 +785,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "Observation"@en . + rdf:type owl:Class; + rdfs:comment "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit."@en; + rdfs:label "Observation"@en . rdf:type owl:DatatypeProperty; @@ -848,14 +867,16 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "GermplasmParent"@en . + rdf:type owl:Class; + rdfs:comment "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes."@en; + rdfs:label "GermplasmParent"@en . - rdf:type owl:DatatypeProperty; - rdfs:domain ; - rdfs:label "publicationReference"@en; - rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; + rdfs:comment "The publication reference."@en; + rdfs:domain ; + rdfs:label "publicationReference"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -864,10 +885,6 @@ PREFIX xsd: rdfs:label "references"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; @@ -883,8 +900,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "ObservationUnitPosition"@en . + rdf:type owl:Class; + rdfs:comment "All positional and layout information related to this Observation Unit"@en; + rdfs:label "ObservationUnitPosition"@en . rdf:type owl:DatatypeProperty; @@ -895,7 +913,7 @@ PREFIX xsd: rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties."@en; + rdfs:comment "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties."@en; rdfs:domain ; rdfs:label "germplasmPUI"@en; rdfs:range xsd:string . @@ -907,10 +925,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format"@en; @@ -919,8 +933,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "GermplasmAttributeValue"@en . + rdf:type owl:Class; + rdfs:comment "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit."@en; + rdfs:label "GermplasmAttributeValue"@en . rdf:type owl:ObjectProperty; @@ -952,8 +967,9 @@ PREFIX xsd: rdfs:range xsd:integer . - rdf:type owl:Class; - rdfs:label "Call"@en . + rdf:type owl:Class; + rdfs:comment "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345."@en; + rdfs:label "Call"@en . rdf:type owl:DatatypeProperty; @@ -962,13 +978,10 @@ PREFIX xsd: rdfs:label "copyright"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - rdf:type owl:Class; - rdfs:label "Reference"@en . + rdf:type owl:Class; + rdfs:comment "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable."@en; + rdfs:label "Reference"@en . rdf:type owl:NamedIndividual , . @@ -1035,12 +1048,14 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "DatasetAuthorships"@en . + rdf:type owl:Class; + rdfs:comment "License and citation information for the data in this trial"@en; + rdfs:label "DatasetAuthorships"@en . - rdf:type owl:Class; - rdfs:label "Germplasm"@en . + rdf:type owl:Class; + rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; + rdfs:label "Germplasm"@en . rdf:type owl:DatatypeProperty; @@ -1057,7 +1072,7 @@ PREFIX xsd: rdfs:range . - rdf:type , owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -1074,8 +1089,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "PedigreeNode"@en . + rdf:type owl:Class; + rdfs:comment "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances."@en; + rdfs:label "PedigreeNode"@en . rdf:type owl:DatatypeProperty; @@ -1105,6 +1121,13 @@ PREFIX xsd: rdfs:label "collector"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name or id of the user who uploaded the observation to the database system"@en; + rdfs:domain ; + rdfs:label "uploadedBy"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The unique identifier for a `Reference`"@en; @@ -1126,12 +1149,12 @@ PREFIX xsd: rdfs:label "documentationURL"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name or id of the user who uploaded the observation to the database system"@en; - rdfs:domain ; - rdfs:label "uploadedBy"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -1140,13 +1163,6 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "Genotype metadata associated with a call"@en; @@ -1177,8 +1193,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Pagination"@en . + rdf:type owl:Class; + rdfs:comment "Pagination info for the matrix"@en; + rdfs:label "Pagination"@en . rdf:type owl:DatatypeProperty; @@ -1194,13 +1211,6 @@ PREFIX xsd: rdfs:label "observationVariablePUI"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "email address for this person"@en; - rdfs:domain ; - rdfs:label "emailAddress"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "the germplasm of the cross parent"@en; @@ -1208,6 +1218,13 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "email address for this person"@en; + rdfs:domain ; + rdfs:label "emailAddress"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; @@ -1246,6 +1263,13 @@ PREFIX xsd: rdfs:label "seedLots"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "associated observation Unit"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The string used as a separator for phased allele calls."@en; @@ -1263,6 +1287,11 @@ PREFIX xsd: rdfs:label "traitPUI"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; + rdfs:label "FileFormat"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Unique DbId for the Seed Lot"@en; @@ -1270,11 +1299,6 @@ PREFIX xsd: rdfs:label "seedLotDbId"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; - rdfs:label "FileFormat"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository."@en; @@ -1299,6 +1323,14 @@ PREFIX xsd: rdfs:label "svlen"@en; rdfs:range xsd:integer . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; @@ -1313,10 +1345,6 @@ PREFIX xsd: rdfs:label "pagination"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -1355,17 +1383,10 @@ PREFIX xsd: rdfs:label "taxonIds"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:label "Type"@en . - - rdf:type owl:Class; - rdfs:label "Ontology"@en . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + rdf:type owl:Class; + rdfs:comment "The identifier and metadata needed to reference an external controlled vocabulary"@en; + rdfs:label "Ontology"@en . rdf:type owl:ObjectProperty; @@ -1403,8 +1424,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Analysis"@en . + rdf:type owl:Class; + rdfs:comment "An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used."@en; + rdfs:label "Analysis"@en . rdf:type owl:DatatypeProperty; @@ -1418,11 +1440,12 @@ PREFIX xsd: rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units.\n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; rdfs:domain ; rdfs:label "environmentParameters"@en; - rdfs:range . + rdfs:range . - rdf:type owl:Class; - rdfs:label "Variable"@en . + rdf:type owl:Class; + rdfs:comment "A unique combination of Trait, Method, and Scale to define a clear context for an Observation."@en; + rdfs:label "Variable"@en . rdf:type owl:ObjectProperty; @@ -1444,8 +1467,13 @@ PREFIX xsd: rdfs:label "AdditionalInfo"@en . - rdf:type owl:Class; - rdfs:label "Location"@en . + rdf:type owl:Class; + rdfs:comment "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc."@en; + rdfs:label "Location"@en . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -1468,6 +1496,10 @@ PREFIX xsd: rdfs:label "crossingProject"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The related observation unit identifier, if relevant."@en; @@ -1483,8 +1515,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Sample"@en . + rdf:type owl:Class; + rdfs:comment "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)."@en; + rdfs:label "Sample"@en . rdf:type owl:DatatypeProperty; @@ -1501,11 +1534,11 @@ PREFIX xsd: rdfs:range xsd:string . [ rdf:type owl:Class; - owl:oneOf ( ) + owl:oneOf ( ) ] . - rdf:type owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -1526,7 +1559,7 @@ PREFIX xsd: rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below."@en; + rdfs:comment "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below."@en; rdfs:domain ; rdfs:label "germplasmDbId"@en; rdfs:range xsd:string . @@ -1538,10 +1571,6 @@ PREFIX xsd: rdfs:label "calls"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; @@ -1578,8 +1607,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "GermplasmAttribute"@en . + rdf:type owl:Class; + rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; + rdfs:label "GermplasmAttribute"@en . rdf:type owl:ObjectProperty; @@ -1596,7 +1626,7 @@ PREFIX xsd: rdfs:range . - rdf:type , owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -1669,7 +1699,7 @@ PREFIX xsd: rdfs:range . - rdf:type , owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -1735,12 +1765,14 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "MetadataField"@en . + rdf:type owl:Class; + rdfs:comment "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; + rdfs:label "MetadataField"@en . - rdf:type owl:Class; - rdfs:label "Method"@en . + rdf:type owl:Class; + rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; + rdfs:label "Method"@en . rdf:type owl:DatatypeProperty; @@ -1794,10 +1826,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -1915,8 +1943,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Donor"@en . + rdf:type owl:Class; + rdfs:comment "Identifier assigned to an accession by the material donor."@en; + rdfs:label "Donor"@en . rdf:type owl:DatatypeProperty; @@ -1930,6 +1959,10 @@ PREFIX xsd: rdfs:comment "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; rdfs:label "SampleType"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a Reference"@en; @@ -2018,8 +2051,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "GenotypeMetadata"@en . + rdf:type owl:Class; + rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; + rdfs:label "GenotypeMetadata"@en . rdf:type owl:DatatypeProperty; @@ -2150,6 +2184,20 @@ PREFIX xsd: rdfs:label "callSets"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Numerical or categorical value\n\nMIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment."@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human-readable value of the environment parameter (defined above) constant within the experiment"@en; + rdfs:domain ; + rdfs:label "environmentParametersDbId"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "General category for the attribute. very similar to Trait class."@en; @@ -2223,17 +2271,6 @@ PREFIX xsd: rdfs:label "programDbId"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)"@en; - rdfs:domain ; - rdfs:label "expandHomozygotes"@en; - rdfs:range xsd:boolean . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -2241,12 +2278,12 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor."@en; - rdfs:domain ; - rdfs:label "factor"@en; - rdfs:range xsd:string . + rdfs:comment "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)"@en; + rdfs:domain ; + rdfs:label "expandHomozygotes"@en; + rdfs:range xsd:boolean . rdf:type owl:ObjectProperty; @@ -2279,6 +2316,10 @@ PREFIX xsd: rdfs:label "scale"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "crossingProjects"@en; @@ -2286,13 +2327,6 @@ PREFIX xsd: rdfs:label "crossingProjects"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "the unique identifier for a cross"@en; - rdfs:domain ; - rdfs:label "crossDbId"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow."@en; @@ -2319,9 +2353,23 @@ PREFIX xsd: rdfs:label "analysisName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the unique identifier for a cross"@en; + rdfs:domain ; + rdfs:label "crossDbId"@en; + rdfs:range xsd:string . + rdf:type owl:NamedIndividual , . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "the human readable name of a cross attribute"@en; @@ -2339,13 +2387,6 @@ PREFIX xsd: rdfs:comment "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; rdfs:label "GeoJSONPoint"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "Persons last name"@en; @@ -2374,10 +2415,6 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "the human readable name for a planned cross"@en; @@ -2414,8 +2451,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "PlannedCross"@en . + rdf:type owl:Class; + rdfs:comment "Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field."@en; + rdfs:label "PlannedCross"@en . rdf:type owl:ObjectProperty; @@ -2452,13 +2490,6 @@ PREFIX xsd: rdfs:label "imageLocation"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "the requested page number (zero indexed)"@en; - rdfs:domain ; - rdfs:label "page"@en; - rdfs:range xsd:integer . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -2466,6 +2497,13 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the requested page number (zero indexed)"@en; + rdfs:domain ; + rdfs:label "page"@en; + rdfs:range xsd:integer . + rdf:type owl:NamedIndividual , . @@ -2513,15 +2551,9 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - rdf:type owl:Class; - rdfs:label "GenomeMap"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "markerPositions"@en; - rdfs:domain ; - rdfs:label "markerPositions"@en; - rdfs:range . + rdf:type owl:Class; + rdfs:comment "The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map."@en; + rdfs:label "GenomeMap"@en . rdf:type owl:ObjectProperty; @@ -2531,16 +2563,24 @@ PREFIX xsd: rdfs:range . - rdf:type owl:DatatypeProperty; - rdfs:domain ; - rdfs:label "publicationPUI"@en; - rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; + rdfs:comment "The permanent unique identifier of the publication."@en; + rdfs:domain ; + rdfs:label "publicationPUI"@en; + rdfs:range xsd:string . - + + rdf:type owl:ObjectProperty; + rdfs:comment "markerPositions"@en; + rdfs:domain ; + rdfs:label "markerPositions"@en; + rdfs:range . + + rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; - rdfs:domain ; - rdfs:label "description"@en; + rdfs:comment "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. "@en; + rdfs:domain ; + rdfs:label "modality"@en; rdfs:range xsd:string . @@ -2581,16 +2621,24 @@ PREFIX xsd: rdfs:label "plate"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; - rdfs:comment "Pollination events associated with a cross"@en; + rdfs:comment "The Cross associated with this Pollination Event"@en; rdfs:domain ; rdfs:label "cross"@en; rdfs:range . - rdf:type owl:Class; - rdfs:label "PollinationEvent"@en . + rdf:type owl:Class; + rdfs:comment "A Pollination Event that was used or attempted for a Cross."@en; + rdfs:label "PollinationEvent"@en . rdf:type owl:DatatypeProperty; @@ -2606,10 +2654,10 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . - + rdf:type owl:ObjectProperty; - rdfs:comment "Environment parameters associated with a study"@en; - rdfs:domain ; + rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; + rdfs:domain ; rdfs:label "study"@en; rdfs:range . @@ -2620,13 +2668,6 @@ PREFIX xsd: rdfs:label "end"@en; rdfs:range xsd:integer . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "phone number of this person"@en; @@ -2673,8 +2714,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "Person"@en . + rdf:type owl:Class; + rdfs:comment "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program."@en; + rdfs:label "Person"@en . rdf:type owl:DatatypeProperty; @@ -2683,10 +2725,6 @@ PREFIX xsd: rdfs:label "variantSetName"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:label "EnvironmentParameters"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; @@ -2753,16 +2791,10 @@ PREFIX xsd: rdfs:label "variantType"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "associated observation Unit"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - rdf:type owl:Class; - rdfs:label "LastUpdate"@en . + rdf:type owl:Class; + rdfs:comment "The date and time when this study was last modified"@en; + rdfs:label "LastUpdate"@en . rdf:type owl:ObjectProperty; @@ -2823,6 +2855,9 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; @@ -2830,9 +2865,6 @@ PREFIX xsd: rdfs:label "sampleType"@en; rdfs:range . - - rdf:type , owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)"@en; @@ -2848,10 +2880,11 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; - rdfs:domain ; - rdfs:label "timestamp"@en; - rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; + rdfs:comment "The timestamp of the update."@en; + rdfs:domain ; + rdfs:label "timestamp"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -2995,8 +3028,9 @@ PREFIX xsd: rdfs:range xsd:boolean . - rdf:type owl:Class; - rdfs:label "TaxonId"@en . + rdf:type owl:Class; + rdfs:comment "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended."@en; + rdfs:label "TaxonId"@en . rdf:type owl:DatatypeProperty; @@ -3012,22 +3046,11 @@ PREFIX xsd: rdfs:label "variantSets"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; - rdfs:domain ; - rdfs:label "geometry"@en; - rdfs:range , . - rdf:type owl:Class; rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; rdfs:label "PlannedCrossStatus"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature."@en; @@ -3042,6 +3065,13 @@ PREFIX xsd: rdfs:label "methodName"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; + rdfs:domain ; + rdfs:label "geometry"@en; + rdfs:range , . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of institution submitting the variable"@en; @@ -3056,6 +3086,13 @@ PREFIX xsd: rdfs:label "submissionTimestamp"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human-readable value of the environment parameter (defined above) constant within the experiment"@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; @@ -3112,22 +3149,19 @@ PREFIX xsd: rdfs:label "tissueType"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . - rdf:type owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type , owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "URI pointing to an ontology class for the parameter value"@en; - rdfs:domain ; - rdfs:label "valuePUI"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3181,8 +3215,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "OntologyReference"@en . + rdf:type owl:Class; + rdfs:comment "MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:label "OntologyReference"@en . rdf:type owl:DatatypeProperty; @@ -3213,19 +3248,13 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "List"@en . + rdf:type owl:Class; + rdfs:comment "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study."@en; + rdfs:label "List"@en . rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "URI pointing to an ontology class for the parameter"@en; - rdfs:domain ; - rdfs:label "parameterPUI"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The timestamp when the pollination took place"@en; @@ -3233,12 +3262,6 @@ PREFIX xsd: rdfs:label "pollinationTimeStamp"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:label "Treatment"@en . - - rdf:type owl:Ontology . - rdf:type owl:DatatypeProperty; rdfs:comment "The unique identifier for this pollination event"@en; @@ -3246,12 +3269,7 @@ PREFIX xsd: rdfs:label "pollinationNumber"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time at which this record was created, in ISO 8601 format."@en; - rdfs:domain ; - rdfs:label "created"@en; - rdfs:range xsd:string . + rdf:type owl:Ontology . rdf:type owl:DatatypeProperty; @@ -3260,17 +3278,18 @@ PREFIX xsd: rdfs:label "commonCropName"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:label "ValidValuesCategory"@en . - - + rdf:type owl:DatatypeProperty; - rdfs:comment "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. "@en; - rdfs:domain ; - rdfs:label "parameterName"@en; + rdfs:comment "The time at which this record was created, in ISO 8601 format."@en; + rdfs:domain ; + rdfs:label "created"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; + rdfs:label "ValidValuesCategory"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; @@ -3293,7 +3312,7 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type , owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -3345,6 +3364,13 @@ PREFIX xsd: rdfs:comment "The dimension of the matrix being paginated"@en; rdfs:label "Dimension"@en . + + rdf:type owl:ObjectProperty; + rdfs:comment "Set of custom attributes associated with a cross"@en; + rdfs:domain ; + rdfs:label "crossAttributes"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "the human readable identifier for this breeding method"@en; @@ -3359,12 +3385,11 @@ PREFIX xsd: rdfs:label "version"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "Set of custom attributes associated with a cross"@en; - rdfs:domain ; - rdfs:label "crossAttributes"@en; - rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "validValues"@en; + rdfs:range . rdf:type owl:NamedIndividual , . @@ -3376,12 +3401,6 @@ PREFIX xsd: rdfs:label "studyType"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "validValues"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc"@en; @@ -3391,7 +3410,7 @@ PREFIX xsd: rdf:type owl:ObjectProperty; - rdfs:comment "The list of pollination events that occurred for this cross"@en; + rdfs:comment "The list of pollination events that occurred for this cross."@en; rdfs:domain ; rdfs:label "pollinationEvents"@en; rdfs:range . @@ -3410,13 +3429,6 @@ PREFIX xsd: rdfs:label "genotypeMetadata"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology's list of authors (no specific format)"@en; - rdfs:domain ; - rdfs:label "authors"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; @@ -3443,6 +3455,13 @@ PREFIX xsd: rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; rdfs:label "StorageTypeCode"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology's list of authors (no specific format)"@en; + rdfs:domain ; + rdfs:label "authors"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The date this call set was created"@en; @@ -3474,16 +3493,21 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; - rdfs:comment "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; + rdfs:comment "The type of positional coordinate used for the X coordinate of the position."@en; rdfs:domain ; rdfs:label "positionCoordinateXType"@en; - rdfs:range . + rdfs:range . - rdf:type owl:Class; - rdfs:label "Plate"@en . + rdf:type owl:Class; + rdfs:comment "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis."@en; + rdfs:label "Plate"@en . rdf:type owl:ObjectProperty; @@ -3513,16 +3537,6 @@ PREFIX xsd: rdfs:label "coordinateUncertainty"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human-readable value of the environment parameter (defined above) constant within the experiment"@en; - rdfs:domain ; - rdfs:label "environmentParametersDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "Order-independent MD5 checksum which identifies this `ReferenceSet`.\n\nTo compute this checksum, make a list of `Reference.md5checksum` for all\n`Reference` s in this set. Then sort that list, and take the MD5 hash of\nall the strings concatenated together. Express the hash as a lower-case\nhexadecimal string."@en; @@ -3537,6 +3551,9 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The type of analysis."@en; @@ -3545,8 +3562,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Study"@en . + rdf:type owl:Class; + rdfs:comment "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies."@en; + rdfs:label "Study"@en . rdf:type owl:DatatypeProperty; @@ -3583,13 +3601,6 @@ PREFIX xsd: rdfs:label "trial"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human-readable value of the environment parameter (defined above) constant within the experiment"@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The value of this genotype call"@en; @@ -3597,6 +3608,10 @@ PREFIX xsd: rdfs:label "genotypeValue"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3633,8 +3648,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "ContentMixture"@en . + rdf:type owl:Class; + rdfs:comment "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100."@en; + rdfs:label "ContentMixture"@en . rdf:type owl:DatatypeProperty; @@ -3661,8 +3677,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "CrossParent"@en . + rdf:type owl:Class; + rdfs:comment "The identifying information gor the parent material of a cross."@en; + rdfs:label "CrossParent"@en . rdf:type owl:DatatypeProperty; @@ -3711,10 +3728,6 @@ PREFIX xsd: rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. "@en; rdfs:label "ParentType"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -3743,10 +3756,6 @@ PREFIX xsd: rdfs:label "parent2"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; @@ -3813,7 +3822,7 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type , owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -3872,19 +3881,13 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "DataMatrix"@en . + rdf:type owl:Class; + rdfs:comment "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; + rdfs:label "DataMatrix"@en . rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The value of the data collected as an observation"@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "plannedCrosses"@en; @@ -3892,6 +3895,13 @@ PREFIX xsd: rdfs:label "plannedCrosses"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of the data collected as an observation"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Other variable names"@en; @@ -3968,13 +3978,22 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing."@en; + rdfs:label "Trial"@en . + - rdf:type owl:Class; - rdfs:label "Image"@en . + rdf:type owl:Class; + rdfs:comment "The metadata for an image file that is connected to some phenotypic observation data."@en; + rdfs:label "Image"@en . - - rdf:type owl:Class; - rdfs:label "Trial"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -3983,16 +4002,17 @@ PREFIX xsd: rdfs:label "callSetCount"@en; rdfs:range xsd:integer . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; + rdfs:comment "Unit of the value for this parameter"@en; + rdfs:domain ; + rdfs:label "unit"@en; rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Contact"@en . + rdf:type owl:Class; + rdfs:comment "A persons contact information"@en; + rdfs:label "Contact"@en . rdf:type owl:ObjectProperty; @@ -4023,8 +4043,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "SeedLot"@en . + rdf:type owl:Class; + rdfs:comment "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program."@en; + rdfs:label "SeedLot"@en . rdf:type owl:ObjectProperty; @@ -4048,10 +4069,11 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range . + rdf:type owl:ObjectProperty; + rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -4060,13 +4082,6 @@ PREFIX xsd: rdfs:label "publications"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "URI pointing to an ontology class for the unit"@en; - rdfs:domain ; - rdfs:label "unitPUI"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; @@ -4098,7 +4113,7 @@ PREFIX xsd: rdf:type owl:ObjectProperty; - rdfs:comment "the unique identifier for a planned cross"@en; + rdfs:comment "The Cross that was used in the planning of this one."@en; rdfs:domain ; rdfs:label "plannedCross"@en; rdfs:range . @@ -4158,13 +4173,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Numerical or categorical value\n\nMIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment."@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -4227,6 +4235,11 @@ PREFIX xsd: rdfs:label "variant"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor."@en; + rdfs:label "ObservationTreatment"@en . + rdf:type owl:ObjectProperty; rdfs:comment "associated germplasm"@en; @@ -4255,6 +4268,9 @@ PREFIX xsd: rdfs:label "type"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; @@ -4262,19 +4278,10 @@ PREFIX xsd: rdfs:label "defaultValue"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - - rdf:type owl:Class; - rdfs:label "AvailableFormat"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The full name of this contact person\n\nMIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)"@en; - rdfs:domain ; - rdfs:label "name"@en; - rdfs:range xsd:string . + rdf:type owl:Class; + rdfs:comment "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other."@en; + rdfs:label "AvailableFormat"@en . rdf:type owl:DatatypeProperty; @@ -4283,6 +4290,13 @@ PREFIX xsd: rdfs:label "donorAccessionNumber"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The full name of this contact person\n\nMIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)"@en; + rdfs:domain ; + rdfs:label "name"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study."@en; @@ -4297,6 +4311,10 @@ PREFIX xsd: rdfs:label "plates"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "associated event"@en; @@ -4305,8 +4323,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "Trait"@en . + rdf:type owl:Class; + rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; + rdfs:label "Trait"@en . rdf:type owl:DatatypeProperty; @@ -4315,6 +4334,13 @@ PREFIX xsd: rdfs:label "active"@en; rdfs:range xsd:boolean . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor."@en; + rdfs:domain ; + rdfs:label "factor"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -4337,12 +4363,14 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "ReferenceSet"@en . + rdf:type owl:Class; + rdfs:comment "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data."@en; + rdfs:label "ReferenceSet"@en . - rdf:type owl:Class; - rdfs:label "Event"@en . + rdf:type owl:Class; + rdfs:comment "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other"@en; + rdfs:label "Event"@en . rdf:type owl:DatatypeProperty; @@ -4376,7 +4404,7 @@ PREFIX xsd: rdfs:range xsd:boolean . - rdf:type owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:NamedIndividual , . @@ -4431,15 +4459,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Scale"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . + rdf:type owl:Class; + rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; + rdfs:label "Scale"@en . rdf:type owl:ObjectProperty; @@ -4448,6 +4470,13 @@ PREFIX xsd: rdfs:label "events"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The crossing project used to generate this germplasm"@en; @@ -4545,6 +4574,13 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of markers present in a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "markerCount"@en; + rdfs:range xsd:integer . + rdf:type owl:ObjectProperty; rdfs:comment "the second parent used in the cross"@en; @@ -4552,12 +4588,12 @@ PREFIX xsd: rdfs:label "parent2"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The number of markers present in a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "markerCount"@en; - rdfs:range xsd:integer . + rdfs:comment "A short human readable code for a study"@en; + rdfs:domain ; + rdfs:label "studyCode"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -4566,12 +4602,10 @@ PREFIX xsd: rdfs:label "plannedCrossDbId"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A short human readable code for a study"@en; - rdfs:domain ; - rdfs:label "studyCode"@en; - rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "Alternative names or IDs used to reference this germplasm"@en; + rdfs:label "Synonym"@en . rdf:type owl:DatatypeProperty; @@ -4580,13 +4614,10 @@ PREFIX xsd: rdfs:label "exposure"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:label "Synonym"@en . - - rdf:type owl:Class; - rdfs:label "ExperimentalDesign"@en . + rdf:type owl:Class; + rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; + rdfs:label "ExperimentalDesign"@en . rdf:type owl:DatatypeProperty; @@ -4617,12 +4648,14 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "GrowthFacility"@en . + rdf:type owl:Class; + rdfs:comment "Short description of the facility in which the study was carried out."@en; + rdfs:label "GrowthFacility"@en . - rdf:type owl:Class; - rdfs:label "OntologyTerm"@en . + rdf:type owl:Class; + rdfs:comment "A pointer to an ontology used by a genomic reference"@en; + rdfs:label "OntologyTerm"@en . rdf:type owl:DatatypeProperty; @@ -4694,10 +4727,6 @@ PREFIX xsd: rdfs:label "alleleMatrices"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The date and time the image was taken"@en; @@ -4748,10 +4777,11 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "season"@en; - rdfs:range . + rdf:type owl:ObjectProperty; + rdfs:comment "The season for this Observation"@en; + rdfs:domain ; + rdfs:label "season"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -4767,6 +4797,13 @@ PREFIX xsd: rdfs:label "growthStage"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. "@en; + rdfs:domain ; + rdfs:label "parameterName"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "The identifier for the Seed Lot being transferred into"@en; @@ -4793,6 +4830,17 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; + rdfs:domain ; + rdfs:label "code"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; @@ -4800,12 +4848,12 @@ PREFIX xsd: rdfs:label "eventParameters"@en; rdfs:range . - + rdf:type owl:ObjectProperty; - rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; - rdfs:domain ; - rdfs:label "code"@en; - rdfs:range . + rdfs:comment "the first parent used in the cross"@en; + rdfs:domain ; + rdfs:label "parent1"@en; + rdfs:range . rdf:type owl:NamedIndividual , . @@ -4827,13 +4875,6 @@ PREFIX xsd: rdfs:label "variantSetDbId"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "the first parent used in the cross"@en; - rdfs:domain ; - rdfs:label "parent1"@en; - rdfs:range . - rdf:type owl:NamedIndividual , . @@ -4861,20 +4902,24 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:Class; - rdfs:label "EventDateRange"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:Class; + rdfs:comment "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; + rdfs:label "PositionCoordinateType"@en . - rdf:type owl:Class; - rdfs:label "CrossingProject"@en . + rdf:type owl:Class; + rdfs:comment "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented."@en; + rdfs:label "CrossingProject"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies an observation"@en; - rdfs:domain ; - rdfs:label "observationDbId"@en; - rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)"@en; + rdfs:label "EventDateRange"@en . rdf:type owl:ObjectProperty; @@ -4887,6 +4932,13 @@ PREFIX xsd: rdf:type owl:Class; rdfs:label "ExternalReference"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies an observation"@en; + rdfs:domain ; + rdfs:label "observationDbId"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The time at which this call set was last updated"@en; @@ -5046,12 +5098,14 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "VariantSet"@en . + rdf:type owl:Class; + rdfs:comment "A VariantSet is a collection of variants and variant calls intended to be analyzed together."@en; + rdfs:label "VariantSet"@en . - rdf:type owl:Class; - rdfs:label "Cross"@en . + rdf:type owl:Class; + rdfs:comment "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present."@en; + rdfs:label "Cross"@en . rdf:type owl:DatatypeProperty; @@ -5082,8 +5136,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "CrossAttribute"@en . + rdf:type owl:Class; + rdfs:comment "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'"@en; + rdfs:label "CrossAttribute"@en . rdf:type owl:DatatypeProperty; @@ -5113,13 +5168,6 @@ PREFIX xsd: rdfs:label "units"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. "@en; - rdfs:domain ; - rdfs:label "modality"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "A permanent identifier for a trial. Could be DOI or other URI formatted identifier."@en; @@ -5238,6 +5286,10 @@ PREFIX xsd: rdfs:label "trial"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -5266,10 +5318,6 @@ PREFIX xsd: rdfs:label "eventTypeDbId"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -5289,10 +5337,6 @@ PREFIX xsd: rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; rdfs:label "ObservationUnitHierarchyLevel"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; @@ -5412,7 +5456,7 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - rdf:type , owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:NamedIndividual , . @@ -5424,9 +5468,14 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + - rdf:type owl:Class; - rdfs:label "DataLink"@en . + rdf:type owl:Class; + rdfs:comment "A link to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; + rdfs:label "DataLink"@en . rdf:type owl:DatatypeProperty; @@ -5470,16 +5519,17 @@ PREFIX xsd: rdfs:label "personDbId"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Unit of the value for this parameter"@en; - rdfs:domain ; - rdfs:label "unit"@en; + rdfs:comment "URI pointing to an ontology class for the parameter value"@en; + rdfs:domain ; + rdfs:label "valuePUI"@en; rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "Variant"@en . + rdf:type owl:Class; + rdfs:comment "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF."@en; + rdfs:label "Variant"@en . rdf:type owl:DatatypeProperty; @@ -5501,12 +5551,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:domain ; - rdfs:label "URL"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The description of the source where this material was originally collected (wild, nursery, etc)"@en; @@ -5514,6 +5558,13 @@ PREFIX xsd: rdfs:label "sourceCollection"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The URL or URI to the documentation"@en; + rdfs:domain ; + rdfs:label "URL"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space."@en; @@ -5571,8 +5622,9 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:Class; - rdfs:label "EventParameter"@en . + rdf:type owl:Class; + rdfs:comment "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event."@en; + rdfs:label "EventParameter"@en . rdf:type owl:DatatypeProperty; @@ -5617,8 +5669,9 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "StorageType"@en . + rdf:type owl:Class; + rdfs:comment "The type of storage this germplasm is kept in at a genebank."@en; + rdfs:label "StorageType"@en . rdf:type owl:DatatypeProperty; @@ -5669,11 +5722,6 @@ PREFIX xsd: rdfs:label "samples"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; - rdfs:label "PositionCoordinateXType"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "Description of a List"@en; @@ -5710,7 +5758,7 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type , owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -5741,8 +5789,16 @@ PREFIX xsd: rdfs:range . - rdf:type owl:Class; - rdfs:label "MarkerPosition"@en . + rdf:type owl:Class; + rdfs:comment "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap."@en; + rdfs:label "MarkerPosition"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "URI pointing to an ontology class for the parameter"@en; + rdfs:domain ; + rdfs:label "parameterPUI"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -5824,8 +5880,14 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:Class; + rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; + rdfs:label "EnvironmentParameter"@en . rdf:type owl:DatatypeProperty; @@ -5834,6 +5896,13 @@ PREFIX xsd: rdfs:label "scientist"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the entity was first created"@en; @@ -5900,13 +5969,6 @@ PREFIX xsd: rdfs:label "sample"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; - rdfs:domain ; - rdfs:label "status"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "Geometry associated with an image"@en; @@ -5914,6 +5976,13 @@ PREFIX xsd: rdfs:label "observationUnit"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; + rdfs:domain ; + rdfs:label "status"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "description of this person"@en; @@ -5952,6 +6021,9 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; @@ -5959,9 +6031,6 @@ PREFIX xsd: rdfs:label "instituteAddress"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value."@en; @@ -5969,17 +6038,15 @@ PREFIX xsd: rdfs:label "filtersApplied"@en; rdfs:range xsd:boolean . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - rdf:type owl:Class; - rdfs:label "ObservationUnit"@en . + rdf:type owl:Class; + rdfs:comment "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples."@en; + rdfs:label "ObservationUnit"@en . - rdf:type owl:Class; - rdfs:label "Program"@en . + rdf:type owl:Class; + rdfs:comment "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies."@en; + rdfs:label "Program"@en . rdf:type owl:NamedIndividual , . @@ -5991,6 +6058,10 @@ PREFIX xsd: rdfs:label "well"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\""@en; @@ -6005,12 +6076,9 @@ PREFIX xsd: rdfs:label "mainAbbreviation"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -6019,9 +6087,12 @@ PREFIX xsd: rdfs:label "PUI"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "observations"@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -6091,7 +6162,7 @@ PREFIX xsd: rdfs:comment "List of treatments applied to an observation unit.\n\nMIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit."@en; rdfs:domain ; rdfs:label "treatments"@en; - rdfs:range . + rdfs:range . rdf:type owl:NamedIndividual , . diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index 27803a2c..0ee9d91a 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -449,16 +449,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/AlleleMatrixResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/AlleleMatrixResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Use this endpoint to retrieve a two dimensional matrix of genotype data", @@ -696,16 +727,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Germplasm Attributes", @@ -740,16 +802,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new Germplasm Attributes", @@ -806,13 +899,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Categories of Germplasm Attributes", @@ -847,16 +964,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the details for a specific Germplasm Attribute", @@ -898,16 +1046,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update an existing Germplasm Attribute", @@ -1045,16 +1224,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Germplasm Attribute Values", @@ -1089,16 +1299,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new Germplasm Attribute Values", @@ -1133,16 +1374,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the details for a specific Germplasm Attribute", @@ -1184,16 +1456,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update an existing Germplasm Attribute Value", @@ -1250,13 +1553,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Breeding Methods", @@ -1301,16 +1628,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Breeding Method", @@ -1439,16 +1798,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CallsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a filtered list of `Calls`", @@ -1483,16 +1873,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/CallsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update existing `Calls` with new genotype value or metadata", @@ -1609,16 +2030,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CallSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallSetsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a filtered list of `CallSet` JSON objects.", @@ -1663,16 +2115,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a `CallSet` by ID.", @@ -1781,16 +2265,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CallsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a list of `Calls` associated with a `CallSet`.", @@ -1847,13 +2362,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Common Crop Names", @@ -1991,16 +2530,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CrossesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossesListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Cross entities", @@ -2035,16 +2605,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/CrossesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossesListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new Cross entities on this server", @@ -2134,16 +2735,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/CrossesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossesListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update existing Cross entities on this server", @@ -2271,16 +2903,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CrossingProjectsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossingProjectsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Crossing Projects", @@ -2315,16 +2978,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/CrossingProjectsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossingProjectsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new Crossing Project entities on this server", @@ -2359,16 +3053,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CrossingProjectsSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossingProjectsSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Crossing Projects", @@ -2410,16 +3135,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/CrossingProjectsSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CrossingProjectsSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update an existing Crossing Project", @@ -2453,16 +3209,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ImageDeleteResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageDeleteResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a delete request for `Images`", @@ -2496,16 +3283,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationDeleteResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationDeleteResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a delete request for `Observations`", @@ -2624,13 +3442,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Events", @@ -2858,16 +3700,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Germplasm", @@ -2902,16 +3775,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new Germplasm entities on this server", @@ -2946,19 +3850,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Germplasm", @@ -3000,19 +3943,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update the details of an existing Germplasm", @@ -3057,16 +4039,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Germplasm in MCPD format", @@ -3132,16 +4146,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "**Deprecated in v2.1** Please use `GET /pedigree?germplasmDbId={germplasmDbId}`. Github issue number #481 \n
Get the pedigree details of a specific Germplasm", @@ -3187,16 +4233,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "**Deprecated in v2.1** Please use `GET /pedigree?germplasmDbId={germplasmDbId}`. Github issue number #481 \n
Get the progeny details of a specific Germplasm", @@ -3344,16 +4422,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ImageListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the image metadata summaries", @@ -3388,16 +4497,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ImageListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new image metadata records", @@ -3432,19 +4572,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ImageSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the an image metadata summary", @@ -3486,19 +4665,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ImageSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing image metadata record", @@ -3543,19 +4761,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ImageSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Attach an image binary file to an existing image metadata record", @@ -3693,16 +4950,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ListsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get filtered set of generic lists", @@ -3737,16 +5025,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ListsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create New List Objects", @@ -3781,19 +5100,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ListsSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListsSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific List", @@ -3835,19 +5193,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ListsSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListsSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing generic list", @@ -3905,16 +5302,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Add new data members to a specific List", @@ -3973,16 +5402,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Add Items to a specific List", @@ -4130,16 +5591,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/LocationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Locations", @@ -4174,16 +5666,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/LocationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new Locations", @@ -4218,19 +5741,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/LocationSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Location", @@ -4272,19 +5834,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/LocationSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update the details for an existing Location", @@ -4421,13 +6022,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Genomic Maps", @@ -4472,16 +6097,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Genomic Map", @@ -4548,16 +6205,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the Linkage Groups of a specific Genomic Map", @@ -4654,16 +6343,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/MarkerPositionListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MarkerPositionListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get marker position info", @@ -4791,16 +6511,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/MethodListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MethodListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Methods", @@ -4835,16 +6586,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/MethodListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MethodListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new Methods", @@ -4879,19 +6661,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/MethodSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MethodSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details for a specific Method", @@ -4933,19 +6754,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/MethodSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MethodSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Method", @@ -5032,13 +6892,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Observation Levels", @@ -5308,16 +7192,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered set of Observations", @@ -5352,19 +7267,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Add new Observation entities", @@ -5447,19 +7401,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update multiple Observation entities", @@ -5688,16 +7681,59 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationTableResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationTableResponse" + } + }, + "text/csv" : { + "example" : "\"observationUnitDbId\",\"observationUnitName\",\"studyDbId\",\"studyName\",\"germplasmDbId\",\"germplasmName\",\"positionCoordinateX\",\"positionCoordinateY\",\"year\",\"field\",\"plot\",\"sub-plot\",\"plant\",\"pot\",\"block\",\"entry\",\"rep\",\"f959a77d\",\"8341dee0\",\"84c9fd86\",\"93d80c95\"\n\n\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Plant height\",\"Carotenoid\",\"Root color\",\"Virus severity\"\n \n\"2019-09-10T18:13:27.223Z\",\"f3a8a3db\",\"Plant Alpha\", \"0fe3e48b\",\"2017 Plant Study\",\"06307ec0\",\"A0043001\",\"76.50106681\",\"42.44409301\",\"2017\",\"Field_1\",\"Plot_11\",\"SubPlot_111\",\"Plant_1111\",\"Pot_1111\",\"Block_11\",\"Entry_11\",\"Rep_11\",\"25.3\",\"\", \"\",\"\"\n\n\"2019-09-10T18:14:27.223Z\",\"f3a8a3db\",\"Plant Alpha\", \"0fe3e48b\",\"2017 Plant Study\",\"06307ec0\",\"A0043001\",\"76.50106681\",\"42.44409301\",\"2017\",\"Field_1\",\"Plot_11\",\"SubPlot_111\",\"Plant_1111\",\"Pot_1111\",\"Block_11\",\"Entry_11\",\"Rep_11\",\"\", \"3\",\"\",\"\"\n\n\"2019-09-10T18:15:54.868Z\",\"05d1b011\",\"Plant Beta\", \"0fe3e48b\",\"2017 Plant Study\",\"59d435cd\",\"A0043002\",\"76.50106683\",\"42.44409301\",\"2017\",\"Field_1\",\"Plot_11\",\"SubPlot_112\",\"Plant_1122\",\"Pot_1122\",\"Block_11\",\"Entry_11\",\"Rep_12\",\"27.9\",\"\", \"\",\"\"\n\n\"2019-09-10T18:16:54.868Z\",\"05d1b011\",\"Plant Beta\", \"0fe3e48b\",\"2017 Plant Study\",\"59d435cd\",\"A0043002\",\"76.50106683\",\"42.44409301\",\"2017\",\"Field_1\",\"Plot_11\",\"SubPlot_112\",\"Plant_1122\",\"Pot_1122\",\"Block_11\",\"Entry_11\",\"Rep_12\",\"\", \"1\",\"\",\"\"\n\n\"2019-09-10T18:17:34.433Z\",\"67e2d87c\",\"Plant Gamma\", \"0fe3e48b\",\"2017 Plant Study\",\"06307ec0\",\"A0043001\",\"76.50106681\",\"42.44409356\",\"2017\",\"Field_1\",\"Plot_12\",\"SubPlot_123\",\"Plant_1233\",\"Pot_1233\",\"Block_12\",\"Entry_12\",\"Rep_11\",\"\", \"3\",\"\",\"\"\n\n\"2019-09-10T18:18:34.433Z\",\"67e2d87c\",\"Plant Gamma\", \"0fe3e48b\",\"2017 Plant Study\",\"06307ec0\",\"A0043001\",\"76.50106681\",\"42.44409356\",\"2017\",\"Field_1\",\"Plot_12\",\"SubPlot_123\",\"Plant_1233\",\"Pot_1233\",\"Block_12\",\"Entry_12\",\"Rep_11\",\"25.5\",\"\", \"\",\"\"\n\n\"2019-09-10T18:19:15.629Z\",\"d98d0d4c\",\"Plant Epsilon\",\"0fe3e48b\",\"2017 Plant Study\",\"59d435cd\",\"A0043002\",\"76.50106683\",\"42.44409356\",\"2017\",\"Field_1\",\"Plot_12\",\"SubPlot_124\",\"Plant_1244\",\"Pot_1244\",\"Block_12\",\"Entry_12\",\"Rep_12\",\"28.9\",\"\", \"\",\"\"\n\n\"2019-09-10T18:20:15.629Z\",\"d98d0d4c\",\"Plant Epsilon\",\"0fe3e48b\",\"2017 Plant Study\",\"59d435cd\",\"A0043002\",\"76.50106683\",\"42.44409356\",\"2017\",\"Field_1\",\"Plot_12\",\"SubPlot_124\",\"Plant_1244\",\"Pot_1244\",\"Block_12\",\"Entry_12\",\"Rep_12\",\"\", \"0\",\"\",\"\"", + "schema" : { + "type" : "string" + } + }, + "text/tsv" : { + "example" : "\"observationUnitDbId\"\\t\"observationUnitName\"\\t\"studyDbId\"\\t\"studyName\"\\t\"germplasmDbId\"\\t\"germplasmName\"\\t\"positionCoordinateX\"\\t\"positionCoordinateY\"\\t\"year\"\\t\"field\"\\t\"plot\"\\t\"sub-plot\"\\t\"plant\"\\t\"pot\"\\t\"block\"\\t\"entry\"\\t\"rep\"\\t\"f959a77d\"\\t\"8341dee0\"\\t\"84c9fd86\"\\t\"93d80c95\"\n\n\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"Plant height\"\\t\"Carotenoid\"\\t\"Root color\"\\t\"Virus severity\"\n \n\"2019-09-10T18:13:27.223Z\"\\t\"f3a8a3db\"\\t\"Plant Alpha\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"06307ec0\"\\t\"A0043001\"\\t\"76.50106681\"\\t\"42.44409301\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_11\"\\t\"SubPlot_111\"\\t\"Plant_1111\"\\t\"Pot_1111\"\\t\"Block_11\"\\t\"Entry_11\"\\t\"Rep_11\"\\t\"25.3\"\\t\"\"\\t \"\"\\t\"\"\n\n\"2019-09-10T18:14:27.223Z\"\\t\"f3a8a3db\"\\t\"Plant Alpha\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"06307ec0\"\\t\"A0043001\"\\t\"76.50106681\"\\t\"42.44409301\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_11\"\\t\"SubPlot_111\"\\t\"Plant_1111\"\\t\"Pot_1111\"\\t\"Block_11\"\\t\"Entry_11\"\\t\"Rep_11\"\\t\"\"\\t \"3\"\\t\"\"\\t\"\"\n\n\"2019-09-10T18:15:54.868Z\"\\t\"05d1b011\"\\t\"Plant Beta\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"59d435cd\"\\t\"A0043002\"\\t\"76.50106683\"\\t\"42.44409301\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_11\"\\t\"SubPlot_112\"\\t\"Plant_1122\"\\t\"Pot_1122\"\\t\"Block_11\"\\t\"Entry_11\"\\t\"Rep_12\"\\t\"27.9\"\\t\"\"\\t \"\"\\t\"\"\n\n\"2019-09-10T18:16:54.868Z\"\\t\"05d1b011\"\\t\"Plant Beta\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"59d435cd\"\\t\"A0043002\"\\t\"76.50106683\"\\t\"42.44409301\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_11\"\\t\"SubPlot_112\"\\t\"Plant_1122\"\\t\"Pot_1122\"\\t\"Block_11\"\\t\"Entry_11\"\\t\"Rep_12\"\\t\"\"\\t \"1\"\\t\"\"\\t\"\"\n\n\"2019-09-10T18:17:34.433Z\"\\t\"67e2d87c\"\\t\"Plant Gamma\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"06307ec0\"\\t\"A0043001\"\\t\"76.50106681\"\\t\"42.44409356\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_12\"\\t\"SubPlot_123\"\\t\"Plant_1233\"\\t\"Pot_1233\"\\t\"Block_12\"\\t\"Entry_12\"\\t\"Rep_11\"\\t\"\"\\t \"3\"\\t\"\"\\t\"\"\n\n\"2019-09-10T18:18:34.433Z\"\\t\"67e2d87c\"\\t\"Plant Gamma\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"06307ec0\"\\t\"A0043001\"\\t\"76.50106681\"\\t\"42.44409356\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_12\"\\t\"SubPlot_123\"\\t\"Plant_1233\"\\t\"Pot_1233\"\\t\"Block_12\"\\t\"Entry_12\"\\t\"Rep_11\"\\t\"25.5\"\\t\"\"\\t \"\"\\t\"\"\n\n\"2019-09-10T18:19:15.629Z\"\\t\"d98d0d4c\"\\t\"Plant Epsilon\"\\t\"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"59d435cd\"\\t\"A0043002\"\\t\"76.50106683\"\\t\"42.44409356\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_12\"\\t\"SubPlot_124\"\\t\"Plant_1244\"\\t\"Pot_1244\"\\t\"Block_12\"\\t\"Entry_12\"\\t\"Rep_12\"\\t\"28.9\"\\t\"\"\\t \"\"\\t\"\"\n\n\"2019-09-10T18:20:15.629Z\"\\t\"d98d0d4c\"\\t\"Plant Epsilon\"\\t\"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"59d435cd\"\\t\"A0043002\"\\t\"76.50106683\"\\t\"42.44409356\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_12\"\\t\"SubPlot_124\"\\t\"Plant_1244\"\\t\"Pot_1244\"\\t\"Block_12\"\\t\"Entry_12\"\\t\"Rep_12\"\\t\"\"\\t \"0\"\\t\"\"\\t\"\"", + "schema" : { + "type" : "string" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a list of Observations in a table format", @@ -5732,19 +7768,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Observations", @@ -5786,19 +7861,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Observation", @@ -6046,16 +8160,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered set of Observation Units", @@ -6090,16 +8235,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new Observation Units", @@ -6248,16 +8424,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update a set of Observation Units", @@ -6454,16 +8661,59 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitTableResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitTableResponse" + } + }, + "text/csv" : { + "example" : "\"observationUnitDbId\",\"observationUnitName\",\"studyDbId\",\"studyName\",\"germplasmDbId\",\"germplasmName\",\"positionCoordinateX\",\"positionCoordinateY\",\"year\",\"field\",\"plot\",\"sub-plot\",\"plant\",\"pot\",\"block\",\"entry\",\"rep\",\"f959a77d\",\"8341dee0\",\"84c9fd86\"\n\n\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Plant Height\",\"Virus severity\",\"Carotenoid\"\n\n\"f3a8a3db\",\"Plant Alpha\", \"0fe3e48b\",\"2017 Plant Study\",\"06307ec0\",\"A0043001\",\"76.50106681\",\"42.44409301\",\"2017\",\"Field_1\",\"Plot_11\",\"SubPlot_111\",\"Plant_1111\",\"Pot_1111\",\"Block_11\",\"Entry_11\",\"Rep_11\",\"25.3\",\"3\",\"50.75\"\n\n\"05d1b011\",\"Plant Beta\", \"0fe3e48b\",\"2017 Plant Study\",\"59d435cd\",\"A0043002\",\"76.50106683\",\"42.44409301\",\"2017\",\"Field_1\",\"Plot_11\",\"SubPlot_112\",\"Plant_1122\",\"Pot_1122\",\"Block_11\",\"Entry_11\",\"Rep_12\",\"27.9\",\"1\",\"45.345\"\n\n\"67e2d87c\",\"Plant Gamma\", \"0fe3e48b\",\"2017 Plant Study\",\"06307ec0\",\"A0043001\",\"76.50106681\",\"42.44409356\",\"2017\",\"Field_1\",\"Plot_12\",\"SubPlot_123\",\"Plant_1233\",\"Pot_1233\",\"Block_12\",\"Entry_12\",\"Rep_11\",\"25.5\",\"3\",\"50.76\"\n\n\"d98d0d4c\",\"Plant Epsilon\",\"0fe3e48b\",\"2017 Plant Study\",\"59d435cd\",\"A0043002\",\"76.50106683\",\"42.44409356\",\"2017\",\"Field_1\",\"Plot_12\",\"SubPlot_124\",\"Plant_1244\",\"Pot_1244\",\"Block_12\",\"Entry_12\",\"Rep_12\",\"28.9\",\"0\",\"46.5\"", + "schema" : { + "type" : "string" + } + }, + "text/tsv" : { + "example" : "\"observationUnitDbId\"\\t\"observationUnitName\"\\t\"studyDbId\"\\t\"studyName\"\\t\"germplasmDbId\"\\t\"germplasmName\"\\t\"positionCoordinateX\"\\t\"positionCoordinateY\"\\t\"year\"\\t\"field\"\\t\"plot\"\\t\"sub-plot\"\\t\"plant\"\\t\"pot\"\\t\"block\"\\t\"entry\"\\t\"rep\"\\t\"f959a77d\"\\t\"8341dee0\"\\t\"84c9fd86\"\n\n\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"\"\\t\"Plant Height\"\\t\"Virus severity\"\\t\"Carotenoid\"\n\n\"f3a8a3db\"\\t\"Plant Alpha\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"06307ec0\"\\t\"A0043001\"\\t\"76.50106681\"\\t\"42.44409301\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_11\"\\t\"SubPlot_111\"\\t\"Plant_1111\"\\t\"Pot_1111\"\\t\"Block_11\"\\t\"Entry_11\"\\t\"Rep_11\"\\t\"25.3\"\\t\"3\"\\t\"50.75\"\n\n\"05d1b011\"\\t\"Plant Beta\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"59d435cd\"\\t\"A0043002\"\\t\"76.50106683\"\\t\"42.44409301\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_11\"\\t\"SubPlot_112\"\\t\"Plant_1122\"\\t\"Pot_1122\"\\t\"Block_11\"\\t\"Entry_11\"\\t\"Rep_12\"\\t\"27.9\"\\t\"1\"\\t\"45.345\"\n\n\"67e2d87c\"\\t\"Plant Gamma\"\\t \"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"06307ec0\"\\t\"A0043001\"\\t\"76.50106681\"\\t\"42.44409356\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_12\"\\t\"SubPlot_123\"\\t\"Plant_1233\"\\t\"Pot_1233\"\\t\"Block_12\"\\t\"Entry_12\"\\t\"Rep_11\"\\t\"25.5\"\\t\"3\"\\t\"50.76\"\n\n\"d98d0d4c\"\\t\"Plant Epsilon\"\\t\"0fe3e48b\"\\t\"2017 Plant Study\"\\t\"59d435cd\"\\t\"A0043002\"\\t\"76.50106683\"\\t\"42.44409356\"\\t\"2017\"\\t\"Field_1\"\\t\"Plot_12\"\\t\"SubPlot_124\"\\t\"Plant_1244\"\\t\"Pot_1244\"\\t\"Block_12\"\\t\"Entry_12\"\\t\"Rep_12\"\\t\"28.9\"\\t\"0\"\\t\"46.5\"", + "schema" : { + "type" : "string" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a list of Observations in a table format", @@ -6498,16 +8748,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the details of a specific Observation Unit", @@ -6549,16 +8830,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update an existing Observation Units", @@ -6625,16 +8937,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/OntologyListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/OntologyListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Ontologies", @@ -6669,16 +9012,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/OntologyListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/OntologyListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create a new Ontology record in the database", @@ -6713,16 +9087,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/OntologySingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/OntologySingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a specific Ontology record by its ontologyDbId", @@ -6764,16 +9169,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/OntologySingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/OntologySingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update a specific Ontology record", @@ -7040,19 +9476,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PedigreeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PedigreeListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get a filtered list of pedigree nodes which represent a subset of a pedigree tree", @@ -7087,19 +9562,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PedigreeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PedigreeListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Send a list of new pedigree nodes to a server", @@ -7207,19 +9721,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PedigreeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PedigreeListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Send a list of pedigree nodes to update existing information on a server", @@ -7357,16 +9910,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PersonListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get filtered list of People", @@ -7401,16 +9985,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PersonListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new People", @@ -7445,19 +10060,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PersonSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details for a specific Person", @@ -7499,19 +10153,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PersonSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Person", @@ -7660,16 +10353,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PlannedCrossesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlannedCrossesListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Planned Cross entities", @@ -7704,16 +10428,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PlannedCrossesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlannedCrossesListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new Planned Cross entities on this server", @@ -7803,16 +10558,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PlannedCrossesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlannedCrossesListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update existing Planned Cross entities on this server", @@ -8000,16 +10786,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PlateListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlateListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Plates.", @@ -8044,16 +10861,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PlateListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlateListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit new Plate entities to the server", @@ -8112,19 +10960,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PlateListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlateListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update the details of existing Plates", @@ -8159,19 +11046,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PlateSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlateSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Plate.", @@ -8300,16 +11226,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ProgramListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of breeding Programs", @@ -8344,16 +11301,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ProgramListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new breeding Programs to the database", @@ -8388,16 +11376,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ProgramSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a breeding Program by Id", @@ -8439,16 +11458,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ProgramSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update an existing Program", @@ -8625,16 +11675,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ReferencesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ReferencesListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a filtered list of `Reference` objects.", @@ -8679,16 +11760,48 @@ "description" : "A successful response." }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a `Reference` by ID.", @@ -8763,16 +11876,48 @@ "description" : "A successful response." }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Lists `Reference` bases by ID and optional range.", @@ -8919,16 +12064,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ReferenceSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ReferenceSetsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a list of `ReferenceSets`.", @@ -9158,16 +12334,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SampleListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Samples", @@ -9202,16 +12409,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SampleListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new Samples", @@ -9294,19 +12532,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SampleListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update the details of existing Samples", @@ -9341,19 +12618,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SampleSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Sample", @@ -9396,19 +12712,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SampleSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update the details of an existing Sample", @@ -9536,16 +12891,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ScaleListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ScaleListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Scales", @@ -9580,16 +12966,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ScaleListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ScaleListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new Scales", @@ -9624,19 +13041,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ScaleSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ScaleSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Scale", @@ -9678,19 +13134,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ScaleSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ScaleSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Scale", @@ -9725,19 +13220,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/AlleleMatrixResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/AlleleMatrixResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for a Allele Matrix", @@ -9772,19 +13305,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/AlleleMatrixResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/AlleleMatrixResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a Allele Matrix search request", @@ -9818,19 +13389,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for Germplasm `Attributes`", @@ -9887,22 +13496,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a Germplasm `Attributes` search request", @@ -9936,19 +13591,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for Germplasm `AttributeValues`", @@ -10005,22 +13698,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a Germplasm `AttributeValues` search request", @@ -10055,19 +13794,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/CallsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Calls`", @@ -10136,19 +13913,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CallsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `Calls` search request", @@ -10183,19 +13998,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/CallSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallSetsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `CallSets`", @@ -10252,19 +14105,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CallSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallSetsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `CallSets` search request", @@ -10298,19 +14189,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Germplasm`", @@ -10367,22 +14296,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/GermplasmListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Germplasm` search request", @@ -10416,19 +14391,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ImageListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `XXEntitiesXX`", @@ -10485,22 +14498,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ImageListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Images` search request", @@ -10534,19 +14593,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ListsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for Lists", @@ -10603,19 +14700,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ListsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `List` search request", @@ -10649,19 +14784,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/LocationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Locations`", @@ -10718,19 +14891,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/LocationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `Locations` search request", @@ -10764,19 +14975,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/MarkerPositionListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MarkerPositionListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `MarkerPositions`", @@ -10833,19 +15082,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/MarkerPositionListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MarkerPositionListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `MarkerPositions` search request", @@ -10879,19 +15166,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Observations`", @@ -10959,19 +15284,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `Observations` search request", @@ -11005,19 +15368,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `ObservationUnits`", @@ -11074,22 +15475,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `ObservationUnits` search request", @@ -11123,19 +15570,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PedigreeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PedigreeListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Pedigree`", @@ -11192,22 +15677,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PedigreeListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PedigreeListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Pedigree` search request", @@ -11241,20 +15772,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PersonListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" - } + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" + } }, "summary" : "Submit a search request for `People`", "tags" : [ "People" ] @@ -11310,19 +15879,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PersonListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `People` search request", @@ -11356,19 +15963,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PlateListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlateListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Plates`", @@ -11425,22 +16070,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/PlateListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlateListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Plates` search request", @@ -11474,19 +16165,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ProgramListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Programs`", @@ -11543,22 +16272,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ProgramListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Programs` search request", @@ -11593,19 +16368,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ReferencesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ReferencesListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `References`", @@ -11662,19 +16475,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ReferencesListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ReferencesListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `References` search request", @@ -11709,19 +16560,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ReferenceSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ReferenceSetsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `ReferenceSets`", @@ -11778,19 +16667,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ReferenceSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ReferenceSetsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `ReferenceSets` search request", @@ -11824,19 +16751,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SampleListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Samples`", @@ -11893,22 +16858,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SampleListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Samples` search request", @@ -11943,19 +16954,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/StudyListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudyListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Studies`", @@ -12012,22 +17061,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/StudyListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudyListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Studies` search request", @@ -12061,19 +17156,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/TrialListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Trials`", @@ -12130,22 +17263,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/TrialListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Trials` search request", @@ -12179,19 +17358,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for Observation `Variables`", @@ -12248,22 +17465,68 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a Observation `variables` search request", @@ -12298,19 +17561,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/VariantsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `Variants`", @@ -12379,19 +17680,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/VariantsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `Variants` search request", @@ -12426,19 +17765,57 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/VariantSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantSetsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a search request for `VariantSets`", @@ -12495,19 +17872,57 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/VariantSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantSetsListResponse" + } + } + }, + "description" : "OK" }, "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse" + } + } + }, + "description" : "Accepted" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the results of a `VariantSets` search request", @@ -12598,16 +18013,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SeasonListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeasonListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Seasons", @@ -12642,16 +18088,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SeasonListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeasonListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "POST new Seasons", @@ -12687,16 +18164,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SeasonSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeasonSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the a single Season", @@ -12739,16 +18247,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SeasonSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeasonSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Update existing Seasons", @@ -12896,16 +18435,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SeedLotListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Seed Lot descriptions", @@ -12940,16 +18510,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SeedLotListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new Seed Lot descriptions to a server", @@ -13107,16 +18708,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SeedLotTransactionListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotTransactionListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Seed Lot Transactions", @@ -13151,16 +18783,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SeedLotTransactionListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotTransactionListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new Seed Lot Transaction to be recorded", @@ -13195,19 +18858,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SeedLotSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get a specific Seed Lot", @@ -13249,19 +18951,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/SeedLotSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Seed Lot", @@ -13339,19 +19080,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/SeedLotTransactionListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SeedLotTransactionListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get all Transactions related to a specific Seed Lot", @@ -13407,13 +19187,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the list of implemented Calls", @@ -13643,16 +19447,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/StudyListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudyListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Studies", @@ -13687,16 +19522,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/StudyListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudyListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new Studies.", @@ -13731,19 +19597,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/StudySingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudySingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details for a specific Study", @@ -13785,19 +19690,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/StudySingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudySingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Study", @@ -13854,13 +19798,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Study Types", @@ -13988,16 +19956,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/TraitListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TraitListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Traits", @@ -14032,16 +20031,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/TraitListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TraitListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new Traits", @@ -14076,19 +20106,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/TraitSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TraitSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Trait", @@ -14130,19 +20199,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/TraitSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TraitSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Trait", @@ -14354,16 +20462,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/TrialListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get a filtered list of Trials", @@ -14398,16 +20537,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/TrialListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Create new trials", @@ -14442,19 +20612,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/TrialSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Trial", @@ -14496,19 +20705,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/TrialSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update the details of an existing Trial", @@ -14766,16 +21014,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Get the Observation Variables", @@ -14810,16 +21089,47 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Add new Observation Variables", @@ -14854,19 +21164,58 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details for a specific Observation Variable", @@ -14908,19 +21257,58 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableSingleResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableSingleResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Observation Variable", @@ -15039,16 +21427,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/VariantsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a filtered list of `Variants`.", @@ -15093,16 +21512,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a `Variant` by ID.", @@ -15211,16 +21662,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CallsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a list of `Calls` associated with a `Variant`.", @@ -15367,16 +21849,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/VariantSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantSetsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a filtered list of `VariantSets`.", @@ -15421,16 +21934,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Create new `VariantSet` based on search results", @@ -15475,16 +22020,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a `VariantSet` by ID.", @@ -15593,16 +22170,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CallsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a list of `Calls` associated with a `VariantSet`.", @@ -15679,16 +22287,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/CallSetsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallSetsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a list of `CallSets` associated with a `VariantSet`.", @@ -15767,16 +22406,47 @@ } ], "responses" : { "200" : { - "$ref" : "#/components/responses/VariantsListResponse" + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantsListResponse" + } + } + }, + "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Gets a `Variants` for a given `VariantSet`.", @@ -15853,13 +22523,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "List current available orders", @@ -15901,13 +22595,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit New Order", @@ -15974,16 +22692,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the Plates for a specific Order", @@ -16050,16 +22800,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a specific Order", @@ -16104,16 +22886,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the status of a specific Order", @@ -16157,13 +22971,37 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" } }, "summary" : "Submit a new set of Sample data", @@ -16208,16 +23046,48 @@ "description" : "OK" }, "400" : { - "$ref" : "#/components/responses/400BadRequest" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" }, "401" : { - "$ref" : "#/components/responses/401Unauthorized" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" }, "403" : { - "$ref" : "#/components/responses/403Forbidden" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" }, "404" : { - "$ref" : "#/components/responses/404NotFound" + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the data for a submitted set of plates", @@ -30739,6 +37609,51 @@ }, "type" : "object" }, + "AlleleMatrixResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/AlleleMatrix" + } + }, + "required" : [ "metadata", "result" ], + "title" : "AlleleMatrixResponse", + "type" : "object" + }, + "GermplasmAttributeListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/GermplasmAttribute" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "GermplasmAttributeListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GermplasmAttributeListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmAttributeListResponse", + "type" : "object" + }, "GermplasmAttributeCategoryListResponse_result" : { "properties" : { "data" : { @@ -30769,6 +37684,67 @@ "title" : "GermplasmAttributeCategoryListResponse", "type" : "object" }, + "GermplasmAttributeSingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GermplasmAttribute" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmAttributeSingleResponse", + "type" : "object" + }, + "GermplasmAttributeValueListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/GermplasmAttributeValue" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "GermplasmAttributeValueListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmAttributeValueListResponse", + "type" : "object" + }, + "GermplasmAttributeValueSingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmAttributeValueSingleResponse", + "type" : "object" + }, "BreedingMethodListResponse_result" : { "properties" : { "data" : { @@ -30814,6 +37790,89 @@ "title" : "BreedingMethodSingleResponse", "type" : "object" }, + "CallsListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Call" + }, + "type" : "array" + }, + "expandHomozygotes" : { + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "example" : true, + "nullable" : true, + "type" : "boolean" + }, + "sepPhased" : { + "description" : "The string used as a separator for phased allele calls.", + "example" : "|", + "nullable" : true, + "type" : "string" + }, + "sepUnphased" : { + "description" : "The string used as a separator for unphased allele calls.", + "example" : "/", + "nullable" : true, + "type" : "string" + }, + "unknownString" : { + "description" : "The string used as a representation for missing data.", + "example" : ".", + "nullable" : true, + "type" : "string" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "CallsListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadataTokenPagination" + }, + "result" : { + "$ref" : "#/components/schemas/CallsListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "CallsListResponse", + "type" : "object" + }, + "CallSetsListResponseResult" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/CallSet" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "title" : "CallSetsListResponseResult", + "type" : "object" + }, + "CallSetsListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/CallSetsListResponseResult" + } + }, + "required" : [ "metadata", "result" ], + "title" : "CallSetsListResponse", + "type" : "object" + }, "callSetResponse" : { "properties" : { "@context" : { @@ -30861,6 +37920,140 @@ "title" : "commonCropNamesResponse", "type" : "object" }, + "CrossesListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Cross" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "CrossesListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/CrossesListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "CrossesListResponse", + "type" : "object" + }, + "CrossingProjectsListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/CrossingProject" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "CrossingProjectsListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/CrossingProjectsListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "CrossingProjectsListResponse", + "type" : "object" + }, + "CrossingProjectsSingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/CrossingProject" + } + }, + "required" : [ "metadata", "result" ], + "title" : "CrossingProjectsSingleResponse", + "type" : "object" + }, + "ImageDeleteResponse_result" : { + "properties" : { + "imageDbIds" : { + "description" : "The unique ids of the Image records which have been successfully deleted", + "example" : [ "6a4a59d8", "3ff067e0" ], + "items" : { + "type" : "string" + }, + "type" : "array" + } + }, + "required" : [ "imageDbIds" ], + "type" : "object" + }, + "ImageDeleteResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ImageDeleteResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ImageDeleteResponse", + "type" : "object" + }, + "ObservationDeleteResponse_result" : { + "properties" : { + "observationDbIds" : { + "description" : "The unique ids of the Observation records which have been successfully deleted", + "example" : [ "6a4a59d8", "3ff067e0" ], + "items" : { + "type" : "string" + }, + "type" : "array" + } + }, + "required" : [ "observationDbIds" ], + "type" : "object" + }, + "ObservationDeleteResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ObservationDeleteResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ObservationDeleteResponse", + "type" : "object" + }, "eventsResponse_result" : { "properties" : { "data" : { @@ -30890,6 +38083,51 @@ "title" : "eventsResponse", "type" : "object" }, + "GermplasmListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Germplasm" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "GermplasmListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GermplasmListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmListResponse", + "type" : "object" + }, + "GermplasmSingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Germplasm" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmSingleResponse", + "type" : "object" + }, "GermplasmMCPDResponse" : { "properties" : { "@context" : { @@ -30938,6 +38176,96 @@ "title" : "GermplasmProgenyResponse", "type" : "object" }, + "ImageListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Image" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "ImageListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ImageListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ImageListResponse", + "type" : "object" + }, + "ImageSingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Image" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ImageSingleResponse", + "type" : "object" + }, + "ListsListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/ListSummary" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "ListsListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ListsListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ListsListResponse", + "type" : "object" + }, + "ListsSingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ListDetails" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ListsSingleResponse", + "type" : "object" + }, "listResponse" : { "properties" : { "@context" : { @@ -30954,6 +38282,51 @@ "title" : "listResponse", "type" : "object" }, + "LocationListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Location" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "LocationListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/LocationListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "LocationListResponse", + "type" : "object" + }, + "LocationSingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Location" + } + }, + "required" : [ "metadata", "result" ], + "title" : "LocationSingleResponse", + "type" : "object" + }, "GenomeMapListResponse_result" : { "properties" : { "data" : { @@ -31028,6 +38401,80 @@ "title" : "LinkageGroupListResponse", "type" : "object" }, + "MarkerPositionListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/MarkerPosition" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "MarkerPositionListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/MarkerPositionListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "MarkerPositionListResponse", + "type" : "object" + }, + "MethodListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Method" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "MethodListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/MethodListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "MethodListResponse", + "type" : "object" + }, + "MethodSingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Method" + } + }, + "required" : [ "metadata", "result" ], + "title" : "MethodSingleResponse", + "type" : "object" + }, "ObservationLevelListResponse_result" : { "properties" : { "data" : { @@ -31073,7 +38520,20 @@ "title" : "ObservationLevelListResponse", "type" : "object" }, - "ReferenceSingleResponse" : { + "ObservationListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Observation" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "ObservationListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31082,14 +38542,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/Reference" + "$ref" : "#/components/schemas/ObservationListResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "ReferenceSingleResponse", + "title" : "ObservationListResponse", "type" : "object" }, - "ReferenceBasesResponse" : { + "ObservationTableResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31098,14 +38558,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/ReferenceBases" + "$ref" : "#/components/schemas/ObservationTable" } }, "required" : [ "metadata", "result" ], - "title" : "ReferenceBasesResponse", + "title" : "ObservationTableResponse", "type" : "object" }, - "ReferenceSetsSingleResponse" : { + "ObservationSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31114,554 +38574,207 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/ReferenceSet" + "$ref" : "#/components/schemas/Observation" } }, "required" : [ "metadata", "result" ], - "title" : "ReferenceSetsSingleResponse", + "title" : "ObservationSingleResponse", "type" : "object" }, - "GeoJSON_Geometry_oneOf" : { - "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "ObservationUnitListResponse_result" : { "properties" : { - "coordinates" : { - "description" : "A single position", - "example" : [ -76.506042, 42.417373, 123 ], + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "type" : "number" + "$ref" : "#/components/schemas/ObservationUnit" }, - "minItems" : 2, "type" : "array" - }, - "type" : { - "default" : "Point", - "description" : "The literal string \"Point\"", - "example" : "Point", - "type" : "string" } }, - "required" : [ "coordinates", "type" ], + "required" : [ "data" ], "type" : "object" }, - "GeoJSON_Geometry_oneOf_1" : { - "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "ObservationUnitListResponse" : { "properties" : { - "coordinates" : { - "description" : "An array of linear rings", - "example" : [ [ [ -77.456654, 42.241133, 494 ], [ -75.414133, 41.508282, 571 ], [ -76.506042, 42.417373, 123 ], [ -77.456654, 42.241133, 346 ] ] ], - "items" : { - "description" : "An array of at least four positions where the first equals the last", - "example" : [ [ -77.456654, 42.241133, 494 ], [ -75.414133, 41.508282, 571 ], [ -76.506042, 42.417373, 123 ], [ -77.456654, 42.241133, 346 ] ], - "items" : { - "description" : "A single position", - "example" : [ -76.506042, 42.417373, 123 ], - "items" : { - "type" : "number" - }, - "minItems" : 2, - "type" : "array" - }, - "minItems" : 4, - "type" : "array" - }, - "type" : "array" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "type" : { - "default" : "Polygon", - "description" : "The literal string \"Polygon\"", - "example" : "Polygon", - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ObservationUnitListResponse_result" } }, - "required" : [ "coordinates", "type" ], + "required" : [ "metadata", "result" ], + "title" : "ObservationUnitListResponse", "type" : "object" }, - "GeoJSON_Geometry" : { - "description" : "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed.", - "discriminator" : { - "mapping" : { - "Point" : "#/components/schemas/pointGeometry", - "Polygon" : "#/components/schemas/polygonGeometry" + "ObservationUnitTableResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "propertyName" : "type" - }, - "example" : { - "coordinates" : [ -76.506042, 42.417373, 123 ], - "type" : "Point" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ObservationUnitTable" + } }, - "oneOf" : [ { - "$ref" : "#/components/schemas/GeoJSON_Geometry_oneOf" - }, { - "$ref" : "#/components/schemas/GeoJSON_Geometry_oneOf_1" - } ], - "title" : "GeoJSON Geometry", + "required" : [ "metadata", "result" ], + "title" : "ObservationUnitTableResponse", "type" : "object" }, - "GeoJSONSearchArea" : { - "description" : "A GeoJSON Polygon which describes an area to search for other GeoJSON objects. All contained Points and intersecting Polygons should be returned as search results. \n\nAll coordinates are decimal values on the WGS84 geographic coordinate reference system.", - "example" : { - "geometry" : { - "coordinates" : [ [ [ -77.456654, 42.241133 ], [ -75.414133, 41.508282 ], [ -76.506042, 42.417373 ], [ -77.456654, 42.241133 ] ] ], - "type" : "Polygon" - }, - "type" : "Feature" - }, + "ObservationUnitSingleResponse" : { "properties" : { - "geometry" : { - "$ref" : "#/components/schemas/GeoJSON_Geometry" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "type" : { - "default" : "Feature", - "description" : "The literal string \"Feature\"", - "example" : "Feature", - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ObservationUnit" } }, - "title" : "GeoJSONSearchArea", + "required" : [ "metadata", "result" ], + "title" : "ObservationUnitSingleResponse", "type" : "object" }, - "_search_images_post_request" : { + "OntologyListResponse_result" : { "properties" : { - "commonCropNames" : { - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "example" : [ "Tomatillo", "Paw Paw" ], + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "type" : "string" + "$ref" : "#/components/schemas/Ontology" }, "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "OntologyListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "descriptiveOntologyTerms" : { - "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", - "example" : [ "doi:10.1002/0470841559", "Red", "ncbi:0300294" ], - "items" : { - "type" : "string" - }, - "type" : "array" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "externalReferenceIDs" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "example" : [ "doi:10.155454/12341234", "14a19841" ], - "items" : { - "type" : "string" - }, - "type" : "array" + "result" : { + "$ref" : "#/components/schemas/OntologyListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "OntologyListResponse", + "type" : "object" + }, + "OntologySingleResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "externalReferenceIds" : { - "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "example" : [ "doi:10.155454/12341234", "14a19841" ], - "items" : { - "type" : "string" - }, - "type" : "array" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "externalReferenceSources" : { - "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", - "example" : [ "DOI", "Field App Name" ], + "result" : { + "$ref" : "#/components/schemas/Ontology" + } + }, + "required" : [ "metadata", "result" ], + "title" : "OntologySingleResponse", + "type" : "object" + }, + "PedigreeListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "type" : "string" + "$ref" : "#/components/schemas/PedigreeNode" }, "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "PedigreeListResponse" : { + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "imageDbIds" : { - "description" : "A list of image Ids to search for", - "example" : [ "564b64a6", "0d122d1d" ], - "items" : { - "type" : "string" - }, - "type" : "array" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "imageFileNames" : { - "description" : "Image file names to search for.", - "example" : [ "image_01032019.jpg", "picture_field_1234.jpg" ], + "result" : { + "$ref" : "#/components/schemas/PedigreeListResponse_result" + } + }, + "required" : [ "metadata", "result" ], + "title" : "PedigreeListResponse", + "type" : "object" + }, + "PersonListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "type" : "string" - }, - "type" : "array" - }, - "imageFileSizeMax" : { - "description" : "A maximum image file size to search for.", - "example" : 20000000, - "type" : "integer" - }, - "imageFileSizeMin" : { - "description" : "A minimum image file size to search for.", - "example" : 1000, - "type" : "integer" - }, - "imageHeightMax" : { - "description" : "A maximum image height to search for.", - "example" : 1080, - "type" : "integer" - }, - "imageHeightMin" : { - "description" : "A minimum image height to search for.", - "example" : 720, - "type" : "integer" - }, - "imageLocation" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - }, - "imageNames" : { - "description" : "Human readable names to search for.", - "example" : [ "Image 43", "Tractor in field" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "imageTimeStampRangeEnd" : { - "description" : "The latest timestamp to search for.", - "format" : "date-time", - "type" : "string" - }, - "imageTimeStampRangeStart" : { - "description" : "The earliest timestamp to search for.", - "format" : "date-time", - "type" : "string" - }, - "imageWidthMax" : { - "description" : "A maximum image width to search for.", - "example" : 1920, - "type" : "integer" - }, - "imageWidthMin" : { - "description" : "A minimum image width to search for.", - "example" : 1280, - "type" : "integer" - }, - "mimeTypes" : { - "description" : "A set of image file types to search for.", - "example" : [ "image/jpg", "image/jpeg", "image/gif" ], - "items" : { - "pattern" : "image/.*", - "type" : "string" - }, - "type" : "array" - }, - "observationDbIds" : { - "description" : "A list of observation Ids this image is associated with to search for", - "example" : [ "47326456", "fc9823ac" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "observationUnitDbIds" : { - "description" : "A set of observation unit identifiers to search for.", - "example" : [ "f5e4b273", "328c9424" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "page" : { - "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "example" : 0, - "type" : "integer" - }, - "pageSize" : { - "description" : "The size of the pages to be returned. Default is `1000`.", - "example" : 1000, - "type" : "integer" - }, - "programDbIds" : { - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "example" : [ "8f5de35b", "0e2d4a13" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "programNames" : { - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "example" : [ "Better Breeding Program", "Best Breeding Program" ], - "items" : { - "type" : "string" + "$ref" : "#/components/schemas/Person" }, "type" : "array" } }, + "required" : [ "data" ], "type" : "object" }, - "ObservationUnitLevelRelationship_1" : { - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", + "PersonListResponse" : { "properties" : { - "levelCode" : { - "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", - "example" : "Plot_123", - "nullable" : true, - "type" : "string" - }, - "levelName" : { - "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : "plot", - "nullable" : true, - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "levelOrder" : { - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : 2, - "nullable" : true, - "type" : "integer" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "observationUnitDbId" : { - "description" : "The ID which uniquely identifies an observation unit\n
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. \n
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response.", - "example" : "5ab883e9", - "nullable" : true, - "type" : "string" + "result" : { + "$ref" : "#/components/schemas/PersonListResponse_result" } }, - "title" : "ObservationUnitLevelRelationship", + "required" : [ "metadata", "result" ], + "title" : "PersonListResponse", "type" : "object" }, - "ObservationUnitLevel_1" : { - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", + "PersonSingleResponse" : { "properties" : { - "levelCode" : { - "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", - "example" : "Plot_123", - "nullable" : true, - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "levelName" : { - "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : "plot", - "nullable" : true, - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "levelOrder" : { - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : 2, - "nullable" : true, - "type" : "integer" + "result" : { + "$ref" : "#/components/schemas/Person" } }, - "title" : "ObservationUnitLevel", + "required" : [ "metadata", "result" ], + "title" : "PersonSingleResponse", "type" : "object" }, - "_search_observations_post_request" : { + "PlannedCrossesListResponse_result" : { "properties" : { - "commonCropNames" : { - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "example" : [ "Tomatillo", "Paw Paw" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "externalReferenceIDs" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "example" : [ "doi:10.155454/12341234", "14a19841" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "externalReferenceIds" : { - "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "example" : [ "doi:10.155454/12341234", "14a19841" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "externalReferenceSources" : { - "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", - "example" : [ "DOI", "Field App Name" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "germplasmDbIds" : { - "description" : "List of IDs which uniquely identify germplasm to search for", - "example" : [ "e9c6edd7", "1b1df4a6" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "germplasmNames" : { - "description" : "List of human readable names to identify germplasm to search for", - "example" : [ "A0000003", "A0000477" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "locationDbIds" : { - "description" : "The location ids to search for", - "example" : [ "b28911cf", "5071d1e4" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "locationNames" : { - "description" : "A human readable names to search for", - "example" : [ "Location Alpha", "The Large Hadron Collider" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "observationDbIds" : { - "description" : "The unique id of an Observation", - "example" : [ "6a4a59d8", "3ff067e0" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "observationLevelRelationships" : { - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", - "example" : [ { - "levelCode" : "Field_1", - "levelName" : "field" - } ], - "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" - }, - "nullable" : true, - "type" : "array" - }, - "observationLevels" : { - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", - "example" : [ { - "levelCode" : "Plot_123", - "levelName" : "plot" - }, { - "levelCode" : "Plot_456", - "levelName" : "plot" - }, { - "levelCode" : "Plot_789", - "levelName" : "plot" - } ], - "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevel_1" - }, - "nullable" : true, - "type" : "array" - }, - "observationTimeStampRangeEnd" : { - "description" : "Timestamp range end", - "format" : "date-time", - "nullable" : true, - "type" : "string" - }, - "observationTimeStampRangeStart" : { - "description" : "Timestamp range start", - "format" : "date-time", - "nullable" : true, - "type" : "string" - }, - "observationUnitDbIds" : { - "description" : "The unique id of an Observation Unit", - "example" : [ "76f559b5", "066bc5d3" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "observationVariableDbIds" : { - "description" : "The DbIds of Variables to search for", - "example" : [ "a646187d", "6d23513b" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "observationVariableNames" : { - "description" : "The names of Variables to search for", - "example" : [ "Plant Height in meters", "Wheat rust score 1-5" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "observationVariablePUIs" : { - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "example" : [ "http://my-traits.com/trait/CO_123:0008012", "http://my-traits.com/trait/CO_123:0007261" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "page" : { - "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "example" : 0, - "type" : "integer" - }, - "pageSize" : { - "description" : "The size of the pages to be returned. Default is `1000`.", - "example" : 1000, - "type" : "integer" - }, - "programDbIds" : { - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "example" : [ "8f5de35b", "0e2d4a13" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "programNames" : { - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "example" : [ "Better Breeding Program", "Best Breeding Program" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "seasonDbIds" : { - "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", - "example" : [ "Spring 2018", "Season A" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "studyDbIds" : { - "description" : "List of study identifiers to search for", - "example" : [ "cf6c4bd4", "691e69d6" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "studyNames" : { - "description" : "List of study names to filter search results", - "example" : [ "The First Bob Study 2017", "Wheat Yield Trial 246" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "trialDbIds" : { - "description" : "The ID which uniquely identifies a trial to search for", - "example" : [ "d2593dc2", "9431a731" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "trialNames" : { - "description" : "The human readable name of a trial to search for", - "example" : [ "All Yield Trials 2016", "Disease Resistance Study Comparison Group" ], + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "type" : "string" + "$ref" : "#/components/schemas/PlannedCross" }, "type" : "array" } }, + "required" : [ "data" ], "type" : "object" }, - "ServerInfoResponse" : { + "PlannedCrossesListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31670,20 +38783,19 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/ServerInfo" + "$ref" : "#/components/schemas/PlannedCrossesListResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "ServerInfoResponse", + "title" : "PlannedCrossesListResponse", "type" : "object" }, - "studyTypesResponse_result" : { + "PlateListResponse_result" : { "properties" : { "data" : { - "description" : "The list of all StudyTypes available on a given server.", - "example" : [ "Crossing Nursery", "Yield study" ], + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "type" : "string" + "$ref" : "#/components/schemas/Plate" }, "type" : "array" } @@ -31691,23 +38803,7 @@ "required" : [ "data" ], "type" : "object" }, - "studyTypesResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "$ref" : "#/components/schemas/studyTypesResponse_result" - } - }, - "required" : [ "metadata", "result" ], - "title" : "studyTypesResponse", - "type" : "object" - }, - "VariantSingleResponse" : { + "PlateListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31716,14 +38812,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/Variant" + "$ref" : "#/components/schemas/PlateListResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "VariantSingleResponse", + "title" : "PlateListResponse", "type" : "object" }, - "variantSetResponse" : { + "PlateSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31732,19 +38828,19 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VariantSet" + "$ref" : "#/components/schemas/Plate" } }, "required" : [ "metadata", "result" ], - "title" : "variantSetResponse", + "title" : "PlateSingleResponse", "type" : "object" }, - "VendorOrderListResponse_result" : { + "ProgramListResponse_result" : { "properties" : { "data" : { "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "$ref" : "#/components/schemas/VendorOrder" + "$ref" : "#/components/schemas/Program" }, "type" : "array" } @@ -31752,7 +38848,7 @@ "required" : [ "data" ], "type" : "object" }, - "VendorOrderListResponse" : { + "ProgramListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31761,14 +38857,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VendorOrderListResponse_result" + "$ref" : "#/components/schemas/ProgramListResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "VendorOrderListResponse", + "title" : "ProgramListResponse", "type" : "object" }, - "VendorOrderSubmissionSingleResponse" : { + "ProgramSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31777,26 +38873,28 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VendorOrderSubmission" + "$ref" : "#/components/schemas/Program" } }, - "title" : "VendorOrderSubmissionSingleResponse", + "required" : [ "metadata", "result" ], + "title" : "ProgramSingleResponse", "type" : "object" }, - "VendorPlateListResponse_result" : { + "ReferencesListResponseResult" : { "properties" : { "data" : { "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "$ref" : "#/components/schemas/VendorPlate" + "$ref" : "#/components/schemas/Reference" }, "type" : "array" } }, "required" : [ "data" ], + "title" : "ReferencesListResponseResult", "type" : "object" }, - "VendorPlateListResponse" : { + "ReferencesListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31805,27 +38903,30 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VendorPlateListResponse_result" + "$ref" : "#/components/schemas/ReferencesListResponseResult" } }, "required" : [ "metadata", "result" ], - "title" : "VendorPlateListResponse", + "title" : "ReferencesListResponse", "type" : "object" }, - "VendorResultFileListResponse_result" : { + "ReferenceSingleResponse" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/VendorResultFile" - }, - "type" : "array" + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Reference" } }, - "required" : [ "data" ], + "required" : [ "metadata", "result" ], + "title" : "ReferenceSingleResponse", "type" : "object" }, - "VendorResultFileListResponse" : { + "ReferenceBasesResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31834,23 +38935,28 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VendorResultFileListResponse_result" + "$ref" : "#/components/schemas/ReferenceBases" } }, "required" : [ "metadata", "result" ], - "title" : "VendorResultFileListResponse", + "title" : "ReferenceBasesResponse", "type" : "object" }, - "VendorOrderStatusResponse_result" : { + "ReferenceSetsListResponseResult" : { "properties" : { - "status" : { - "enum" : [ "registered", "received", "inProgress", "completed", "rejected" ], - "type" : "string" + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/ReferenceSet" + }, + "type" : "array" } }, + "required" : [ "data" ], + "title" : "ReferenceSetsListResponseResult", "type" : "object" }, - "VendorOrderStatusResponse" : { + "ReferenceSetsListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31859,14 +38965,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VendorOrderStatusResponse_result" + "$ref" : "#/components/schemas/ReferenceSetsListResponseResult" } }, "required" : [ "metadata", "result" ], - "title" : "VendorOrderStatusResponse", + "title" : "ReferenceSetsListResponse", "type" : "object" }, - "VendorPlateSubmissionIdSingleResponse" : { + "ReferenceSetsSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31875,14 +38981,27 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VendorPlateSubmissionId" + "$ref" : "#/components/schemas/ReferenceSet" } }, "required" : [ "metadata", "result" ], - "title" : "VendorPlateSubmissionIdSingleResponse", + "title" : "ReferenceSetsSingleResponse", "type" : "object" }, - "VendorPlateSubmissionSingleResponse" : { + "SampleListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Sample" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "SampleListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31891,14 +39010,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VendorPlateSubmission" + "$ref" : "#/components/schemas/SampleListResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "VendorPlateSubmissionSingleResponse", + "title" : "SampleListResponse", "type" : "object" }, - "VendorSpecificationSingleResponse" : { + "SampleSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -31907,2143 +39026,964 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/VendorSpecification" + "$ref" : "#/components/schemas/Sample" } }, "required" : [ "metadata", "result" ], - "title" : "VendorSpecificationSingleResponse", + "title" : "SampleSingleResponse", "type" : "object" }, - "AlleleMatrix_dataMatrices_inner" : { - "description" : "This is a single data matrix. It could be the allele matrix or an additional layer of metadata associated with each genotype value.", + "ScaleListResponse_result" : { "properties" : { - "dataMatrix" : { - "description" : "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.", - "example" : [ [ "0|0", "1|0", "1/1" ], [ "0|0", "1|0", "1/1" ], [ "0|0", "1|0", "1/1" ] ], + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "description" : "An array of rows in the data matrix", - "items" : { - "description" : "All the values per row (columns) in the data matrix", - "type" : "string" - }, - "type" : "array" + "$ref" : "#/components/schemas/Scale" }, - "nullable" : true, "type" : "array" - }, - "dataMatrixAbbreviation" : { - "description" : "The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word \"GT\" is reserved for the allele matrix. Examples of other metadata matrices include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard.", - "example" : "GT", - "nullable" : true, - "type" : "string" - }, - "dataMatrixName" : { - "description" : "The name of the field represented in this data matrix. The key word \"Genotype\" is reserved for the allele matrix. Examples of other metadata matrices include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard.", - "example" : "Genotype", - "nullable" : true, - "type" : "string" - }, - "dataType" : { - "description" : "The type of field represented in this data matrix. This is intended to help parse the data out of JSON.", - "enum" : [ "string", "integer", "float", "boolean" ], - "example" : "string", - "nullable" : true, - "type" : "string" } }, + "required" : [ "data" ], "type" : "object" }, - "AlleleMatrix_pagination_inner" : { + "ScaleListResponse" : { "properties" : { - "dimension" : { - "description" : "The dimension of the matrix being paginated", - "enum" : [ "CALLSETS", "VARIANTS" ], - "example" : "VARIANTS", - "nullable" : true, - "type" : "string" - }, - "page" : { - "description" : "the requested page number (zero indexed)", - "example" : 0, - "nullable" : true, - "type" : "integer" - }, - "pageSize" : { - "description" : "the maximum number of elements per page in this dimension of the matrix", - "example" : 500, - "nullable" : true, - "type" : "integer" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "totalCount" : { - "description" : "The total number of elements that are available on the server and match the requested query parameters.", - "example" : 10000, - "nullable" : true, - "type" : "integer" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "totalPages" : { - "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", - "example" : 20, - "nullable" : true, - "type" : "integer" + "result" : { + "$ref" : "#/components/schemas/ScaleListResponse_result" } }, + "required" : [ "metadata", "result" ], + "title" : "ScaleListResponse", "type" : "object" }, - "AlleleMatrixSearchRequest_pagination_inner" : { + "ScaleSingleResponse" : { "properties" : { - "dimension" : { - "description" : "the dimension of the matrix being paginated", - "enum" : [ "CALLSETS", "VARIANTS" ], - "example" : "VARIANTS", - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "page" : { - "description" : "the requested page number (zero indexed)", - "example" : 0, - "type" : "integer" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "pageSize" : { - "description" : "the maximum number of elements per page in this dimension of the matrix", - "example" : 500, - "type" : "integer" + "result" : { + "$ref" : "#/components/schemas/Scale" } }, + "required" : [ "metadata", "result" ], + "title" : "ScaleSingleResponse", "type" : "object" }, - "Call_genotypeMetadata_inner" : { + "_202AcceptedSearchResponse_result" : { "properties" : { - "dataType" : { - "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", - "enum" : [ "string", "integer", "float", "boolean" ], - "example" : "integer", - "type" : "string" - }, - "fieldAbbreviation" : { - "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard.", - "example" : "GQ", - "type" : "string" - }, - "fieldName" : { - "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard.", - "example" : "Genotype Quality", - "type" : "string" - }, - "fieldValue" : { - "description" : "The additional metadata value associated with this genotype call", - "example" : "45.2", + "searchResultsDbId" : { + "example" : "551ae08c", "type" : "string" } }, "type" : "object" }, - "Cross_crossAttributes_inner" : { - "description" : "a custom attributes associated with a cross", + "_202AcceptedSearchResponse" : { "properties" : { - "crossAttributeName" : { - "description" : "the human readable name of a cross attribute", - "example" : "Humidity Percentage", - "nullable" : true, - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "crossAttributeValue" : { - "description" : "the value of a cross attribute", - "example" : "45", - "nullable" : true, - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/_202AcceptedSearchResponse_result" } }, + "title" : "202AcceptedSearchResponse", "type" : "object" }, - "ExternalReferences_1_inner" : { + "GeoJSON_Geometry_oneOf" : { + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", "properties" : { - "referenceID" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `referenceId`. Github issue number #460 \n
The external reference ID. Could be a simple string or a URI.", - "nullable" : true, - "type" : "string" - }, - "referenceId" : { - "description" : "The external reference ID. Could be a simple string or a URI.", - "type" : "string" + "coordinates" : { + "description" : "A single position", + "example" : [ -76.506042, 42.417373, 123 ], + "items" : { + "type" : "number" + }, + "minItems" : 2, + "type" : "array" }, - "referenceSource" : { - "description" : "An identifier for the source system or database of this reference", + "type" : { + "default" : "Point", + "description" : "The literal string \"Point\"", + "example" : "Point", "type" : "string" } }, + "required" : [ "coordinates", "type" ], "type" : "object" }, - "Cross_parent1" : { - "nullable" : true, + "GeoJSON_Geometry_oneOf_1" : { + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", "properties" : { - "germplasmDbId" : { - "description" : "the unique identifier for a germplasm", - "example" : "d34b10c3", - "nullable" : true, - "type" : "string" + "coordinates" : { + "description" : "An array of linear rings", + "example" : [ [ [ -77.456654, 42.241133, 494 ], [ -75.414133, 41.508282, 571 ], [ -76.506042, 42.417373, 123 ], [ -77.456654, 42.241133, 346 ] ] ], + "items" : { + "description" : "An array of at least four positions where the first equals the last", + "example" : [ [ -77.456654, 42.241133, 494 ], [ -75.414133, 41.508282, 571 ], [ -76.506042, 42.417373, 123 ], [ -77.456654, 42.241133, 346 ] ], + "items" : { + "description" : "A single position", + "example" : [ -76.506042, 42.417373, 123 ], + "items" : { + "type" : "number" + }, + "minItems" : 2, + "type" : "array" + }, + "minItems" : 4, + "type" : "array" + }, + "type" : "array" }, - "germplasmName" : { - "description" : "the human readable name for a germplasm", - "example" : "TME_419", - "nullable" : true, + "type" : { + "default" : "Polygon", + "description" : "The literal string \"Polygon\"", + "example" : "Polygon", "type" : "string" + } + }, + "required" : [ "coordinates", "type" ], + "type" : "object" + }, + "GeoJSON_Geometry" : { + "description" : "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed.", + "discriminator" : { + "mapping" : { + "Point" : "#/components/schemas/pointGeometry", + "Polygon" : "#/components/schemas/polygonGeometry" }, - "observationUnitDbId" : { - "description" : "the unique identifier for an observation unit", - "example" : "2e1926a7", - "nullable" : true, - "type" : "string" + "propertyName" : "type" + }, + "example" : { + "coordinates" : [ -76.506042, 42.417373, 123 ], + "type" : "Point" + }, + "oneOf" : [ { + "$ref" : "#/components/schemas/GeoJSON_Geometry_oneOf" + }, { + "$ref" : "#/components/schemas/GeoJSON_Geometry_oneOf_1" + } ], + "title" : "GeoJSON Geometry", + "type" : "object" + }, + "GeoJSONSearchArea" : { + "description" : "A GeoJSON Polygon which describes an area to search for other GeoJSON objects. All contained Points and intersecting Polygons should be returned as search results. \n\nAll coordinates are decimal values on the WGS84 geographic coordinate reference system.", + "example" : { + "geometry" : { + "coordinates" : [ [ [ -77.456654, 42.241133 ], [ -75.414133, 41.508282 ], [ -76.506042, 42.417373 ], [ -77.456654, 42.241133 ] ] ], + "type" : "Polygon" }, - "observationUnitName" : { - "description" : "the human readable name for an observation unit", - "example" : "my_Plot_9001", - "nullable" : true, - "type" : "string" + "type" : "Feature" + }, + "properties" : { + "geometry" : { + "$ref" : "#/components/schemas/GeoJSON_Geometry" }, - "parentType" : { - "description" : "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.", - "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION" ], - "example" : "MALE", + "type" : { + "default" : "Feature", + "description" : "The literal string \"Feature\"", + "example" : "Feature", "type" : "string" } }, + "title" : "GeoJSONSearchArea", "type" : "object" }, - "Cross_pollinationEvents_inner" : { + "_search_images_post_request" : { "properties" : { - "pollinationNumber" : { - "description" : "The unique identifier for this pollination event", - "nullable" : true, - "type" : "string" + "commonCropNames" : { + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "example" : [ "Tomatillo", "Paw Paw" ], + "items" : { + "type" : "string" + }, + "type" : "array" }, - "pollinationSuccessful" : { - "description" : "True if the pollination was successful", - "nullable" : true, - "type" : "boolean" + "descriptiveOntologyTerms" : { + "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", + "example" : [ "doi:10.1002/0470841559", "Red", "ncbi:0300294" ], + "items" : { + "type" : "string" + }, + "type" : "array" }, - "pollinationTimeStamp" : { - "description" : "The timestamp when the pollination took place", + "externalReferenceIDs" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "example" : [ "doi:10.155454/12341234", "14a19841" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "externalReferenceIds" : { + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "example" : [ "doi:10.155454/12341234", "14a19841" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "externalReferenceSources" : { + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "example" : [ "DOI", "Field App Name" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "imageDbIds" : { + "description" : "A list of image Ids to search for", + "example" : [ "564b64a6", "0d122d1d" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "imageFileNames" : { + "description" : "Image file names to search for.", + "example" : [ "image_01032019.jpg", "picture_field_1234.jpg" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "imageFileSizeMax" : { + "description" : "A maximum image file size to search for.", + "example" : 20000000, + "type" : "integer" + }, + "imageFileSizeMin" : { + "description" : "A minimum image file size to search for.", + "example" : 1000, + "type" : "integer" + }, + "imageHeightMax" : { + "description" : "A maximum image height to search for.", + "example" : 1080, + "type" : "integer" + }, + "imageHeightMin" : { + "description" : "A minimum image height to search for.", + "example" : 720, + "type" : "integer" + }, + "imageLocation" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + }, + "imageNames" : { + "description" : "Human readable names to search for.", + "example" : [ "Image 43", "Tractor in field" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "imageTimeStampRangeEnd" : { + "description" : "The latest timestamp to search for.", + "format" : "date-time", + "type" : "string" + }, + "imageTimeStampRangeStart" : { + "description" : "The earliest timestamp to search for.", "format" : "date-time", - "nullable" : true, "type" : "string" + }, + "imageWidthMax" : { + "description" : "A maximum image width to search for.", + "example" : 1920, + "type" : "integer" + }, + "imageWidthMin" : { + "description" : "A minimum image width to search for.", + "example" : 1280, + "type" : "integer" + }, + "mimeTypes" : { + "description" : "A set of image file types to search for.", + "example" : [ "image/jpg", "image/jpeg", "image/gif" ], + "items" : { + "pattern" : "image/.*", + "type" : "string" + }, + "type" : "array" + }, + "observationDbIds" : { + "description" : "A list of observation Ids this image is associated with to search for", + "example" : [ "47326456", "fc9823ac" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "observationUnitDbIds" : { + "description" : "A set of observation unit identifiers to search for.", + "example" : [ "f5e4b273", "328c9424" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "page" : { + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "example" : 0, + "type" : "integer" + }, + "pageSize" : { + "description" : "The size of the pages to be returned. Default is `1000`.", + "example" : 1000, + "type" : "integer" + }, + "programDbIds" : { + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "example" : [ "8f5de35b", "0e2d4a13" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "programNames" : { + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "example" : [ "Better Breeding Program", "Best Breeding Program" ], + "items" : { + "type" : "string" + }, + "type" : "array" } }, "type" : "object" }, - "CrossingProject_potentialParents_inner" : { + "ObservationUnitLevelRelationship_1" : { + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", "properties" : { - "germplasmDbId" : { - "description" : "the unique identifier for a germplasm", - "example" : "d34b10c3", + "levelCode" : { + "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", + "example" : "Plot_123", "nullable" : true, "type" : "string" }, - "germplasmName" : { - "description" : "the human readable name for a germplasm", - "example" : "TME_419", + "levelName" : { + "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "example" : "plot", "nullable" : true, "type" : "string" }, - "observationUnitDbId" : { - "description" : "the unique identifier for an observation unit", - "example" : "2e1926a7", + "levelOrder" : { + "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "example" : 2, "nullable" : true, - "type" : "string" + "type" : "integer" }, - "observationUnitName" : { - "description" : "the human readable name for an observation unit", - "example" : "my_Plot_9001", + "observationUnitDbId" : { + "description" : "The ID which uniquely identifies an observation unit\n
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. \n
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response.", + "example" : "5ab883e9", "nullable" : true, "type" : "string" - }, - "parentType" : { - "description" : "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.", - "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION" ], - "example" : "MALE", - "type" : "string" } }, + "title" : "ObservationUnitLevelRelationship", "type" : "object" }, - "Event_eventDateRange" : { - "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)", - "nullable" : true, + "ObservationUnitLevel_1" : { + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", "properties" : { - "discreteDates" : { - "description" : "A list of dates when the event occurred\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", - "example" : [ "2018-10-08T18:15:11Z", "2018-11-09T18:16:12Z", "2018-11-19T18:16:12Z" ], - "items" : { - "format" : "date-time", - "type" : "string" - }, + "levelCode" : { + "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", + "example" : "Plot_123", "nullable" : true, - "type" : "array" + "type" : "string" }, - "endDate" : { - "description" : "The end of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", - "example" : "2018-10-08T18:15:11Z", - "format" : "date-time", + "levelName" : { + "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "example" : "plot", "nullable" : true, "type" : "string" }, - "startDate" : { - "description" : "The beginning of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", - "example" : "2018-10-08T18:15:11Z", - "format" : "date-time", + "levelOrder" : { + "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "example" : 2, "nullable" : true, - "type" : "string" + "type" : "integer" } }, + "title" : "ObservationUnitLevel", "type" : "object" }, - "Event_eventParameters_inner" : { + "_search_observations_post_request" : { "properties" : { - "code" : { - "description" : "The shortened code name of an event parameter\n
ICASA \"Code_Display\"", - "example" : "tiimp", - "nullable" : true, - "type" : "string" - }, - "description" : { - "description" : "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter.", - "example" : "Implement or tool used for tillage", - "nullable" : true, - "type" : "string" + "commonCropNames" : { + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "example" : [ "Tomatillo", "Paw Paw" ], + "items" : { + "type" : "string" + }, + "type" : "array" }, - "key" : { + "externalReferenceIDs" : { "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `name`. Github issue number #440 \n
Specifies the relationship between the event and the given property. E.g. fertilizer, operator", - "example" : "operator", - "nullable" : true, - "type" : "string" + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "example" : [ "doi:10.155454/12341234", "14a19841" ], + "items" : { + "type" : "string" + }, + "type" : "array" }, - "name" : { - "description" : "The full name of an event parameter\n
ICASA \"Variable_Name\"", - "example" : "tillage_implement", + "externalReferenceIds" : { + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "example" : [ "doi:10.155454/12341234", "14a19841" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "externalReferenceSources" : { + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "example" : [ "DOI", "Field App Name" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "germplasmDbIds" : { + "description" : "List of IDs which uniquely identify germplasm to search for", + "example" : [ "e9c6edd7", "1b1df4a6" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "germplasmNames" : { + "description" : "List of human readable names to identify germplasm to search for", + "example" : [ "A0000003", "A0000477" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "locationDbIds" : { + "description" : "The location ids to search for", + "example" : [ "b28911cf", "5071d1e4" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "locationNames" : { + "description" : "A human readable names to search for", + "example" : [ "Location Alpha", "The Large Hadron Collider" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "observationDbIds" : { + "description" : "The unique id of an Observation", + "example" : [ "6a4a59d8", "3ff067e0" ], + "items" : { + "type" : "string" + }, "nullable" : true, - "type" : "string" + "type" : "array" }, - "rdfValue" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `code`. Github issue number #440 \nobservationUnitPosition->observationLevelRelationships", + "example" : [ { + "levelCode" : "Field_1", + "levelName" : "field" + } ], + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" + }, "nullable" : true, - "type" : "string" + "type" : "array" }, - "units" : { - "description" : "The units or data type of the 'value'. \n
If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. \n
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\"", - "example" : "code", + "observationLevels" : { + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "example" : [ { + "levelCode" : "Plot_123", + "levelName" : "plot" + }, { + "levelCode" : "Plot_456", + "levelName" : "plot" + }, { + "levelCode" : "Plot_789", + "levelName" : "plot" + } ], + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevel_1" + }, "nullable" : true, - "type" : "string" + "type" : "array" }, - "value" : { - "description" : "The single value of this event parameter. This single value is accurate for all the dates in the date range. If 'value' is populated then 'valuesByDate' should NOT be populated.", - "example" : "TI001", + "observationTimeStampRangeEnd" : { + "description" : "Timestamp range end", + "format" : "date-time", "nullable" : true, "type" : "string" }, - "valueDescription" : { - "description" : "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value.", - "example" : "Standard V-Ripper (TI001)", + "observationTimeStampRangeStart" : { + "description" : "Timestamp range start", + "format" : "date-time", "nullable" : true, "type" : "string" }, - "valuesByDate" : { - "description" : "An array of values corresponding to each timestamp in the 'discreteDates' array of this event. The 'valuesByDate' array should exactly match the size of the 'discreteDates' array. If 'valuesByDate' is populated then 'value' should NOT be populated.", - "example" : [ "20", "50", "40" ], + "observationUnitDbIds" : { + "description" : "The unique id of an Observation Unit", + "example" : [ "76f559b5", "066bc5d3" ], "items" : { "type" : "string" }, "nullable" : true, "type" : "array" - } - }, - "type" : "object" - }, - "Germplasm_donors_inner" : { - "properties" : { - "donorAccessionNumber" : { - "description" : "The accession number assigned by the donor\n \nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", - "example" : "A0000123", - "nullable" : true, - "type" : "string" }, - "donorInstituteCode" : { - "description" : "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", - "example" : "PER001", + "observationVariableDbIds" : { + "description" : "The DbIds of Variables to search for", + "example" : [ "a646187d", "6d23513b" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "observationVariableNames" : { + "description" : "The names of Variables to search for", + "example" : [ "Plant Height in meters", "Wheat rust score 1-5" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "observationVariablePUIs" : { + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "example" : [ "http://my-traits.com/trait/CO_123:0008012", "http://my-traits.com/trait/CO_123:0007261" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "page" : { + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "example" : 0, + "type" : "integer" + }, + "pageSize" : { + "description" : "The size of the pages to be returned. Default is `1000`.", + "example" : 1000, + "type" : "integer" + }, + "programDbIds" : { + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "example" : [ "8f5de35b", "0e2d4a13" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "programNames" : { + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "example" : [ "Better Breeding Program", "Best Breeding Program" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "seasonDbIds" : { + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "example" : [ "Spring 2018", "Season A" ], + "items" : { + "type" : "string" + }, "nullable" : true, - "type" : "string" + "type" : "array" + }, + "studyDbIds" : { + "description" : "List of study identifiers to search for", + "example" : [ "cf6c4bd4", "691e69d6" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "studyNames" : { + "description" : "List of study names to filter search results", + "example" : [ "The First Bob Study 2017", "Wheat Yield Trial 246" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "trialDbIds" : { + "description" : "The ID which uniquely identifies a trial to search for", + "example" : [ "d2593dc2", "9431a731" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "trialNames" : { + "description" : "The human readable name of a trial to search for", + "example" : [ "All Yield Trials 2016", "Disease Resistance Study Comparison Group" ], + "items" : { + "type" : "string" + }, + "type" : "array" } }, "type" : "object" }, - "GeoJSON" : { - "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "nullable" : true, + "StudyListResponse_result" : { "properties" : { - "geometry" : { - "$ref" : "#/components/schemas/GeoJSON_Geometry" - }, - "type" : { - "default" : "Feature", - "description" : "The literal string \"Feature\"", - "example" : "Feature", - "type" : "string" + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Study" + }, + "type" : "array" } }, - "title" : "GeoJSON", + "required" : [ "data" ], "type" : "object" }, - "Germplasm_germplasmOrigin_inner" : { - "description" : "MIAPPE V1.1 (DM-52) \n\nMIAPPE V1.1 (DM-53) \n\nMIAPPE V1.1 (DM-54) \n\nMIAPPE V1.1 (DM-55)\n\nMCPD (v2.1) (COORDUNCERT) 15.5 \n\nMCPD (v2.1) (ELEVATION) 16. \n\nMCPD (v2.1) (GEOREFMETH) 15.7 \n\nMCPD (v2.1) (DECLATITUDE) 15.1 \n\nMCPD (v2.1) (DECLONGITUDE) 15.3 ", + "StudyListResponse" : { "properties" : { - "coordinateUncertainty" : { - "description" : "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", - "example" : "20", - "nullable" : true, - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "coordinates" : { - "$ref" : "#/components/schemas/GeoJSON" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/StudyListResponse_result" } }, + "required" : [ "metadata", "result" ], + "title" : "StudyListResponse", "type" : "object" }, - "Germplasm_storageTypes_inner" : { + "TrialListResponse_result" : { "properties" : { - "code" : { - "description" : "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", - "enum" : [ "10", "11", "12", "13", "20", "30", "40", "50", "99" ], - "example" : "11", - "nullable" : true, - "type" : "string" - }, - "description" : { - "description" : "A supplemental text description of the storage type", - "example" : "Short term", - "nullable" : true, - "type" : "string" + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Trial" + }, + "type" : "array" } }, + "required" : [ "data" ], "type" : "object" }, - "Germplasm_synonyms_inner" : { + "TrialListResponse" : { "properties" : { - "synonym" : { - "description" : "Alternative name or ID used to reference this germplasm", - "example" : "variety_1", - "nullable" : true, - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "type" : { - "description" : "A descriptive classification for this synonym", - "example" : "Pre-Code", - "nullable" : true, - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/TrialListResponse_result" } }, + "required" : [ "metadata", "result" ], + "title" : "TrialListResponse", "type" : "object" }, - "Germplasm_taxonIds_inner" : { + "ObservationVariableListResponse_result" : { "properties" : { - "sourceName" : { - "description" : "The human readable name of the taxonomy provider", - "example" : "NCBI", - "type" : "string" - }, - "taxonId" : { - "description" : "The identifier (name, ID, URI) of a particular taxonomy within the source provider", - "example" : "2026747", - "type" : "string" + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/ObservationVariable" + }, + "type" : "array" } }, - "required" : [ "sourceName", "taxonId" ], + "required" : [ "data" ], "type" : "object" }, - "GermplasmAttribute_method_ontologyReference_documentationLinks_inner" : { + "ObservationVariableListResponse" : { "properties" : { - "URL" : { - "example" : "http://purl.obolibrary.org/obo/ro.owl", - "format" : "uri", - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "type" : { - "enum" : [ "OBO", "RDF", "WEBPAGE" ], - "example" : "OBO", - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ObservationVariableListResponse_result" } }, + "required" : [ "metadata", "result" ], + "title" : "ObservationVariableListResponse", "type" : "object" }, - "GermplasmAttribute_method_ontologyReference" : { - "description" : "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", + "VariantsListResponseResult" : { "properties" : { - "documentationLinks" : { - "description" : "links to various ontology documentation", + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference_documentationLinks_inner" + "$ref" : "#/components/schemas/Variant" }, - "nullable" : true, "type" : "array" - }, - "ontologyDbId" : { - "description" : "Ontology database unique identifier", - "example" : "6b071868", - "type" : "string" - }, - "ontologyName" : { - "description" : "Ontology name", - "example" : "The Crop Ontology", - "type" : "string" - }, - "version" : { - "description" : "Ontology version (no specific format)", - "example" : "7.2.3", - "nullable" : true, - "type" : "string" } }, - "required" : [ "ontologyDbId", "ontologyName" ], + "required" : [ "data" ], + "title" : "VariantsListResponseResult", "type" : "object" }, - "GermplasmAttribute_method" : { - "description" : "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". ", + "VariantsListResponse" : { "properties" : { - "additionalInfo" : { - "additionalProperties" : { - "type" : "string" - }, - "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "nullable" : true, - "type" : "object" - }, - "bibliographicalReference" : { - "description" : "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method.", - "example" : "Smith, 1893, Really Cool Paper, Popular Journal", - "nullable" : true, - "type" : "string" - }, - "description" : { - "description" : "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)", - "example" : "A measuring tape was used", - "nullable" : true, - "type" : "string" - }, - "externalReferences" : { - "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "example" : [ { - "referenceId" : "doi:10.155454/12341234", - "referenceSource" : "DOI" - }, { - "referenceId" : "75a50e76", - "referenceSource" : "Remote Data Collection Upload Tool" - } ], - "items" : { - "$ref" : "#/components/schemas/ExternalReferences_1_inner" - }, - "nullable" : true, - "title" : "ExternalReferences", - "type" : "array" - }, - "formula" : { - "description" : "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation", - "example" : "a^2 + b^2 = c^2", - "nullable" : true, - "type" : "string" - }, - "methodClass" : { - "description" : "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)", - "example" : "Measurement", - "nullable" : true, - "type" : "string" - }, - "methodDbId" : { - "description" : "Method unique identifier", - "example" : "0adb2764", - "type" : "string" - }, - "methodName" : { - "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", - "example" : "Measuring Tape", - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "methodPUI" : { - "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", - "example" : "http://my-traits.com/trait/CO_123:0000212", - "nullable" : true, - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadataTokenPagination" }, - "ontologyReference" : { - "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference" + "result" : { + "$ref" : "#/components/schemas/VariantsListResponseResult" } }, - "required" : [ "methodName" ], + "required" : [ "metadata", "result" ], + "title" : "VariantsListResponse", "type" : "object" }, - "GermplasmAttribute_ontologyReference" : { - "description" : "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", - "nullable" : true, + "VariantSetsListResponseResult" : { "properties" : { - "documentationLinks" : { - "description" : "links to various ontology documentation", + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference_documentationLinks_inner" + "$ref" : "#/components/schemas/VariantSet" }, - "nullable" : true, "type" : "array" - }, - "ontologyDbId" : { - "description" : "Ontology database unique identifier", - "example" : "6b071868", - "type" : "string" - }, - "ontologyName" : { - "description" : "Ontology name", - "example" : "The Crop Ontology", - "type" : "string" - }, - "version" : { - "description" : "Ontology version (no specific format)", - "example" : "7.2.3", - "nullable" : true, - "type" : "string" } }, - "required" : [ "ontologyDbId", "ontologyName" ], + "required" : [ "data" ], + "title" : "VariantSetsListResponseResult", "type" : "object" }, - "GermplasmAttribute_scale_validValues_categories_inner" : { + "VariantSetsListResponse" : { "properties" : { - "label" : { - "description" : "A text label for a category", - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "value" : { - "description" : "The actual value for a category", - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/VariantSetsListResponseResult" } }, + "required" : [ "metadata", "result" ], + "title" : "VariantSetsListResponse", "type" : "object" }, - "GermplasmAttribute_scale_validValues" : { - "nullable" : true, + "SeasonListResponse_result" : { "properties" : { - "categories" : { - "description" : "List of possible values with optional labels", - "example" : [ { - "label" : "low", - "value" : "0" - }, { - "label" : "medium", - "value" : "5" - }, { - "label" : "high", - "value" : "10" - } ], - "items" : { - "$ref" : "#/components/schemas/GermplasmAttribute_scale_validValues_categories_inner" - }, - "type" : "array" - }, - "max" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `maximumValue`. Github issue number #450 \n
Maximum value for numerical scales. Typically used for data capture control and QC.", - "example" : 9999, - "nullable" : true, - "type" : "integer" - }, - "maximumValue" : { - "description" : "Maximum value for numerical, date, and time scales. Typically used for data capture control and QC.", - "example" : "9999", - "nullable" : true, - "type" : "string" - }, - "min" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `minimumValue`. Github issue number #450 \n
Minimum value for numerical scales. Typically used for data capture control and QC.", - "example" : 2, - "nullable" : true, - "type" : "integer" - }, - "minimumValue" : { - "description" : "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC.", - "example" : "2", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "GermplasmAttribute_scale" : { - "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\".", - "properties" : { - "additionalInfo" : { - "additionalProperties" : { - "type" : "string" - }, - "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "nullable" : true, - "type" : "object" - }, - "dataType" : { - "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", - "enum" : [ "Code", "Date", "Duration", "Nominal", "Numerical", "Ordinal", "Text" ], - "example" : "Numerical", - "nullable" : true, - "type" : "string" - }, - "decimalPlaces" : { - "description" : "For numerical, number of decimal places to be reported", - "example" : 2, - "nullable" : true, - "type" : "integer" - }, - "externalReferences" : { - "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "example" : [ { - "referenceId" : "doi:10.155454/12341234", - "referenceSource" : "DOI" - }, { - "referenceId" : "75a50e76", - "referenceSource" : "Remote Data Collection Upload Tool" - } ], - "items" : { - "$ref" : "#/components/schemas/ExternalReferences_1_inner" - }, - "nullable" : true, - "title" : "ExternalReferences", - "type" : "array" - }, - "ontologyReference" : { - "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference" - }, - "scaleDbId" : { - "description" : "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID.", - "example" : "af730171", - "type" : "string" - }, - "scaleName" : { - "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", - "example" : "Meters", - "nullable" : true, - "type" : "string" - }, - "scalePUI" : { - "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", - "example" : "http://my-traits.com/trait/CO_123:0000112", - "nullable" : true, - "type" : "string" - }, - "units" : { - "description" : "This field can be used to describe the units used for this scale. This should be the abbreviated \nform of the units, intended to be displayed with every value using this scale. Usually this only \napplies when `dataType` is Numeric, but could also be included for other dataTypes when applicable.", - "example" : "m", - "nullable" : true, - "type" : "string" - }, - "validValues" : { - "$ref" : "#/components/schemas/GermplasmAttribute_scale_validValues" - } - }, - "required" : [ "scaleDbId", "scaleName" ], - "type" : "object" - }, - "GermplasmAttribute_trait" : { - "description" : "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". ", - "properties" : { - "additionalInfo" : { - "additionalProperties" : { - "type" : "string" - }, - "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "nullable" : true, - "type" : "object" - }, - "alternativeAbbreviations" : { - "description" : "A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention.", - "example" : [ "H", "PH", "H1" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "attribute" : { - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", - "example" : "height", - "nullable" : true, - "type" : "string" - }, - "attributePUI" : { - "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", - "example" : "http://my-traits.com/trait/PO:00012345", - "nullable" : true, - "type" : "string" - }, - "entity" : { - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", - "example" : "Stalk", - "nullable" : true, - "type" : "string" - }, - "entityPUI" : { - "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", - "example" : "http://my-traits.com/trait/PATO:00098765", - "nullable" : true, - "type" : "string" - }, - "externalReferences" : { - "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "example" : [ { - "referenceId" : "doi:10.155454/12341234", - "referenceSource" : "DOI" - }, { - "referenceId" : "75a50e76", - "referenceSource" : "Remote Data Collection Upload Tool" - } ], - "items" : { - "$ref" : "#/components/schemas/ExternalReferences_1_inner" - }, - "nullable" : true, - "title" : "ExternalReferences", - "type" : "array" - }, - "mainAbbreviation" : { - "description" : "A shortened version of the human readable name for a Trait", - "example" : "PH", - "nullable" : true, - "type" : "string" - }, - "ontologyReference" : { - "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference" - }, - "status" : { - "description" : "Trait status (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", - "example" : "recommended", - "nullable" : true, - "type" : "string" - }, - "synonyms" : { - "description" : "Other trait names", - "example" : [ "Height", "Plant Height", "Stalk Height", "Canopy Height" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "traitClass" : { - "description" : "A classification to describe the type of trait and the context it should be considered in.\n
examples- \"morphological\", \"phenological\", \"agronomical\", \"physiological\", \"abiotic stress\", \"biotic stress\", \"biochemical\", \"quality traits\", \"fertility\", etc.", - "example" : "phenological", - "nullable" : true, - "type" : "string" - }, - "traitDbId" : { - "description" : "The ID which uniquely identifies a trait", - "example" : "9b2e34f5", - "type" : "string" - }, - "traitDescription" : { - "description" : "The description of a trait", - "example" : "The height of the plant", - "nullable" : true, - "type" : "string" - }, - "traitName" : { - "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", - "example" : "Height", - "type" : "string" - }, - "traitPUI" : { - "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", - "example" : "http://my-traits.com/trait/CO_123:0000012", - "nullable" : true, - "type" : "string" - } - }, - "required" : [ "traitName" ], - "type" : "object" - }, - "GermplasmMCPD_breedingInstitutes_inner" : { - "properties" : { - "instituteCode" : { - "description" : "MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.", - "example" : "PER001", - "nullable" : true, - "type" : "string" - }, - "instituteName" : { - "description" : "MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available.", - "example" : "The BrAPI Institute", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "GermplasmMCPD_collectingInfo_collectingInstitutes_inner" : { - "properties" : { - "instituteAddress" : { - "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", - "example" : "123 Main Street, Lima, Peru, 5555", - "nullable" : true, - "type" : "string" - }, - "instituteCode" : { - "description" : "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.", - "example" : "PER001", - "nullable" : true, - "type" : "string" - }, - "instituteName" : { - "description" : "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", - "example" : "The BrAPI Institute", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "GermplasmMCPD_collectingInfo_collectingSite" : { - "description" : "Information about the location where the sample was collected", - "nullable" : true, - "properties" : { - "coordinateUncertainty" : { - "description" : "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.", - "example" : "20", - "nullable" : true, - "type" : "string" - }, - "elevation" : { - "description" : "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.", - "example" : "35", - "nullable" : true, - "type" : "string" - }, - "georeferencingMethod" : { - "description" : "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.", - "example" : "WGS84", - "nullable" : true, - "type" : "string" - }, - "latitudeDecimal" : { - "description" : "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).", - "example" : "+42.445295", - "nullable" : true, - "type" : "string" - }, - "latitudeDegrees" : { - "description" : "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10", - "example" : "42 26 43.1 N", - "nullable" : true, - "type" : "string" - }, - "locationDescription" : { - "description" : "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).", - "example" : "South east hill near institute buildings", - "nullable" : true, - "type" : "string" - }, - "longitudeDecimal" : { - "description" : "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).", - "example" : "-076.471934", - "nullable" : true, - "type" : "string" - }, - "longitudeDegrees" : { - "description" : "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076", - "example" : "76 28 19.0 W", - "nullable" : true, - "type" : "string" - }, - "spatialReferenceSystem" : { - "description" : "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.", - "example" : "WGS84", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "GermplasmMCPD_collectingInfo" : { - "description" : "Information about the collection of a germplasm", - "properties" : { - "collectingDate" : { - "description" : "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", - "format" : "date", - "nullable" : true, - "type" : "string" - }, - "collectingInstitutes" : { - "description" : "Institutes which collected the sample", - "items" : { - "$ref" : "#/components/schemas/GermplasmMCPD_collectingInfo_collectingInstitutes_inner" - }, - "nullable" : true, - "type" : "array" - }, - "collectingMissionIdentifier" : { - "description" : "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\").", - "example" : "CIATFOR_052", - "nullable" : true, - "type" : "string" - }, - "collectingNumber" : { - "description" : "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections.", - "example" : "ab109909", - "nullable" : true, - "type" : "string" - }, - "collectingSite" : { - "$ref" : "#/components/schemas/GermplasmMCPD_collectingInfo_collectingSite" - } - }, - "type" : "object" - }, - "GermplasmMCPD_donorInfo_donorInstitute" : { - "description" : "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", - "properties" : { - "instituteCode" : { - "description" : "MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", - "example" : "PER001", - "nullable" : true, - "type" : "string" - }, - "instituteName" : { - "description" : "MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", - "example" : "The BrAPI Institute", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "GermplasmMCPD_donorInfo" : { - "description" : "Information about an accession donor", - "properties" : { - "donorAccessionNumber" : { - "description" : "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", - "example" : "A0090204", - "nullable" : true, - "type" : "string" - }, - "donorAccessionPui" : { - "description" : "PUI (DOI mostly) of the accession in the donor system.", - "example" : "http://pui.per/accession/A0010025", - "nullable" : true, - "type" : "string" - }, - "donorInstitute" : { - "$ref" : "#/components/schemas/GermplasmMCPD_donorInfo_donorInstitute" - } - }, - "type" : "object" - }, - "GermplasmMCPD_safetyDuplicateInstitutes_inner" : { - "properties" : { - "instituteCode" : { - "description" : "MCPD (v2.1) (DUPLSITE) 25. FAO WIEWS code of the institute(s) where a safety duplicate of the accession is maintained. Follows INSTCODE standard.", - "example" : "PER001", - "nullable" : true, - "type" : "string" - }, - "instituteName" : { - "description" : "MCPD (v2.1) (DUPLINSTNAME) 25.1 Name of the institute where a safety duplicate of the accession is maintained.", - "example" : "The BrAPI Institute", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "ListValue_values_inner" : { - "oneOf" : [ { - "description" : "Represents a boolean value.", - "format" : "boolean", - "type" : "boolean" - }, { - "description" : "Represents a double value.", - "format" : "double", - "type" : "number" - }, { - "description" : "Represents a string value.", - "type" : "string" - } ] - }, - "GeoJSONSearchArea_1" : { - "description" : "A GeoJSON Polygon which describes an area to search for other GeoJSON objects. All contained Points and intersecting Polygons should be returned as search results. \n\nAll coordinates are decimal values on the WGS84 geographic coordinate reference system.", - "example" : { - "geometry" : { - "coordinates" : [ [ [ -77.456654, 42.241133 ], [ -75.414133, 41.508282 ], [ -76.506042, 42.417373 ], [ -77.456654, 42.241133 ] ] ], - "type" : "Polygon" - }, - "type" : "Feature" - }, - "nullable" : true, - "properties" : { - "geometry" : { - "$ref" : "#/components/schemas/GeoJSON_Geometry" - }, - "type" : { - "default" : "Feature", - "description" : "The literal string \"Feature\"", - "example" : "Feature", - "type" : "string" - } - }, - "title" : "GeoJSONSearchArea", - "type" : "object" - }, - "Observation_season" : { - "nullable" : true, - "properties" : { - "season" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `seasonName`. Github issue number #456 \n
Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.", - "example" : "Spring", - "nullable" : true, - "type" : "string" - }, - "seasonDbId" : { - "description" : "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'", - "example" : "Spring_2018", - "nullable" : true, - "type" : "string" - }, - "seasonName" : { - "description" : "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.", - "example" : "Spring", - "nullable" : true, - "type" : "string" - }, - "year" : { - "description" : "The 4 digit year of the season.", - "example" : 2018, - "nullable" : true, - "type" : "integer" - } - }, - "required" : [ "seasonDbId" ], - "type" : "object" - }, - "ObservationTable_observationVariables_inner" : { - "properties" : { - "observationVariableDbId" : { - "description" : "Variable unique identifier", - "example" : "367aa1a9", - "type" : "string" - }, - "observationVariableName" : { - "description" : "Variable name (usually a short name)", - "example" : "Plant height", - "type" : "string" - } - }, - "type" : "object" - }, - "ObservationUnitLevel_2" : { - "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", - "properties" : { - "levelCode" : { - "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", - "example" : "Plot_123", - "nullable" : true, - "type" : "string" - }, - "levelName" : { - "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : "plot", - "nullable" : true, - "type" : "string" - }, - "levelOrder" : { - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : 2, - "nullable" : true, - "type" : "integer" - } - }, - "title" : "ObservationUnitLevel", - "type" : "object" - }, - "ObservationUnit_observationUnitPosition" : { - "description" : "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section.", - "nullable" : true, - "properties" : { - "entryType" : { - "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", - "enum" : [ "CHECK", "TEST", "FILLER" ], - "example" : "TEST", - "nullable" : true, - "type" : "string" - }, - "geoCoordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "observationLevel" : { - "$ref" : "#/components/schemas/ObservationUnitLevel_2" - }, - "observationLevelRelationships" : { - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", - "example" : [ { - "levelCode" : "Field_1", - "levelName" : "field", - "levelOrder" : 0 - }, { - "levelCode" : "Block_12", - "levelName" : "block", - "levelOrder" : 1 - }, { - "levelCode" : "Plot_123", - "levelName" : "plot", - "levelOrder" : 2 - } ], - "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" - }, - "nullable" : true, - "type" : "array" - }, - "positionCoordinateX" : { - "description" : "The X position coordinate for an observation unit. Different systems may use different coordinate systems.", - "example" : "74", - "nullable" : true, - "type" : "string" - }, - "positionCoordinateXType" : { - "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independant or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", - "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ], - "example" : "GRID_COL", - "nullable" : true, - "type" : "string" - }, - "positionCoordinateY" : { - "description" : "The Y position coordinate for an observation unit. Different systems may use different coordinate systems.", - "example" : "03", - "nullable" : true, - "type" : "string" - }, - "positionCoordinateYType" : { - "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independant or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", - "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ], - "example" : "GRID_ROW", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "Observation_1" : { - "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit.", - "properties" : { - "additionalInfo" : { - "additionalProperties" : { - "type" : "string" - }, - "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "nullable" : true, - "type" : "object" - }, - "collector" : { - "description" : "The name or identifier of the entity which collected the observation", - "example" : "917d3ae0", - "nullable" : true, - "type" : "string" - }, - "externalReferences" : { - "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "example" : [ { - "referenceId" : "doi:10.155454/12341234", - "referenceSource" : "DOI" - }, { - "referenceId" : "75a50e76", - "referenceSource" : "Remote Data Collection Upload Tool" - } ], - "items" : { - "$ref" : "#/components/schemas/ExternalReferences_1_inner" - }, - "nullable" : true, - "title" : "ExternalReferences", - "type" : "array" - }, - "geoCoordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "germplasmDbId" : { - "description" : "The ID which uniquely identifies a germplasm", - "example" : "2408ab11", - "nullable" : true, - "type" : "string" - }, - "germplasmName" : { - "description" : "Name of the germplasm. It can be the preferred name and does not have to be unique.", - "example" : "A0000003", - "nullable" : true, - "type" : "string" - }, - "observationDbId" : { - "description" : "The ID which uniquely identifies an observation", - "example" : "ef24b615", - "type" : "string" - }, - "observationTimeStamp" : { - "description" : "The date and time when this observation was made", - "format" : "date-time", - "nullable" : true, - "type" : "string" - }, - "observationUnitDbId" : { - "description" : "The ID which uniquely identifies an observation unit", - "example" : "598111d4", - "nullable" : true, - "type" : "string" - }, - "observationUnitName" : { - "description" : "A human readable name for an observation unit", - "example" : "Plot 1", - "nullable" : true, - "type" : "string" - }, - "observationVariableDbId" : { - "description" : "The ID which uniquely identifies an observation variable", - "example" : "c403d107", - "nullable" : true, - "type" : "string" - }, - "observationVariableName" : { - "description" : "A human readable name for an observation variable", - "example" : "Plant Height in meters", - "nullable" : true, - "type" : "string" - }, - "season" : { - "$ref" : "#/components/schemas/Observation_season" - }, - "studyDbId" : { - "description" : "The ID which uniquely identifies a study within the given database server", - "example" : "ef2829db", - "nullable" : true, - "type" : "string" - }, - "uploadedBy" : { - "description" : "The name or id of the user who uploaded the observation to the database system", - "example" : "a2f7f60b", - "nullable" : true, - "type" : "string" - }, - "value" : { - "description" : "The value of the data collected as an observation", - "example" : "2.3", - "nullable" : true, - "type" : "string" - } - }, - "required" : [ "observationDbId" ], - "title" : "Observation", - "type" : "object", - "x-brapi-metadata" : { - "module" : "BrAPI-Phenotyping", - "primaryModel" : true - } - }, - "ObservationUnit_treatments_inner" : { - "properties" : { - "factor" : { - "description" : "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.", - "example" : "fertilizer", - "nullable" : true, - "type" : "string" - }, - "modality" : { - "description" : "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ", - "example" : "low fertilizer", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "PedigreeNode_parents_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "The ID which uniquely identifies a germplasm", - "example" : "a55847ed", - "type" : "string" - }, - "germplasmName" : { - "description" : "A human readable name for a germplasm", - "example" : "A0000592", - "nullable" : true, - "type" : "string" - }, - "parentType" : { - "$ref" : "#/components/schemas/ParentType" - } - }, - "required" : [ "germplasmDbId", "parentType" ], - "type" : "object" - }, - "PedigreeNode_siblings_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "The ID which uniquely identifies a germplasm", - "example" : "a55847ed", - "type" : "string" - }, - "germplasmName" : { - "description" : "A human readable name for a germplasm", - "example" : "A0000592", - "nullable" : true, - "type" : "string" - } - }, - "required" : [ "germplasmDbId" ], - "type" : "object" - }, - "PedigreeNodeDEP_parents_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "The germplasm DbId of the parent of this germplasm", - "example" : "a55847ed", - "type" : "string" - }, - "germplasmName" : { - "description" : "the human readable name of the parent of this germplasm", - "example" : "A0000592", - "nullable" : true, - "type" : "string" - }, - "parentType" : { - "$ref" : "#/components/schemas/ParentTypeDEP" - } - }, - "type" : "object" - }, - "PedigreeNodeDEP_siblings_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "the germplasm DbId of the sibling", - "type" : "string" - }, - "germplasmName" : { - "description" : "the germplasm name of the sibling", - "type" : "string" - } - }, - "type" : "object" - }, - "ProgenyNodeDEP_progeny_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "The unique identifier of a progeny germplasm", - "example" : "e8d5dad7", - "type" : "string" - }, - "germplasmName" : { - "description" : "The human readable name of a progeny germplasm", - "example" : "A0021011", - "nullable" : true, - "type" : "string" - }, - "parentType" : { - "$ref" : "#/components/schemas/ParentTypeDEP" - } - }, - "required" : [ "germplasmDbId", "parentType" ], - "type" : "object" - }, - "Reference_sourceGermplasm_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "The ID which uniquely identifies a `Germplasm` within the given database server", - "example" : "d4076594", - "type" : "string" - }, - "germplasmName" : { - "description" : "The human readable name of a `Germplasm`", - "example" : "A0000003", - "type" : "string" - } - }, - "type" : "object" - }, - "ReferenceSet_sourceGermplasm_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "The ID which uniquely identifies a germplasm within the given database server", - "example" : "d4076594", - "type" : "string" - }, - "germplasmName" : { - "description" : "The human readable name of a germplasm", - "example" : "A0000003", - "type" : "string" - } - }, - "type" : "object" - }, - "SeedLot_contentMixture_inner" : { - "properties" : { - "crossDbId" : { - "description" : "The unique DbId for a cross contained in this seed lot", - "example" : "d105fd6f", - "nullable" : true, - "type" : "string" - }, - "crossName" : { - "description" : "The human readable name for a cross contained in this seed lot", - "example" : "my_Crosses_2018_01", - "nullable" : true, - "type" : "string" - }, - "germplasmDbId" : { - "description" : "The unique DbId of the Germplasm contained in this Seed Lot", - "example" : "029d705d", - "nullable" : true, - "type" : "string" - }, - "germplasmName" : { - "description" : "The human readable name of the Germplasm contained in this Seed Lot", - "example" : "A0000003", - "nullable" : true, - "type" : "string" - }, - "mixturePercentage" : { - "description" : "The percentage of the given germplasm in the seed lot mixture.", - "example" : 100, - "nullable" : true, - "type" : "integer" - } - }, - "type" : "object" - }, - "Study_contacts_inner" : { - "properties" : { - "contactDbId" : { - "description" : "The ID which uniquely identifies this contact\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.", - "example" : "5f4e5509", - "type" : "string" - }, - "email" : { - "description" : "The contacts email address\n\nMIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person.", - "example" : "bob@bob.com", - "nullable" : true, - "type" : "string" - }, - "instituteName" : { - "description" : "The name of the institution which this contact is part of\n\nMIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to", - "example" : "The BrAPI Institute", - "nullable" : true, - "type" : "string" - }, - "name" : { - "description" : "The full name of this contact person\n\nMIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)", - "example" : "Bob Robertson", - "nullable" : true, - "type" : "string" - }, - "orcid" : { - "description" : "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.", - "example" : "http://orcid.org/0000-0001-8640-1750", - "nullable" : true, - "type" : "string" - }, - "type" : { - "description" : "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation", - "example" : "PI", - "nullable" : true, - "type" : "string" - } - }, - "required" : [ "contactDbId" ], - "type" : "object" - }, - "Study_dataLinks_inner" : { - "properties" : { - "dataFormat" : { - "description" : "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", - "example" : "Image Archive", - "nullable" : true, - "type" : "string" - }, - "description" : { - "description" : "The general description of this data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", - "example" : "Raw drone images collected for this study", - "nullable" : true, - "type" : "string" - }, - "fileFormat" : { - "description" : "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", - "example" : "application/zip", - "nullable" : true, - "type" : "string" - }, - "name" : { - "description" : "The name of the external data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", - "example" : "image-archive.zip", - "nullable" : true, - "type" : "string" - }, - "provenance" : { - "description" : "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow.", - "example" : "Image Processing Pipeline, built at the University of Antarctica: https://github.com/antarctica/pipeline", - "nullable" : true, - "type" : "string" - }, - "scientificType" : { - "description" : "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc", - "example" : "Environmental", - "nullable" : true, - "type" : "string" - }, - "url" : { - "description" : "URL describing the location of this data file to view or download\n\nMIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission.", - "example" : "https://brapi.org/image-archive.zip", - "format" : "uri", - "nullable" : true, - "type" : "string" - }, - "version" : { - "description" : "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data).", - "example" : "1.0.3", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "Study_environmentParameters_inner" : { - "properties" : { - "description" : { - "description" : "Human-readable value of the environment parameter (defined above) constant within the experiment", - "example" : "the soil type was clay", - "type" : "string" - }, - "parameterName" : { - "description" : "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. ", - "example" : "soil type", - "type" : "string" - }, - "parameterPUI" : { - "description" : "URI pointing to an ontology class for the parameter", - "example" : "PECO:0007155", - "nullable" : true, - "type" : "string" - }, - "unit" : { - "description" : "Unit of the value for this parameter", - "example" : "pH", - "nullable" : true, - "type" : "string" - }, - "unitPUI" : { - "description" : "URI pointing to an ontology class for the unit", - "example" : "PECO:0007059", - "nullable" : true, - "type" : "string" - }, - "value" : { - "description" : "Numerical or categorical value\n\nMIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment.", - "example" : "clay soil", - "nullable" : true, - "type" : "string" - }, - "valuePUI" : { - "description" : "URI pointing to an ontology class for the parameter value", - "example" : "ENVO:00002262", - "nullable" : true, - "type" : "string" - } - }, - "required" : [ "description", "parameterName" ], - "type" : "object" - }, - "Study_experimentalDesign" : { - "description" : "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology", - "nullable" : true, - "properties" : { - "PUI" : { - "description" : "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.", - "example" : "CO_715:0000145", - "nullable" : true, - "type" : "string" - }, - "description" : { - "description" : "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.", - "example" : "Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information.", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "Study_growthFacility" : { - "description" : "Short description of the facility in which the study was carried out.", - "nullable" : true, - "properties" : { - "PUI" : { - "description" : "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.", - "example" : "CO_715:0000162", - "type" : "string" - }, - "description" : { - "description" : "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.", - "example" : "field environment condition, greenhouse", - "type" : "string" - } - }, - "type" : "object" - }, - "Study_lastUpdate" : { - "description" : "The date and time when this study was last modified", - "nullable" : true, - "properties" : { - "timestamp" : { - "format" : "date-time", - "nullable" : true, - "type" : "string" - }, - "version" : { - "example" : "1.2.3", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "ObservationUnitHierarchyLevel_1" : { - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "properties" : { - "levelName" : { - "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : "plot", - "nullable" : true, - "type" : "string" - }, - "levelOrder" : { - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : 2, - "nullable" : true, - "type" : "integer" - } - }, - "title" : "ObservationUnitHierarchyLevel", - "type" : "object" - }, - "Trial_datasetAuthorships_inner" : { - "properties" : { - "datasetPUI" : { - "description" : "The DOI or other permanent unique identifier for this published dataset", - "example" : "doi:10.15454/312953986E3", - "nullable" : true, - "type" : "string" - }, - "license" : { - "description" : "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended.", - "example" : "https://CreativeCommons.org/licenses/by/4.0", - "nullable" : true, - "type" : "string" - }, - "publicReleaseDate" : { - "description" : "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described.", - "format" : "date", - "nullable" : true, - "type" : "string" - }, - "submissionDate" : { - "description" : "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository.", - "format" : "date", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, - "Trial_publications_inner" : { - "properties" : { - "publicationPUI" : { - "example" : "doi:10.15454/312953986E3", - "nullable" : true, - "type" : "string" - }, - "publicationReference" : { - "example" : "Selby, BrAPI - An application programming interface for plant breeding applications, Bioinformatics, https://doi.org/10.1093/bioinformatics/190", - "nullable" : true, - "type" : "string" + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Season" + }, + "type" : "array" } }, + "required" : [ "data" ], "type" : "object" }, - "VariantSet_metadataFields_inner" : { - "description" : "This represents a type of genotyping data or metadata available in this VariantSet", - "nullable" : true, + "SeasonListResponse" : { "properties" : { - "dataType" : { - "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", - "enum" : [ "string", "integer", "float", "boolean" ], - "example" : "integer", - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "fieldAbbreviation" : { - "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"", - "example" : "GQ", - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "fieldName" : { - "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"", - "example" : "Genotype Quality", - "type" : "string" + "result" : { + "$ref" : "#/components/schemas/SeasonListResponse_result" } }, + "required" : [ "metadata", "result" ], + "title" : "SeasonListResponse", "type" : "object" }, - "ShipmentForm" : { + "SeasonSingleResponse" : { "properties" : { - "fileDescription" : { - "description" : "The human readable long description for this form", - "example" : "This is a shipment manifest form", - "nullable" : true, - "type" : "string" - }, - "fileName" : { - "description" : "The human readable name for this form", - "example" : "Shipment Manifest", - "nullable" : true, - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "fileURL" : { - "description" : "The URL to download this form", - "example" : "https://vendor.org/forms/manifest.pdf", - "format" : "uri", - "nullable" : true, - "type" : "string" - } - }, - "required" : [ "fileURL" ], - "title" : "ShipmentForm", - "type" : "object" - }, - "VendorOrderSubmissionRequest_plates_inner_samples_inner_concentration" : { - "description" : "A value with units", - "properties" : { - "units" : { - "description" : "Units (example: \"ng/ul\")", - "example" : "ng/ul", - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "value" : { - "description" : "Value (example: \"2.3\")", - "example" : 2.3, - "type" : "number" + "result" : { + "$ref" : "#/components/schemas/Season" } }, + "required" : [ "metadata", "result" ], + "title" : "SeasonSingleResponse", "type" : "object" }, - "VendorOrderSubmissionRequest_plates_inner_samples_inner_volume" : { - "description" : "A value with units", - "nullable" : true, + "SeedLotListResponse_result" : { "properties" : { - "units" : { - "description" : "Units (example: \"ng/ul\")", - "example" : "ng/ul", - "type" : "string" - }, - "value" : { - "description" : "Value (example: \"2.3\")", - "example" : 2.3, - "type" : "number" + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/SeedLot" + }, + "type" : "array" } }, + "required" : [ "data" ], "type" : "object" }, - "VendorOrderSubmissionRequest_plates_inner_samples_inner" : { + "SeedLotListResponse" : { "properties" : { - "clientSampleBarCode" : { - "description" : "(Optional) The value of the bar code attached to this sample", - "example" : "7c07e527", - "nullable" : true, - "type" : "string" - }, - "clientSampleId" : { - "description" : "The ID which uniquely identifies this sample to the client making the request", - "example" : "bd96bd69", - "type" : "string" - }, - "column" : { - "description" : "The Column identifier for this samples location in the plate", - "example" : 6, - "maximum" : 12, - "minimum" : 1, - "nullable" : true, - "type" : "integer" - }, - "comments" : { - "description" : "Generic comments about this sample for the vendor", - "example" : "This is my favorite sample, please be extra careful with it.", - "nullable" : true, - "type" : "string" - }, - "concentration" : { - "$ref" : "#/components/schemas/VendorOrderSubmissionRequest_plates_inner_samples_inner_concentration" - }, - "organismName" : { - "description" : "Scientific organism name", - "example" : "Aspergillus fructus", - "nullable" : true, - "type" : "string" - }, - "row" : { - "description" : "The Row identifier for this samples location in the plate", - "example" : "B", - "nullable" : true, - "type" : "string" - }, - "speciesName" : { - "description" : "Scientific species name", - "example" : "Aspergillus fructus", - "nullable" : true, - "type" : "string" - }, - "taxonomyOntologyReference" : { - "$ref" : "#/components/schemas/GermplasmAttribute_ontologyReference" - }, - "tissueType" : { - "description" : "The type of tissue in this sample. List of accepted tissue types can be found in the Vendor Specs.", - "example" : "Root", - "nullable" : true, - "type" : "string" - }, - "tissueTypeOntologyReference" : { - "$ref" : "#/components/schemas/GermplasmAttribute_ontologyReference" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "volume" : { - "$ref" : "#/components/schemas/VendorOrderSubmissionRequest_plates_inner_samples_inner_volume" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "well" : { - "description" : "The Well identifier for this samples location in the plate. Usually a concatenation of Row and Column, or just a number if the samples are not part of an ordered plate.", - "example" : "B6", - "nullable" : true, - "type" : "string" + "result" : { + "$ref" : "#/components/schemas/SeedLotListResponse_result" } }, - "required" : [ "clientSampleId" ], + "required" : [ "metadata", "result" ], + "title" : "SeedLotListResponse", "type" : "object" }, - "VendorOrderSubmissionRequest_plates_inner" : { + "SeedLotTransactionListResponse_result" : { "properties" : { - "clientPlateBarcode" : { - "description" : "(Optional) The value of the bar code attached to this plate", - "example" : "6ebf3f25", - "nullable" : true, - "type" : "string" - }, - "clientPlateId" : { - "description" : "The ID which uniquely identifies this plate to the client making the request", - "example" : "02a8d6f0", - "type" : "string" - }, - "sampleSubmissionFormat" : { - "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", - "enum" : [ "PLATE_96", "TUBES" ], - "example" : "PLATE_96", - "nullable" : true, - "type" : "string" - }, - "samples" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "$ref" : "#/components/schemas/VendorOrderSubmissionRequest_plates_inner_samples_inner" + "$ref" : "#/components/schemas/SeedLotTransaction" }, - "nullable" : true, "type" : "array" } }, + "required" : [ "data" ], "type" : "object" }, - "VendorPlateSubmission_plates_inner" : { + "SeedLotTransactionListResponse" : { "properties" : { - "clientPlateBarcode" : { - "description" : "(Optional) The value of the bar code attached to this plate", - "example" : "bfb33593", - "nullable" : true, - "type" : "string" - }, - "clientPlateId" : { - "description" : "The ID which uniquely identifies this plate to the client making the request", - "example" : "dae8f49d", - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "sampleSubmissionFormat" : { - "$ref" : "#/components/schemas/PlateFormat" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "samples" : { - "items" : { - "$ref" : "#/components/schemas/VendorSample" - }, - "type" : "array" + "result" : { + "$ref" : "#/components/schemas/SeedLotTransactionListResponse_result" } }, + "required" : [ "metadata", "result" ], + "title" : "SeedLotTransactionListResponse", "type" : "object" }, - "VendorSpecificationService_specificRequirements_inner" : { + "SeedLotSingleResponse" : { "properties" : { - "description" : { - "description" : "The value of a key-value entry in a map of Vendor specific requirements", - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "key" : { - "description" : "The key of a key-value entry in a map of Vendor specific requirements", - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/SeedLot" } }, + "required" : [ "metadata", "result" ], + "title" : "SeedLotSingleResponse", "type" : "object" }, - "metadata_datafiles_inner" : { - "description" : "A dataFile contains a URL and the relevant file metadata to represent a file", + "ServerInfoResponse" : { "properties" : { - "fileDescription" : { - "description" : "A human readable description of the file contents", - "example" : "This is an Excel data file", - "type" : "string" - }, - "fileMD5Hash" : { - "description" : "The MD5 Hash of the file contents to be used as a check sum", - "example" : "c2365e900c81a89cf74d83dab60df146", - "type" : "string" - }, - "fileName" : { - "description" : "The name of the file", - "example" : "datafile.xlsx", - "type" : "string" - }, - "fileSize" : { - "description" : "The size of the file in bytes", - "example" : 4398, - "type" : "integer" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "fileType" : { - "description" : "The type or format of the file. Preferably MIME Type.", - "example" : "application/vnd.ms-excel", - "type" : "string" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "fileURL" : { - "description" : "The absolute URL where the file is located", - "example" : "https://wiki.brapi.org/examples/datafile.xlsx", - "format" : "uri", - "type" : "string" + "result" : { + "$ref" : "#/components/schemas/ServerInfo" } }, - "required" : [ "fileURL" ], + "required" : [ "metadata", "result" ], + "title" : "ServerInfoResponse", "type" : "object" }, - "metadata_pagination" : { - "description" : "The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Pages are zero indexed, so the first page will be page 0 (zero).", + "StudySingleResponse" : { "properties" : { - "currentPage" : { - "default" : 0, - "description" : "The index number for the returned page of data. This should always match the requested page number or the default page (0).", - "example" : 0, - "type" : "integer" - }, - "pageSize" : { - "default" : 1000, - "description" : "The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned.", - "example" : 1000, - "type" : "integer" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "totalCount" : { - "description" : "The total number of elements that are available on the server and match the requested query parameters.", - "example" : 10, - "type" : "integer" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "totalPages" : { - "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", - "example" : 1, - "type" : "integer" + "result" : { + "$ref" : "#/components/schemas/Study" } }, - "required" : [ "currentPage", "pageSize" ], + "required" : [ "metadata", "result" ], + "title" : "StudySingleResponse", "type" : "object" }, - "metadata_status_inner" : { - "description" : "An array of status messages to convey technical logging information from the server to the client.", + "studyTypesResponse_result" : { "properties" : { - "message" : { - "description" : "A short message concerning the status of this request/response", - "example" : "Request accepted, response successful", - "type" : "string" - }, - "messageType" : { - "description" : "The logging level for the attached message", - "enum" : [ "DEBUG", "ERROR", "WARNING", "INFO" ], - "example" : "INFO", - "type" : "string" + "data" : { + "description" : "The list of all StudyTypes available on a given server.", + "example" : [ "Crossing Nursery", "Yield study" ], + "items" : { + "type" : "string" + }, + "type" : "array" } }, - "required" : [ "message", "messageType" ], + "required" : [ "data" ], "type" : "object" }, - "metadataTokenPagination_pagination" : { - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken to construct an additional query and move to the next or previous page respectively. ", - "example" : { - "currentPage" : 0, - "pageSize" : 1000, - "totalCount" : 10, - "totalPages" : 1 - }, + "studyTypesResponse" : { "properties" : { - "currentPage" : { - "default" : 0, - "description" : "The index number for the returned page of data. This should always match the requested page number or the default page (0).", - "example" : 0, - "type" : "integer" - }, - "currentPageToken" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the current page of data.", - "example" : "48bc6ac1", - "type" : "string" - }, - "nextPageToken" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the next page of data.", - "example" : "cb668f63", - "type" : "string" - }, - "pageSize" : { - "default" : 1000, - "description" : "The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned.", - "example" : 1000, - "type" : "integer" - }, - "prevPageToken" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the previous page of data.", - "example" : "9659857e", - "type" : "string" + "@context" : { + "$ref" : "#/components/schemas/Context" }, - "totalCount" : { - "description" : "The total number of elements that are available on the server and match the requested query parameters.", - "example" : 10, - "type" : "integer" + "metadata" : { + "$ref" : "#/components/schemas/metadata" }, - "totalPages" : { - "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", - "example" : 1, - "type" : "integer" + "result" : { + "$ref" : "#/components/schemas/studyTypesResponse_result" } }, - "required" : [ "currentPage", "nextPageToken", "pageSize" ], + "required" : [ "metadata", "result" ], + "title" : "studyTypesResponse", "type" : "object" }, - "_202AcceptedSearchResponse_result" : { + "TraitListResponse_result" : { "properties" : { - "searchResultsDbId" : { - "example" : "551ae08c", - "type" : "string" + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/Trait" + }, + "type" : "array" } }, + "required" : [ "data" ], "type" : "object" }, - "_202AcceptedSearchResponse" : { + "TraitListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34052,13 +39992,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/_202AcceptedSearchResponse_result" + "$ref" : "#/components/schemas/TraitListResponse_result" } }, - "title" : "202AcceptedSearchResponse", + "required" : [ "metadata", "result" ], + "title" : "TraitListResponse", "type" : "object" }, - "AlleleMatrixResponse" : { + "TraitSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34067,110 +40008,62 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/AlleleMatrix" + "$ref" : "#/components/schemas/Trait" } }, "required" : [ "metadata", "result" ], - "title" : "AlleleMatrixResponse", - "type" : "object" - }, - "CallSetsListResponseResult" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/CallSet" - }, - "type" : "array" - } - }, - "required" : [ "data" ], - "title" : "CallSetsListResponseResult", + "title" : "TraitSingleResponse", "type" : "object" }, - "CallSetsListResponse" : { + "TrialSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" }, "metadata" : { "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "$ref" : "#/components/schemas/CallSetsListResponseResult" - } - }, - "required" : [ "metadata", "result" ], - "title" : "CallSetsListResponse", - "type" : "object" - }, - "CallsListResponse_result" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Call" - }, - "type" : "array" - }, - "expandHomozygotes" : { - "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", - "example" : true, - "nullable" : true, - "type" : "boolean" - }, - "sepPhased" : { - "description" : "The string used as a separator for phased allele calls.", - "example" : "|", - "nullable" : true, - "type" : "string" - }, - "sepUnphased" : { - "description" : "The string used as a separator for unphased allele calls.", - "example" : "/", - "nullable" : true, - "type" : "string" - }, - "unknownString" : { - "description" : "The string used as a representation for missing data.", - "example" : ".", - "nullable" : true, - "type" : "string" + }, + "result" : { + "$ref" : "#/components/schemas/Trial" } }, - "required" : [ "data" ], + "required" : [ "metadata", "result" ], + "title" : "TrialSingleResponse", "type" : "object" }, - "CallsListResponse" : { + "ObservationVariableSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" }, "metadata" : { - "$ref" : "#/components/schemas/metadataTokenPagination" + "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/CallsListResponse_result" + "$ref" : "#/components/schemas/ObservationVariable" } }, "required" : [ "metadata", "result" ], - "title" : "CallsListResponse", + "title" : "ObservationVariableSingleResponse", "type" : "object" }, - "CrossesListResponse_result" : { + "VariantSingleResponse" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Cross" - }, - "type" : "array" + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Variant" } }, - "required" : [ "data" ], + "required" : [ "metadata", "result" ], + "title" : "VariantSingleResponse", "type" : "object" }, - "CrossesListResponse" : { + "variantSetResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34179,19 +40072,19 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/CrossesListResponse_result" + "$ref" : "#/components/schemas/VariantSet" } }, "required" : [ "metadata", "result" ], - "title" : "CrossesListResponse", + "title" : "variantSetResponse", "type" : "object" }, - "CrossingProjectsListResponse_result" : { + "VendorOrderListResponse_result" : { "properties" : { "data" : { "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "$ref" : "#/components/schemas/CrossingProject" + "$ref" : "#/components/schemas/VendorOrder" }, "type" : "array" } @@ -34199,7 +40092,7 @@ "required" : [ "data" ], "type" : "object" }, - "CrossingProjectsListResponse" : { + "VendorOrderListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34208,14 +40101,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/CrossingProjectsListResponse_result" + "$ref" : "#/components/schemas/VendorOrderListResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "CrossingProjectsListResponse", + "title" : "VendorOrderListResponse", "type" : "object" }, - "CrossingProjectsSingleResponse" : { + "VendorOrderSubmissionSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34224,19 +40117,18 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/CrossingProject" + "$ref" : "#/components/schemas/VendorOrderSubmission" } }, - "required" : [ "metadata", "result" ], - "title" : "CrossingProjectsSingleResponse", + "title" : "VendorOrderSubmissionSingleResponse", "type" : "object" }, - "GermplasmAttributeListResponse_result" : { + "VendorPlateListResponse_result" : { "properties" : { "data" : { "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { - "$ref" : "#/components/schemas/GermplasmAttribute" + "$ref" : "#/components/schemas/VendorPlate" }, "type" : "array" } @@ -34244,7 +40136,7 @@ "required" : [ "data" ], "type" : "object" }, - "GermplasmAttributeListResponse" : { + "VendorPlateListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34253,14 +40145,27 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/GermplasmAttributeListResponse_result" + "$ref" : "#/components/schemas/VendorPlateListResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "GermplasmAttributeListResponse", + "title" : "VendorPlateListResponse", "type" : "object" }, - "GermplasmAttributeSingleResponse" : { + "VendorResultFileListResponse_result" : { + "properties" : { + "data" : { + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "items" : { + "$ref" : "#/components/schemas/VendorResultFile" + }, + "type" : "array" + } + }, + "required" : [ "data" ], + "type" : "object" + }, + "VendorResultFileListResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34269,27 +40174,23 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/GermplasmAttribute" + "$ref" : "#/components/schemas/VendorResultFileListResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "GermplasmAttributeSingleResponse", + "title" : "VendorResultFileListResponse", "type" : "object" }, - "GermplasmAttributeValueListResponse_result" : { + "VendorOrderStatusResponse_result" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/GermplasmAttributeValue" - }, - "type" : "array" + "status" : { + "enum" : [ "registered", "received", "inProgress", "completed", "rejected" ], + "type" : "string" } }, - "required" : [ "data" ], "type" : "object" }, - "GermplasmAttributeValueListResponse" : { + "VendorOrderStatusResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34298,14 +40199,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/GermplasmAttributeValueListResponse_result" + "$ref" : "#/components/schemas/VendorOrderStatusResponse_result" } }, "required" : [ "metadata", "result" ], - "title" : "GermplasmAttributeValueListResponse", + "title" : "VendorOrderStatusResponse", "type" : "object" }, - "GermplasmAttributeValueSingleResponse" : { + "VendorPlateSubmissionIdSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34314,27 +40215,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/GermplasmAttributeValue" + "$ref" : "#/components/schemas/VendorPlateSubmissionId" } }, "required" : [ "metadata", "result" ], - "title" : "GermplasmAttributeValueSingleResponse", - "type" : "object" - }, - "GermplasmListResponse_result" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Germplasm" - }, - "type" : "array" - } - }, - "required" : [ "data" ], + "title" : "VendorPlateSubmissionIdSingleResponse", "type" : "object" }, - "GermplasmListResponse" : { + "VendorPlateSubmissionSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34343,14 +40231,14 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/GermplasmListResponse_result" + "$ref" : "#/components/schemas/VendorPlateSubmission" } }, "required" : [ "metadata", "result" ], - "title" : "GermplasmListResponse", + "title" : "VendorPlateSubmissionSingleResponse", "type" : "object" }, - "GermplasmSingleResponse" : { + "VendorSpecificationSingleResponse" : { "properties" : { "@context" : { "$ref" : "#/components/schemas/Context" @@ -34359,1149 +40247,2131 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/Germplasm" + "$ref" : "#/components/schemas/VendorSpecification" } }, "required" : [ "metadata", "result" ], - "title" : "GermplasmSingleResponse", + "title" : "VendorSpecificationSingleResponse", "type" : "object" }, - "ImageDeleteResponse_result" : { + "AlleleMatrix_dataMatrices_inner" : { + "description" : "This is a single data matrix. It could be the allele matrix or an additional layer of metadata associated with each genotype value.", "properties" : { - "imageDbIds" : { - "description" : "The unique ids of the Image records which have been successfully deleted", - "example" : [ "6a4a59d8", "3ff067e0" ], + "dataMatrix" : { + "description" : "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.", + "example" : [ [ "0|0", "1|0", "1/1" ], [ "0|0", "1|0", "1/1" ], [ "0|0", "1|0", "1/1" ] ], "items" : { - "type" : "string" + "description" : "An array of rows in the data matrix", + "items" : { + "description" : "All the values per row (columns) in the data matrix", + "type" : "string" + }, + "type" : "array" }, + "nullable" : true, "type" : "array" + }, + "dataMatrixAbbreviation" : { + "description" : "The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word \"GT\" is reserved for the allele matrix. Examples of other metadata matrices include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard.", + "example" : "GT", + "nullable" : true, + "type" : "string" + }, + "dataMatrixName" : { + "description" : "The name of the field represented in this data matrix. The key word \"Genotype\" is reserved for the allele matrix. Examples of other metadata matrices include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard.", + "example" : "Genotype", + "nullable" : true, + "type" : "string" + }, + "dataType" : { + "description" : "The type of field represented in this data matrix. This is intended to help parse the data out of JSON.", + "enum" : [ "string", "integer", "float", "boolean" ], + "example" : "string", + "nullable" : true, + "type" : "string" } }, - "required" : [ "imageDbIds" ], "type" : "object" }, - "ImageDeleteResponse" : { + "AlleleMatrix_pagination_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "dimension" : { + "description" : "The dimension of the matrix being paginated", + "enum" : [ "CALLSETS", "VARIANTS" ], + "example" : "VARIANTS", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "page" : { + "description" : "the requested page number (zero indexed)", + "example" : 0, + "nullable" : true, + "type" : "integer" }, - "result" : { - "$ref" : "#/components/schemas/ImageDeleteResponse_result" + "pageSize" : { + "description" : "the maximum number of elements per page in this dimension of the matrix", + "example" : 500, + "nullable" : true, + "type" : "integer" + }, + "totalCount" : { + "description" : "The total number of elements that are available on the server and match the requested query parameters.", + "example" : 10000, + "nullable" : true, + "type" : "integer" + }, + "totalPages" : { + "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", + "example" : 20, + "nullable" : true, + "type" : "integer" } }, - "required" : [ "metadata", "result" ], - "title" : "ImageDeleteResponse", "type" : "object" }, - "ImageListResponse_result" : { + "AlleleMatrixSearchRequest_pagination_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Image" - }, - "type" : "array" + "dimension" : { + "description" : "the dimension of the matrix being paginated", + "enum" : [ "CALLSETS", "VARIANTS" ], + "example" : "VARIANTS", + "type" : "string" + }, + "page" : { + "description" : "the requested page number (zero indexed)", + "example" : 0, + "type" : "integer" + }, + "pageSize" : { + "description" : "the maximum number of elements per page in this dimension of the matrix", + "example" : 500, + "type" : "integer" } }, - "required" : [ "data" ], "type" : "object" }, - "ImageListResponse" : { + "Call_genotypeMetadata_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "dataType" : { + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "enum" : [ "string", "integer", "float", "boolean" ], + "example" : "integer", + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "fieldAbbreviation" : { + "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard.", + "example" : "GQ", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ImageListResponse_result" + "fieldName" : { + "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard.", + "example" : "Genotype Quality", + "type" : "string" + }, + "fieldValue" : { + "description" : "The additional metadata value associated with this genotype call", + "example" : "45.2", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ImageListResponse", "type" : "object" }, - "ImageSingleResponse" : { + "Cross_crossAttributes_inner" : { + "description" : "a custom attributes associated with a cross", "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "crossAttributeName" : { + "description" : "the human readable name of a cross attribute", + "example" : "Humidity Percentage", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "crossAttributeValue" : { + "description" : "the value of a cross attribute", + "example" : "45", + "nullable" : true, + "type" : "string" + } + }, + "type" : "object" + }, + "ExternalReferences_1_inner" : { + "properties" : { + "referenceID" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `referenceId`. Github issue number #460 \n
The external reference ID. Could be a simple string or a URI.", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Image" + "referenceId" : { + "description" : "The external reference ID. Could be a simple string or a URI.", + "type" : "string" + }, + "referenceSource" : { + "description" : "An identifier for the source system or database of this reference", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ImageSingleResponse", "type" : "object" }, - "ListsListResponse_result" : { + "Cross_parent1" : { + "nullable" : true, "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "germplasmDbId" : { + "description" : "the unique identifier for a germplasm", + "example" : "d34b10c3", + "nullable" : true, + "type" : "string" + }, + "germplasmName" : { + "description" : "the human readable name for a germplasm", + "example" : "TME_419", + "nullable" : true, + "type" : "string" + }, + "observationUnitDbId" : { + "description" : "the unique identifier for an observation unit", + "example" : "2e1926a7", + "nullable" : true, + "type" : "string" + }, + "observationUnitName" : { + "description" : "the human readable name for an observation unit", + "example" : "my_Plot_9001", + "nullable" : true, + "type" : "string" + }, + "parentType" : { + "description" : "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION" ], + "example" : "MALE", + "type" : "string" + } + }, + "type" : "object" + }, + "Cross_pollinationEvents_inner" : { + "properties" : { + "pollinationNumber" : { + "description" : "The unique identifier for this pollination event", + "nullable" : true, + "type" : "string" + }, + "pollinationSuccessful" : { + "description" : "True if the pollination was successful", + "nullable" : true, + "type" : "boolean" + }, + "pollinationTimeStamp" : { + "description" : "The timestamp when the pollination took place", + "format" : "date-time", + "nullable" : true, + "type" : "string" + } + }, + "type" : "object" + }, + "CrossingProject_potentialParents_inner" : { + "properties" : { + "germplasmDbId" : { + "description" : "the unique identifier for a germplasm", + "example" : "d34b10c3", + "nullable" : true, + "type" : "string" + }, + "germplasmName" : { + "description" : "the human readable name for a germplasm", + "example" : "TME_419", + "nullable" : true, + "type" : "string" + }, + "observationUnitDbId" : { + "description" : "the unique identifier for an observation unit", + "example" : "2e1926a7", + "nullable" : true, + "type" : "string" + }, + "observationUnitName" : { + "description" : "the human readable name for an observation unit", + "example" : "my_Plot_9001", + "nullable" : true, + "type" : "string" + }, + "parentType" : { + "description" : "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION" ], + "example" : "MALE", + "type" : "string" + } + }, + "type" : "object" + }, + "Event_eventDateRange" : { + "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)", + "nullable" : true, + "properties" : { + "discreteDates" : { + "description" : "A list of dates when the event occurred\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", + "example" : [ "2018-10-08T18:15:11Z", "2018-11-09T18:16:12Z", "2018-11-19T18:16:12Z" ], "items" : { - "$ref" : "#/components/schemas/ListSummary" + "format" : "date-time", + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "endDate" : { + "description" : "The end of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", + "example" : "2018-10-08T18:15:11Z", + "format" : "date-time", + "nullable" : true, + "type" : "string" + }, + "startDate" : { + "description" : "The beginning of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", + "example" : "2018-10-08T18:15:11Z", + "format" : "date-time", + "nullable" : true, + "type" : "string" + } + }, + "type" : "object" + }, + "Event_eventParameters_inner" : { + "properties" : { + "code" : { + "description" : "The shortened code name of an event parameter\n
ICASA \"Code_Display\"", + "example" : "tiimp", + "nullable" : true, + "type" : "string" + }, + "description" : { + "description" : "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter.", + "example" : "Implement or tool used for tillage", + "nullable" : true, + "type" : "string" + }, + "key" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `name`. Github issue number #440 \n
Specifies the relationship between the event and the given property. E.g. fertilizer, operator", + "example" : "operator", + "nullable" : true, + "type" : "string" + }, + "name" : { + "description" : "The full name of an event parameter\n
ICASA \"Variable_Name\"", + "example" : "tillage_implement", + "nullable" : true, + "type" : "string" + }, + "rdfValue" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `code`. Github issue number #440 \nIf the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. \n
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\"", + "example" : "code", + "nullable" : true, + "type" : "string" + }, + "value" : { + "description" : "The single value of this event parameter. This single value is accurate for all the dates in the date range. If 'value' is populated then 'valuesByDate' should NOT be populated.", + "example" : "TI001", + "nullable" : true, + "type" : "string" + }, + "valueDescription" : { + "description" : "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value.", + "example" : "Standard V-Ripper (TI001)", + "nullable" : true, + "type" : "string" + }, + "valuesByDate" : { + "description" : "An array of values corresponding to each timestamp in the 'discreteDates' array of this event. The 'valuesByDate' array should exactly match the size of the 'discreteDates' array. If 'valuesByDate' is populated then 'value' should NOT be populated.", + "example" : [ "20", "50", "40" ], + "items" : { + "type" : "string" }, + "nullable" : true, "type" : "array" } }, - "required" : [ "data" ], "type" : "object" }, - "ListsListResponse" : { + "Germplasm_donors_inner" : { + "properties" : { + "donorAccessionNumber" : { + "description" : "The accession number assigned by the donor\n \nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "example" : "A0000123", + "nullable" : true, + "type" : "string" + }, + "donorInstituteCode" : { + "description" : "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", + "example" : "PER001", + "nullable" : true, + "type" : "string" + } + }, + "type" : "object" + }, + "GeoJSON" : { + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "nullable" : true, + "properties" : { + "geometry" : { + "$ref" : "#/components/schemas/GeoJSON_Geometry" + }, + "type" : { + "default" : "Feature", + "description" : "The literal string \"Feature\"", + "example" : "Feature", + "type" : "string" + } + }, + "title" : "GeoJSON", + "type" : "object" + }, + "Germplasm_germplasmOrigin_inner" : { + "description" : "MIAPPE V1.1 (DM-52) \n\nMIAPPE V1.1 (DM-53) \n\nMIAPPE V1.1 (DM-54) \n\nMIAPPE V1.1 (DM-55)\n\nMCPD (v2.1) (COORDUNCERT) 15.5 \n\nMCPD (v2.1) (ELEVATION) 16. \n\nMCPD (v2.1) (GEOREFMETH) 15.7 \n\nMCPD (v2.1) (DECLATITUDE) 15.1 \n\nMCPD (v2.1) (DECLONGITUDE) 15.3 ", "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "coordinateUncertainty" : { + "description" : "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", + "example" : "20", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ListsListResponse_result" + "coordinates" : { + "$ref" : "#/components/schemas/GeoJSON" } }, - "required" : [ "metadata", "result" ], - "title" : "ListsListResponse", "type" : "object" }, - "ListsSingleResponse" : { + "Germplasm_storageTypes_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "code" : { + "description" : "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", + "enum" : [ "10", "11", "12", "13", "20", "30", "40", "50", "99" ], + "example" : "11", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ListDetails" + "description" : { + "description" : "A supplemental text description of the storage type", + "example" : "Short term", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ListsSingleResponse", "type" : "object" }, - "LocationListResponse_result" : { + "Germplasm_synonyms_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Location" - }, - "type" : "array" + "synonym" : { + "description" : "Alternative name or ID used to reference this germplasm", + "example" : "variety_1", + "nullable" : true, + "type" : "string" + }, + "type" : { + "description" : "A descriptive classification for this synonym", + "example" : "Pre-Code", + "nullable" : true, + "type" : "string" } }, - "required" : [ "data" ], "type" : "object" }, - "LocationListResponse" : { + "Germplasm_taxonIds_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "sourceName" : { + "description" : "The human readable name of the taxonomy provider", + "example" : "NCBI", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/LocationListResponse_result" + "taxonId" : { + "description" : "The identifier (name, ID, URI) of a particular taxonomy within the source provider", + "example" : "2026747", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "LocationListResponse", + "required" : [ "sourceName", "taxonId" ], "type" : "object" }, - "LocationSingleResponse" : { + "GermplasmAttribute_method_ontologyReference_documentationLinks_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "URL" : { + "example" : "http://purl.obolibrary.org/obo/ro.owl", + "format" : "uri", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Location" + "type" : { + "enum" : [ "OBO", "RDF", "WEBPAGE" ], + "example" : "OBO", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "LocationSingleResponse", "type" : "object" }, - "MarkerPositionListResponse_result" : { + "GermplasmAttribute_method_ontologyReference" : { + "description" : "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "documentationLinks" : { + "description" : "links to various ontology documentation", "items" : { - "$ref" : "#/components/schemas/MarkerPosition" + "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference_documentationLinks_inner" }, + "nullable" : true, "type" : "array" - } - }, - "required" : [ "data" ], - "type" : "object" - }, - "MarkerPositionListResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "ontologyDbId" : { + "description" : "Ontology database unique identifier", + "example" : "6b071868", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/MarkerPositionListResponse_result" + "ontologyName" : { + "description" : "Ontology name", + "example" : "The Crop Ontology", + "type" : "string" + }, + "version" : { + "description" : "Ontology version (no specific format)", + "example" : "7.2.3", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "MarkerPositionListResponse", + "required" : [ "ontologyDbId", "ontologyName" ], "type" : "object" }, - "MethodListResponse_result" : { + "GermplasmAttribute_method" : { + "description" : "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". ", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "additionalInfo" : { + "additionalProperties" : { + "type" : "string" + }, + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "nullable" : true, + "type" : "object" + }, + "bibliographicalReference" : { + "description" : "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method.", + "example" : "Smith, 1893, Really Cool Paper, Popular Journal", + "nullable" : true, + "type" : "string" + }, + "description" : { + "description" : "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)", + "example" : "A measuring tape was used", + "nullable" : true, + "type" : "string" + }, + "externalReferences" : { + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "example" : [ { + "referenceId" : "doi:10.155454/12341234", + "referenceSource" : "DOI" + }, { + "referenceId" : "75a50e76", + "referenceSource" : "Remote Data Collection Upload Tool" + } ], "items" : { - "$ref" : "#/components/schemas/Method" + "$ref" : "#/components/schemas/ExternalReferences_1_inner" }, + "nullable" : true, + "title" : "ExternalReferences", "type" : "array" + }, + "formula" : { + "description" : "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation", + "example" : "a^2 + b^2 = c^2", + "nullable" : true, + "type" : "string" + }, + "methodClass" : { + "description" : "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)", + "example" : "Measurement", + "nullable" : true, + "type" : "string" + }, + "methodDbId" : { + "description" : "Method unique identifier", + "example" : "0adb2764", + "type" : "string" + }, + "methodName" : { + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "example" : "Measuring Tape", + "type" : "string" + }, + "methodPUI" : { + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "example" : "http://my-traits.com/trait/CO_123:0000212", + "nullable" : true, + "type" : "string" + }, + "ontologyReference" : { + "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference" } }, - "required" : [ "data" ], + "required" : [ "methodName" ], "type" : "object" }, - "MethodListResponse" : { + "GermplasmAttribute_ontologyReference" : { + "description" : "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", + "nullable" : true, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "documentationLinks" : { + "description" : "links to various ontology documentation", + "items" : { + "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference_documentationLinks_inner" + }, + "nullable" : true, + "type" : "array" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "ontologyDbId" : { + "description" : "Ontology database unique identifier", + "example" : "6b071868", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/MethodListResponse_result" + "ontologyName" : { + "description" : "Ontology name", + "example" : "The Crop Ontology", + "type" : "string" + }, + "version" : { + "description" : "Ontology version (no specific format)", + "example" : "7.2.3", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "MethodListResponse", + "required" : [ "ontologyDbId", "ontologyName" ], "type" : "object" }, - "MethodSingleResponse" : { + "GermplasmAttribute_scale_validValues_categories_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "label" : { + "description" : "A text label for a category", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Method" + "value" : { + "description" : "The actual value for a category", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "MethodSingleResponse", "type" : "object" }, - "ObservationDeleteResponse_result" : { + "GermplasmAttribute_scale_validValues" : { + "nullable" : true, "properties" : { - "observationDbIds" : { - "description" : "The unique ids of the Observation records which have been successfully deleted", - "example" : [ "6a4a59d8", "3ff067e0" ], + "categories" : { + "description" : "List of possible values with optional labels", + "example" : [ { + "label" : "low", + "value" : "0" + }, { + "label" : "medium", + "value" : "5" + }, { + "label" : "high", + "value" : "10" + } ], "items" : { - "type" : "string" + "$ref" : "#/components/schemas/GermplasmAttribute_scale_validValues_categories_inner" }, "type" : "array" + }, + "max" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `maximumValue`. Github issue number #450 \n
Maximum value for numerical scales. Typically used for data capture control and QC.", + "example" : 9999, + "nullable" : true, + "type" : "integer" + }, + "maximumValue" : { + "description" : "Maximum value for numerical, date, and time scales. Typically used for data capture control and QC.", + "example" : "9999", + "nullable" : true, + "type" : "string" + }, + "min" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `minimumValue`. Github issue number #450 \n
Minimum value for numerical scales. Typically used for data capture control and QC.", + "example" : 2, + "nullable" : true, + "type" : "integer" + }, + "minimumValue" : { + "description" : "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC.", + "example" : "2", + "nullable" : true, + "type" : "string" } }, - "required" : [ "observationDbIds" ], "type" : "object" }, - "ObservationDeleteResponse" : { + "GermplasmAttribute_scale" : { + "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\".", "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "additionalInfo" : { + "additionalProperties" : { + "type" : "string" + }, + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "nullable" : true, + "type" : "object" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "dataType" : { + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "enum" : [ "Code", "Date", "Duration", "Nominal", "Numerical", "Ordinal", "Text" ], + "example" : "Numerical", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ObservationDeleteResponse_result" + "decimalPlaces" : { + "description" : "For numerical, number of decimal places to be reported", + "example" : 2, + "nullable" : true, + "type" : "integer" + }, + "externalReferences" : { + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "example" : [ { + "referenceId" : "doi:10.155454/12341234", + "referenceSource" : "DOI" + }, { + "referenceId" : "75a50e76", + "referenceSource" : "Remote Data Collection Upload Tool" + } ], + "items" : { + "$ref" : "#/components/schemas/ExternalReferences_1_inner" + }, + "nullable" : true, + "title" : "ExternalReferences", + "type" : "array" + }, + "ontologyReference" : { + "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference" + }, + "scaleDbId" : { + "description" : "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID.", + "example" : "af730171", + "type" : "string" + }, + "scaleName" : { + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "example" : "Meters", + "nullable" : true, + "type" : "string" + }, + "scalePUI" : { + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "example" : "http://my-traits.com/trait/CO_123:0000112", + "nullable" : true, + "type" : "string" + }, + "units" : { + "description" : "This field can be used to describe the units used for this scale. This should be the abbreviated \nform of the units, intended to be displayed with every value using this scale. Usually this only \napplies when `dataType` is Numeric, but could also be included for other dataTypes when applicable.", + "example" : "m", + "nullable" : true, + "type" : "string" + }, + "validValues" : { + "$ref" : "#/components/schemas/GermplasmAttribute_scale_validValues" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationDeleteResponse", + "required" : [ "scaleDbId", "scaleName" ], "type" : "object" }, - "ObservationListResponse_result" : { + "GermplasmAttribute_trait" : { + "description" : "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". ", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "additionalInfo" : { + "additionalProperties" : { + "type" : "string" + }, + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "nullable" : true, + "type" : "object" + }, + "alternativeAbbreviations" : { + "description" : "A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention.", + "example" : [ "H", "PH", "H1" ], "items" : { - "$ref" : "#/components/schemas/Observation" + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "attribute" : { + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "example" : "height", + "nullable" : true, + "type" : "string" + }, + "attributePUI" : { + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "example" : "http://my-traits.com/trait/PO:00012345", + "nullable" : true, + "type" : "string" + }, + "entity" : { + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "example" : "Stalk", + "nullable" : true, + "type" : "string" + }, + "entityPUI" : { + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "example" : "http://my-traits.com/trait/PATO:00098765", + "nullable" : true, + "type" : "string" + }, + "externalReferences" : { + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "example" : [ { + "referenceId" : "doi:10.155454/12341234", + "referenceSource" : "DOI" + }, { + "referenceId" : "75a50e76", + "referenceSource" : "Remote Data Collection Upload Tool" + } ], + "items" : { + "$ref" : "#/components/schemas/ExternalReferences_1_inner" + }, + "nullable" : true, + "title" : "ExternalReferences", + "type" : "array" + }, + "mainAbbreviation" : { + "description" : "A shortened version of the human readable name for a Trait", + "example" : "PH", + "nullable" : true, + "type" : "string" + }, + "ontologyReference" : { + "$ref" : "#/components/schemas/GermplasmAttribute_method_ontologyReference" + }, + "status" : { + "description" : "Trait status (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", + "example" : "recommended", + "nullable" : true, + "type" : "string" + }, + "synonyms" : { + "description" : "Other trait names", + "example" : [ "Height", "Plant Height", "Stalk Height", "Canopy Height" ], + "items" : { + "type" : "string" }, + "nullable" : true, "type" : "array" + }, + "traitClass" : { + "description" : "A classification to describe the type of trait and the context it should be considered in.\n
examples- \"morphological\", \"phenological\", \"agronomical\", \"physiological\", \"abiotic stress\", \"biotic stress\", \"biochemical\", \"quality traits\", \"fertility\", etc.", + "example" : "phenological", + "nullable" : true, + "type" : "string" + }, + "traitDbId" : { + "description" : "The ID which uniquely identifies a trait", + "example" : "9b2e34f5", + "type" : "string" + }, + "traitDescription" : { + "description" : "The description of a trait", + "example" : "The height of the plant", + "nullable" : true, + "type" : "string" + }, + "traitName" : { + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "example" : "Height", + "type" : "string" + }, + "traitPUI" : { + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "example" : "http://my-traits.com/trait/CO_123:0000012", + "nullable" : true, + "type" : "string" } }, - "required" : [ "data" ], + "required" : [ "traitName" ], "type" : "object" }, - "ObservationListResponse" : { + "GermplasmMCPD_breedingInstitutes_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "instituteCode" : { + "description" : "MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.", + "example" : "PER001", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ObservationListResponse_result" + "instituteName" : { + "description" : "MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available.", + "example" : "The BrAPI Institute", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationListResponse", "type" : "object" }, - "ObservationSingleResponse" : { + "GermplasmMCPD_collectingInfo_collectingInstitutes_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "instituteAddress" : { + "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "example" : "123 Main Street, Lima, Peru, 5555", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "instituteCode" : { + "description" : "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.", + "example" : "PER001", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Observation" + "instituteName" : { + "description" : "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "example" : "The BrAPI Institute", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationSingleResponse", "type" : "object" }, - "ObservationTableResponse" : { + "GermplasmMCPD_collectingInfo_collectingSite" : { + "description" : "Information about the location where the sample was collected", + "nullable" : true, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "coordinateUncertainty" : { + "description" : "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.", + "example" : "20", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "elevation" : { + "description" : "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.", + "example" : "35", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ObservationTable" + "georeferencingMethod" : { + "description" : "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.", + "example" : "WGS84", + "nullable" : true, + "type" : "string" + }, + "latitudeDecimal" : { + "description" : "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).", + "example" : "+42.445295", + "nullable" : true, + "type" : "string" + }, + "latitudeDegrees" : { + "description" : "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10", + "example" : "42 26 43.1 N", + "nullable" : true, + "type" : "string" + }, + "locationDescription" : { + "description" : "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).", + "example" : "South east hill near institute buildings", + "nullable" : true, + "type" : "string" + }, + "longitudeDecimal" : { + "description" : "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).", + "example" : "-076.471934", + "nullable" : true, + "type" : "string" + }, + "longitudeDegrees" : { + "description" : "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076", + "example" : "76 28 19.0 W", + "nullable" : true, + "type" : "string" + }, + "spatialReferenceSystem" : { + "description" : "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.", + "example" : "WGS84", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationTableResponse", "type" : "object" }, - "ObservationUnitListResponse_result" : { + "GermplasmMCPD_collectingInfo" : { + "description" : "Information about the collection of a germplasm", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "collectingDate" : { + "description" : "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "format" : "date", + "nullable" : true, + "type" : "string" + }, + "collectingInstitutes" : { + "description" : "Institutes which collected the sample", "items" : { - "$ref" : "#/components/schemas/ObservationUnit" + "$ref" : "#/components/schemas/GermplasmMCPD_collectingInfo_collectingInstitutes_inner" }, + "nullable" : true, "type" : "array" - } - }, - "required" : [ "data" ], - "type" : "object" - }, - "ObservationUnitListResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "collectingMissionIdentifier" : { + "description" : "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\").", + "example" : "CIATFOR_052", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ObservationUnitListResponse_result" + "collectingNumber" : { + "description" : "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections.", + "example" : "ab109909", + "nullable" : true, + "type" : "string" + }, + "collectingSite" : { + "$ref" : "#/components/schemas/GermplasmMCPD_collectingInfo_collectingSite" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationUnitListResponse", "type" : "object" }, - "ObservationUnitSingleResponse" : { + "GermplasmMCPD_donorInfo_donorInstitute" : { + "description" : "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "instituteCode" : { + "description" : "MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", + "example" : "PER001", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ObservationUnit" + "instituteName" : { + "description" : "MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", + "example" : "The BrAPI Institute", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationUnitSingleResponse", "type" : "object" }, - "ObservationUnitTableResponse" : { + "GermplasmMCPD_donorInfo" : { + "description" : "Information about an accession donor", "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "donorAccessionNumber" : { + "description" : "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "example" : "A0090204", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "donorAccessionPui" : { + "description" : "PUI (DOI mostly) of the accession in the donor system.", + "example" : "http://pui.per/accession/A0010025", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ObservationUnitTable" + "donorInstitute" : { + "$ref" : "#/components/schemas/GermplasmMCPD_donorInfo_donorInstitute" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationUnitTableResponse", "type" : "object" }, - "ObservationVariableListResponse_result" : { + "GermplasmMCPD_safetyDuplicateInstitutes_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/ObservationVariable" - }, - "type" : "array" + "instituteCode" : { + "description" : "MCPD (v2.1) (DUPLSITE) 25. FAO WIEWS code of the institute(s) where a safety duplicate of the accession is maintained. Follows INSTCODE standard.", + "example" : "PER001", + "nullable" : true, + "type" : "string" + }, + "instituteName" : { + "description" : "MCPD (v2.1) (DUPLINSTNAME) 25.1 Name of the institute where a safety duplicate of the accession is maintained.", + "example" : "The BrAPI Institute", + "nullable" : true, + "type" : "string" } }, - "required" : [ "data" ], "type" : "object" }, - "ObservationVariableListResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "ListValue_values_inner" : { + "oneOf" : [ { + "description" : "Represents a boolean value.", + "format" : "boolean", + "type" : "boolean" + }, { + "description" : "Represents a double value.", + "format" : "double", + "type" : "number" + }, { + "description" : "Represents a string value.", + "type" : "string" + } ] + }, + "GeoJSONSearchArea_1" : { + "description" : "A GeoJSON Polygon which describes an area to search for other GeoJSON objects. All contained Points and intersecting Polygons should be returned as search results. \n\nAll coordinates are decimal values on the WGS84 geographic coordinate reference system.", + "example" : { + "geometry" : { + "coordinates" : [ [ [ -77.456654, 42.241133 ], [ -75.414133, 41.508282 ], [ -76.506042, 42.417373 ], [ -77.456654, 42.241133 ] ] ], + "type" : "Polygon" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "type" : "Feature" + }, + "nullable" : true, + "properties" : { + "geometry" : { + "$ref" : "#/components/schemas/GeoJSON_Geometry" }, - "result" : { - "$ref" : "#/components/schemas/ObservationVariableListResponse_result" + "type" : { + "default" : "Feature", + "description" : "The literal string \"Feature\"", + "example" : "Feature", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationVariableListResponse", + "title" : "GeoJSONSearchArea", "type" : "object" }, - "ObservationVariableSingleResponse" : { + "Observation_season" : { + "nullable" : true, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "season" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `seasonName`. Github issue number #456 \n
Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.", + "example" : "Spring", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "seasonDbId" : { + "description" : "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'", + "example" : "Spring_2018", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ObservationVariable" + "seasonName" : { + "description" : "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.", + "example" : "Spring", + "nullable" : true, + "type" : "string" + }, + "year" : { + "description" : "The 4 digit year of the season.", + "example" : 2018, + "nullable" : true, + "type" : "integer" } }, - "required" : [ "metadata", "result" ], - "title" : "ObservationVariableSingleResponse", + "required" : [ "seasonDbId" ], "type" : "object" }, - "OntologyListResponse_result" : { + "ObservationTable_observationVariables_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Ontology" - }, - "type" : "array" + "observationVariableDbId" : { + "description" : "Variable unique identifier", + "example" : "367aa1a9", + "type" : "string" + }, + "observationVariableName" : { + "description" : "Variable name (usually a short name)", + "example" : "Plant height", + "type" : "string" } }, - "required" : [ "data" ], "type" : "object" }, - "OntologyListResponse" : { + "ObservationUnitLevel_2" : { + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "levelCode" : { + "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", + "example" : "Plot_123", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "levelName" : { + "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "example" : "plot", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/OntologyListResponse_result" + "levelOrder" : { + "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "example" : 2, + "nullable" : true, + "type" : "integer" } }, - "required" : [ "metadata", "result" ], - "title" : "OntologyListResponse", + "title" : "ObservationUnitLevel", "type" : "object" }, - "OntologySingleResponse" : { + "ObservationUnit_observationUnitPosition" : { + "description" : "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section.", + "nullable" : true, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "entryType" : { + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ], + "example" : "TEST", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "geoCoordinates" : { + "$ref" : "#/components/schemas/GeoJSON" }, - "result" : { - "$ref" : "#/components/schemas/Ontology" - } - }, - "required" : [ "metadata", "result" ], - "title" : "OntologySingleResponse", - "type" : "object" - }, - "PedigreeListResponse_result" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "observationLevel" : { + "$ref" : "#/components/schemas/ObservationUnitLevel_2" + }, + "observationLevelRelationships" : { + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", + "example" : [ { + "levelCode" : "Field_1", + "levelName" : "field", + "levelOrder" : 0 + }, { + "levelCode" : "Block_12", + "levelName" : "block", + "levelOrder" : 1 + }, { + "levelCode" : "Plot_123", + "levelName" : "plot", + "levelOrder" : 2 + } ], "items" : { - "$ref" : "#/components/schemas/PedigreeNode" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" }, + "nullable" : true, "type" : "array" - } - }, - "required" : [ "data" ], - "type" : "object" - }, - "PedigreeListResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "positionCoordinateX" : { + "description" : "The X position coordinate for an observation unit. Different systems may use different coordinate systems.", + "example" : "74", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/PedigreeListResponse_result" + "positionCoordinateXType" : { + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independant or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ], + "example" : "GRID_COL", + "nullable" : true, + "type" : "string" + }, + "positionCoordinateY" : { + "description" : "The Y position coordinate for an observation unit. Different systems may use different coordinate systems.", + "example" : "03", + "nullable" : true, + "type" : "string" + }, + "positionCoordinateYType" : { + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independant or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ], + "example" : "GRID_ROW", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "PedigreeListResponse", "type" : "object" }, - "PersonListResponse_result" : { + "Observation_1" : { + "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit.", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "additionalInfo" : { + "additionalProperties" : { + "type" : "string" + }, + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "nullable" : true, + "type" : "object" + }, + "collector" : { + "description" : "The name or identifier of the entity which collected the observation", + "example" : "917d3ae0", + "nullable" : true, + "type" : "string" + }, + "externalReferences" : { + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "example" : [ { + "referenceId" : "doi:10.155454/12341234", + "referenceSource" : "DOI" + }, { + "referenceId" : "75a50e76", + "referenceSource" : "Remote Data Collection Upload Tool" + } ], "items" : { - "$ref" : "#/components/schemas/Person" + "$ref" : "#/components/schemas/ExternalReferences_1_inner" }, + "nullable" : true, + "title" : "ExternalReferences", "type" : "array" + }, + "geoCoordinates" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "germplasmDbId" : { + "description" : "The ID which uniquely identifies a germplasm", + "example" : "2408ab11", + "nullable" : true, + "type" : "string" + }, + "germplasmName" : { + "description" : "Name of the germplasm. It can be the preferred name and does not have to be unique.", + "example" : "A0000003", + "nullable" : true, + "type" : "string" + }, + "observationDbId" : { + "description" : "The ID which uniquely identifies an observation", + "example" : "ef24b615", + "type" : "string" + }, + "observationTimeStamp" : { + "description" : "The date and time when this observation was made", + "format" : "date-time", + "nullable" : true, + "type" : "string" + }, + "observationUnitDbId" : { + "description" : "The ID which uniquely identifies an observation unit", + "example" : "598111d4", + "nullable" : true, + "type" : "string" + }, + "observationUnitName" : { + "description" : "A human readable name for an observation unit", + "example" : "Plot 1", + "nullable" : true, + "type" : "string" + }, + "observationVariableDbId" : { + "description" : "The ID which uniquely identifies an observation variable", + "example" : "c403d107", + "nullable" : true, + "type" : "string" + }, + "observationVariableName" : { + "description" : "A human readable name for an observation variable", + "example" : "Plant Height in meters", + "nullable" : true, + "type" : "string" + }, + "season" : { + "$ref" : "#/components/schemas/Observation_season" + }, + "studyDbId" : { + "description" : "The ID which uniquely identifies a study within the given database server", + "example" : "ef2829db", + "nullable" : true, + "type" : "string" + }, + "uploadedBy" : { + "description" : "The name or id of the user who uploaded the observation to the database system", + "example" : "a2f7f60b", + "nullable" : true, + "type" : "string" + }, + "value" : { + "description" : "The value of the data collected as an observation", + "example" : "2.3", + "nullable" : true, + "type" : "string" } }, - "required" : [ "data" ], - "type" : "object" + "required" : [ "observationDbId" ], + "title" : "Observation", + "type" : "object", + "x-brapi-metadata" : { + "module" : "BrAPI-Phenotyping", + "primaryModel" : true + } }, - "PersonListResponse" : { + "ObservationUnit_treatments_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "factor" : { + "description" : "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.", + "example" : "fertilizer", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/PersonListResponse_result" + "modality" : { + "description" : "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ", + "example" : "low fertilizer", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "PersonListResponse", "type" : "object" }, - "PersonSingleResponse" : { + "PedigreeNode_parents_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "germplasmDbId" : { + "description" : "The ID which uniquely identifies a germplasm", + "example" : "a55847ed", + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "germplasmName" : { + "description" : "A human readable name for a germplasm", + "example" : "A0000592", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Person" + "parentType" : { + "$ref" : "#/components/schemas/ParentType" } }, - "required" : [ "metadata", "result" ], - "title" : "PersonSingleResponse", + "required" : [ "germplasmDbId", "parentType" ], "type" : "object" }, - "PlannedCrossesListResponse_result" : { + "PedigreeNode_siblings_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/PlannedCross" - }, - "type" : "array" + "germplasmDbId" : { + "description" : "The ID which uniquely identifies a germplasm", + "example" : "a55847ed", + "type" : "string" + }, + "germplasmName" : { + "description" : "A human readable name for a germplasm", + "example" : "A0000592", + "nullable" : true, + "type" : "string" } }, - "required" : [ "data" ], + "required" : [ "germplasmDbId" ], "type" : "object" }, - "PlannedCrossesListResponse" : { + "PedigreeNodeDEP_parents_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "germplasmDbId" : { + "description" : "The germplasm DbId of the parent of this germplasm", + "example" : "a55847ed", + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "germplasmName" : { + "description" : "the human readable name of the parent of this germplasm", + "example" : "A0000592", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/PlannedCrossesListResponse_result" + "parentType" : { + "$ref" : "#/components/schemas/ParentTypeDEP" } }, - "required" : [ "metadata", "result" ], - "title" : "PlannedCrossesListResponse", "type" : "object" }, - "PlateListResponse_result" : { + "PedigreeNodeDEP_siblings_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Plate" - }, - "type" : "array" + "germplasmDbId" : { + "description" : "the germplasm DbId of the sibling", + "type" : "string" + }, + "germplasmName" : { + "description" : "the germplasm name of the sibling", + "type" : "string" } }, - "required" : [ "data" ], "type" : "object" }, - "PlateListResponse" : { + "ProgenyNodeDEP_progeny_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "germplasmDbId" : { + "description" : "The unique identifier of a progeny germplasm", + "example" : "e8d5dad7", + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "germplasmName" : { + "description" : "The human readable name of a progeny germplasm", + "example" : "A0021011", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/PlateListResponse_result" + "parentType" : { + "$ref" : "#/components/schemas/ParentTypeDEP" } }, - "required" : [ "metadata", "result" ], - "title" : "PlateListResponse", + "required" : [ "germplasmDbId", "parentType" ], "type" : "object" }, - "PlateSingleResponse" : { + "Reference_sourceGermplasm_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "germplasmDbId" : { + "description" : "The ID which uniquely identifies a `Germplasm` within the given database server", + "example" : "d4076594", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Plate" + "germplasmName" : { + "description" : "The human readable name of a `Germplasm`", + "example" : "A0000003", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "PlateSingleResponse", "type" : "object" }, - "ProgramListResponse_result" : { + "ReferenceSet_sourceGermplasm_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Program" - }, - "type" : "array" + "germplasmDbId" : { + "description" : "The ID which uniquely identifies a germplasm within the given database server", + "example" : "d4076594", + "type" : "string" + }, + "germplasmName" : { + "description" : "The human readable name of a germplasm", + "example" : "A0000003", + "type" : "string" } }, - "required" : [ "data" ], "type" : "object" }, - "ProgramListResponse" : { + "SeedLot_contentMixture_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "crossDbId" : { + "description" : "The unique DbId for a cross contained in this seed lot", + "example" : "d105fd6f", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "crossName" : { + "description" : "The human readable name for a cross contained in this seed lot", + "example" : "my_Crosses_2018_01", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ProgramListResponse_result" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ProgramListResponse", - "type" : "object" - }, - "ProgramSingleResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "germplasmDbId" : { + "description" : "The unique DbId of the Germplasm contained in this Seed Lot", + "example" : "029d705d", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "germplasmName" : { + "description" : "The human readable name of the Germplasm contained in this Seed Lot", + "example" : "A0000003", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Program" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ProgramSingleResponse", - "type" : "object" - }, - "ReferenceSetsListResponseResult" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/ReferenceSet" - }, - "type" : "array" + "mixturePercentage" : { + "description" : "The percentage of the given germplasm in the seed lot mixture.", + "example" : 100, + "nullable" : true, + "type" : "integer" } }, - "required" : [ "data" ], - "title" : "ReferenceSetsListResponseResult", "type" : "object" }, - "ReferenceSetsListResponse" : { + "Study_contacts_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "contactDbId" : { + "description" : "The ID which uniquely identifies this contact\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.", + "example" : "5f4e5509", + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "email" : { + "description" : "The contacts email address\n\nMIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person.", + "example" : "bob@bob.com", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ReferenceSetsListResponseResult" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ReferenceSetsListResponse", - "type" : "object" - }, - "ReferencesListResponseResult" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Reference" - }, - "type" : "array" - } - }, - "required" : [ "data" ], - "title" : "ReferencesListResponseResult", - "type" : "object" - }, - "ReferencesListResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "instituteName" : { + "description" : "The name of the institution which this contact is part of\n\nMIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to", + "example" : "The BrAPI Institute", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "name" : { + "description" : "The full name of this contact person\n\nMIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)", + "example" : "Bob Robertson", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ReferencesListResponseResult" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ReferencesListResponse", - "type" : "object" - }, - "SampleListResponse_result" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Sample" - }, - "type" : "array" + "orcid" : { + "description" : "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.", + "example" : "http://orcid.org/0000-0001-8640-1750", + "nullable" : true, + "type" : "string" + }, + "type" : { + "description" : "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation", + "example" : "PI", + "nullable" : true, + "type" : "string" } }, - "required" : [ "data" ], + "required" : [ "contactDbId" ], "type" : "object" }, - "SampleListResponse" : { + "Study_dataLinks_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "dataFormat" : { + "description" : "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", + "example" : "Image Archive", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "description" : { + "description" : "The general description of this data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", + "example" : "Raw drone images collected for this study", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/SampleListResponse_result" - } - }, - "required" : [ "metadata", "result" ], - "title" : "SampleListResponse", - "type" : "object" - }, - "SampleSingleResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "fileFormat" : { + "description" : "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", + "example" : "application/zip", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "name" : { + "description" : "The name of the external data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", + "example" : "image-archive.zip", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Sample" - } - }, - "required" : [ "metadata", "result" ], - "title" : "SampleSingleResponse", - "type" : "object" - }, - "ScaleListResponse_result" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Scale" - }, - "type" : "array" - } - }, - "required" : [ "data" ], - "type" : "object" - }, - "ScaleListResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "provenance" : { + "description" : "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow.", + "example" : "Image Processing Pipeline, built at the University of Antarctica: https://github.com/antarctica/pipeline", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "scientificType" : { + "description" : "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc", + "example" : "Environmental", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/ScaleListResponse_result" + "url" : { + "description" : "URL describing the location of this data file to view or download\n\nMIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission.", + "example" : "https://brapi.org/image-archive.zip", + "format" : "uri", + "nullable" : true, + "type" : "string" + }, + "version" : { + "description" : "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data).", + "example" : "1.0.3", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "ScaleListResponse", "type" : "object" }, - "ScaleSingleResponse" : { + "Study_environmentParameters_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "description" : { + "description" : "Human-readable value of the environment parameter (defined above) constant within the experiment", + "example" : "the soil type was clay", + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "parameterName" : { + "description" : "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. ", + "example" : "soil type", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Scale" - } - }, - "required" : [ "metadata", "result" ], - "title" : "ScaleSingleResponse", - "type" : "object" - }, - "SeasonListResponse_result" : { - "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Season" - }, - "type" : "array" - } - }, - "required" : [ "data" ], - "type" : "object" - }, - "SeasonListResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "parameterPUI" : { + "description" : "URI pointing to an ontology class for the parameter", + "example" : "PECO:0007155", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "unit" : { + "description" : "Unit of the value for this parameter", + "example" : "pH", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/SeasonListResponse_result" - } - }, - "required" : [ "metadata", "result" ], - "title" : "SeasonListResponse", - "type" : "object" - }, - "SeasonSingleResponse" : { - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "unitPUI" : { + "description" : "URI pointing to an ontology class for the unit", + "example" : "PECO:0007059", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "value" : { + "description" : "Numerical or categorical value\n\nMIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment.", + "example" : "clay soil", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Season" + "valuePUI" : { + "description" : "URI pointing to an ontology class for the parameter value", + "example" : "ENVO:00002262", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "SeasonSingleResponse", + "required" : [ "description", "parameterName" ], "type" : "object" }, - "SeedLotListResponse_result" : { + "Study_experimentalDesign" : { + "description" : "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology", + "nullable" : true, "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/SeedLot" - }, - "type" : "array" + "PUI" : { + "description" : "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.", + "example" : "CO_715:0000145", + "nullable" : true, + "type" : "string" + }, + "description" : { + "description" : "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.", + "example" : "Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information.", + "nullable" : true, + "type" : "string" } }, - "required" : [ "data" ], "type" : "object" }, - "SeedLotListResponse" : { + "Study_growthFacility" : { + "description" : "Short description of the facility in which the study was carried out.", + "nullable" : true, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "PUI" : { + "description" : "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.", + "example" : "CO_715:0000162", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/SeedLotListResponse_result" + "description" : { + "description" : "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.", + "example" : "field environment condition, greenhouse", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "SeedLotListResponse", "type" : "object" }, - "SeedLotSingleResponse" : { + "Study_lastUpdate" : { + "description" : "The date and time when this study was last modified", + "nullable" : true, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "timestamp" : { + "format" : "date-time", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/SeedLot" + "version" : { + "example" : "1.2.3", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "SeedLotSingleResponse", "type" : "object" }, - "SeedLotTransactionListResponse_result" : { + "ObservationUnitHierarchyLevel_1" : { + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/SeedLotTransaction" - }, - "type" : "array" + "levelName" : { + "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "example" : "plot", + "nullable" : true, + "type" : "string" + }, + "levelOrder" : { + "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "example" : 2, + "nullable" : true, + "type" : "integer" } }, - "required" : [ "data" ], + "title" : "ObservationUnitHierarchyLevel", "type" : "object" }, - "SeedLotTransactionListResponse" : { + "Trial_datasetAuthorships_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "datasetPUI" : { + "description" : "The DOI or other permanent unique identifier for this published dataset", + "example" : "doi:10.15454/312953986E3", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "license" : { + "description" : "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended.", + "example" : "https://CreativeCommons.org/licenses/by/4.0", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/SeedLotTransactionListResponse_result" + "publicReleaseDate" : { + "description" : "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described.", + "format" : "date", + "nullable" : true, + "type" : "string" + }, + "submissionDate" : { + "description" : "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository.", + "format" : "date", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "SeedLotTransactionListResponse", "type" : "object" }, - "StudyListResponse_result" : { + "Trial_publications_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Study" - }, - "type" : "array" + "publicationPUI" : { + "example" : "doi:10.15454/312953986E3", + "nullable" : true, + "type" : "string" + }, + "publicationReference" : { + "example" : "Selby, BrAPI - An application programming interface for plant breeding applications, Bioinformatics, https://doi.org/10.1093/bioinformatics/190", + "nullable" : true, + "type" : "string" } }, - "required" : [ "data" ], "type" : "object" }, - "StudyListResponse" : { + "VariantSet_metadataFields_inner" : { + "description" : "This represents a type of genotyping data or metadata available in this VariantSet", + "nullable" : true, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "dataType" : { + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "enum" : [ "string", "integer", "float", "boolean" ], + "example" : "integer", + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "fieldAbbreviation" : { + "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"", + "example" : "GQ", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/StudyListResponse_result" + "fieldName" : { + "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"", + "example" : "Genotype Quality", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "StudyListResponse", "type" : "object" }, - "StudySingleResponse" : { + "ShipmentForm" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "fileDescription" : { + "description" : "The human readable long description for this form", + "example" : "This is a shipment manifest form", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "fileName" : { + "description" : "The human readable name for this form", + "example" : "Shipment Manifest", + "nullable" : true, + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Study" + "fileURL" : { + "description" : "The URL to download this form", + "example" : "https://vendor.org/forms/manifest.pdf", + "format" : "uri", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "StudySingleResponse", + "required" : [ "fileURL" ], + "title" : "ShipmentForm", "type" : "object" }, - "TraitListResponse_result" : { + "VendorOrderSubmissionRequest_plates_inner_samples_inner_concentration" : { + "description" : "A value with units", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Trait" - }, - "type" : "array" + "units" : { + "description" : "Units (example: \"ng/ul\")", + "example" : "ng/ul", + "type" : "string" + }, + "value" : { + "description" : "Value (example: \"2.3\")", + "example" : 2.3, + "type" : "number" } }, - "required" : [ "data" ], "type" : "object" }, - "TraitListResponse" : { + "VendorOrderSubmissionRequest_plates_inner_samples_inner_volume" : { + "description" : "A value with units", + "nullable" : true, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "units" : { + "description" : "Units (example: \"ng/ul\")", + "example" : "ng/ul", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/TraitListResponse_result" + "value" : { + "description" : "Value (example: \"2.3\")", + "example" : 2.3, + "type" : "number" } }, - "required" : [ "metadata", "result" ], - "title" : "TraitListResponse", "type" : "object" }, - "TraitSingleResponse" : { + "VendorOrderSubmissionRequest_plates_inner_samples_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "clientSampleBarCode" : { + "description" : "(Optional) The value of the bar code attached to this sample", + "example" : "7c07e527", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "clientSampleId" : { + "description" : "The ID which uniquely identifies this sample to the client making the request", + "example" : "bd96bd69", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Trait" + "column" : { + "description" : "The Column identifier for this samples location in the plate", + "example" : 6, + "maximum" : 12, + "minimum" : 1, + "nullable" : true, + "type" : "integer" + }, + "comments" : { + "description" : "Generic comments about this sample for the vendor", + "example" : "This is my favorite sample, please be extra careful with it.", + "nullable" : true, + "type" : "string" + }, + "concentration" : { + "$ref" : "#/components/schemas/VendorOrderSubmissionRequest_plates_inner_samples_inner_concentration" + }, + "organismName" : { + "description" : "Scientific organism name", + "example" : "Aspergillus fructus", + "nullable" : true, + "type" : "string" + }, + "row" : { + "description" : "The Row identifier for this samples location in the plate", + "example" : "B", + "nullable" : true, + "type" : "string" + }, + "speciesName" : { + "description" : "Scientific species name", + "example" : "Aspergillus fructus", + "nullable" : true, + "type" : "string" + }, + "taxonomyOntologyReference" : { + "$ref" : "#/components/schemas/GermplasmAttribute_ontologyReference" + }, + "tissueType" : { + "description" : "The type of tissue in this sample. List of accepted tissue types can be found in the Vendor Specs.", + "example" : "Root", + "nullable" : true, + "type" : "string" + }, + "tissueTypeOntologyReference" : { + "$ref" : "#/components/schemas/GermplasmAttribute_ontologyReference" + }, + "volume" : { + "$ref" : "#/components/schemas/VendorOrderSubmissionRequest_plates_inner_samples_inner_volume" + }, + "well" : { + "description" : "The Well identifier for this samples location in the plate. Usually a concatenation of Row and Column, or just a number if the samples are not part of an ordered plate.", + "example" : "B6", + "nullable" : true, + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "TraitSingleResponse", + "required" : [ "clientSampleId" ], "type" : "object" }, - "TrialListResponse_result" : { + "VendorOrderSubmissionRequest_plates_inner" : { "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", + "clientPlateBarcode" : { + "description" : "(Optional) The value of the bar code attached to this plate", + "example" : "6ebf3f25", + "nullable" : true, + "type" : "string" + }, + "clientPlateId" : { + "description" : "The ID which uniquely identifies this plate to the client making the request", + "example" : "02a8d6f0", + "type" : "string" + }, + "sampleSubmissionFormat" : { + "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", + "enum" : [ "PLATE_96", "TUBES" ], + "example" : "PLATE_96", + "nullable" : true, + "type" : "string" + }, + "samples" : { "items" : { - "$ref" : "#/components/schemas/Trial" + "$ref" : "#/components/schemas/VendorOrderSubmissionRequest_plates_inner_samples_inner" }, + "nullable" : true, "type" : "array" } }, - "required" : [ "data" ], "type" : "object" }, - "TrialListResponse" : { + "VendorPlateSubmission_plates_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "clientPlateBarcode" : { + "description" : "(Optional) The value of the bar code attached to this plate", + "example" : "bfb33593", + "nullable" : true, + "type" : "string" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "clientPlateId" : { + "description" : "The ID which uniquely identifies this plate to the client making the request", + "example" : "dae8f49d", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/TrialListResponse_result" + "sampleSubmissionFormat" : { + "$ref" : "#/components/schemas/PlateFormat" + }, + "samples" : { + "items" : { + "$ref" : "#/components/schemas/VendorSample" + }, + "type" : "array" } }, - "required" : [ "metadata", "result" ], - "title" : "TrialListResponse", "type" : "object" }, - "TrialSingleResponse" : { + "VendorSpecificationService_specificRequirements_inner" : { "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "description" : { + "description" : "The value of a key-value entry in a map of Vendor specific requirements", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/Trial" + "key" : { + "description" : "The key of a key-value entry in a map of Vendor specific requirements", + "type" : "string" } }, - "required" : [ "metadata", "result" ], - "title" : "TrialSingleResponse", "type" : "object" }, - "VariantSetsListResponseResult" : { + "metadata_datafiles_inner" : { + "description" : "A dataFile contains a URL and the relevant file metadata to represent a file", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/VariantSet" - }, - "type" : "array" + "fileDescription" : { + "description" : "A human readable description of the file contents", + "example" : "This is an Excel data file", + "type" : "string" + }, + "fileMD5Hash" : { + "description" : "The MD5 Hash of the file contents to be used as a check sum", + "example" : "c2365e900c81a89cf74d83dab60df146", + "type" : "string" + }, + "fileName" : { + "description" : "The name of the file", + "example" : "datafile.xlsx", + "type" : "string" + }, + "fileSize" : { + "description" : "The size of the file in bytes", + "example" : 4398, + "type" : "integer" + }, + "fileType" : { + "description" : "The type or format of the file. Preferably MIME Type.", + "example" : "application/vnd.ms-excel", + "type" : "string" + }, + "fileURL" : { + "description" : "The absolute URL where the file is located", + "example" : "https://wiki.brapi.org/examples/datafile.xlsx", + "format" : "uri", + "type" : "string" } }, - "required" : [ "data" ], - "title" : "VariantSetsListResponseResult", + "required" : [ "fileURL" ], "type" : "object" }, - "VariantSetsListResponse" : { + "metadata_pagination" : { + "description" : "The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Pages are zero indexed, so the first page will be page 0 (zero).", "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "currentPage" : { + "default" : 0, + "description" : "The index number for the returned page of data. This should always match the requested page number or the default page (0).", + "example" : 0, + "type" : "integer" }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" + "pageSize" : { + "default" : 1000, + "description" : "The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned.", + "example" : 1000, + "type" : "integer" }, - "result" : { - "$ref" : "#/components/schemas/VariantSetsListResponseResult" + "totalCount" : { + "description" : "The total number of elements that are available on the server and match the requested query parameters.", + "example" : 10, + "type" : "integer" + }, + "totalPages" : { + "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", + "example" : 1, + "type" : "integer" } }, - "required" : [ "metadata", "result" ], - "title" : "VariantSetsListResponse", + "required" : [ "currentPage", "pageSize" ], "type" : "object" }, - "VariantsListResponseResult" : { + "metadata_status_inner" : { + "description" : "An array of status messages to convey technical logging information from the server to the client.", "properties" : { - "data" : { - "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", - "items" : { - "$ref" : "#/components/schemas/Variant" - }, - "type" : "array" + "message" : { + "description" : "A short message concerning the status of this request/response", + "example" : "Request accepted, response successful", + "type" : "string" + }, + "messageType" : { + "description" : "The logging level for the attached message", + "enum" : [ "DEBUG", "ERROR", "WARNING", "INFO" ], + "example" : "INFO", + "type" : "string" } }, - "required" : [ "data" ], - "title" : "VariantsListResponseResult", + "required" : [ "message", "messageType" ], "type" : "object" }, - "VariantsListResponse" : { + "metadataTokenPagination_pagination" : { + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken to construct an additional query and move to the next or previous page respectively. ", + "example" : { + "currentPage" : 0, + "pageSize" : 1000, + "totalCount" : 10, + "totalPages" : 1 + }, "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" + "currentPage" : { + "default" : 0, + "description" : "The index number for the returned page of data. This should always match the requested page number or the default page (0).", + "example" : 0, + "type" : "integer" }, - "metadata" : { - "$ref" : "#/components/schemas/metadataTokenPagination" + "currentPageToken" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the current page of data.", + "example" : "48bc6ac1", + "type" : "string" }, - "result" : { - "$ref" : "#/components/schemas/VariantsListResponseResult" + "nextPageToken" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the next page of data.", + "example" : "cb668f63", + "type" : "string" + }, + "pageSize" : { + "default" : 1000, + "description" : "The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned.", + "example" : 1000, + "type" : "integer" + }, + "prevPageToken" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the previous page of data.", + "example" : "9659857e", + "type" : "string" + }, + "totalCount" : { + "description" : "The total number of elements that are available on the server and match the requested query parameters.", + "example" : 10, + "type" : "integer" + }, + "totalPages" : { + "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", + "example" : 1, + "type" : "integer" } }, - "required" : [ "metadata", "result" ], - "title" : "VariantsListResponse", + "required" : [ "currentPage", "nextPageToken", "pageSize" ], "type" : "object" } }, diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index 5cb30f24..82ecd7f0 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -31,18 +31,6 @@ > Get the details of a specific Germplasm in MCPD format -##### `GET` /germplasm/{germplasmDbId}/pedigree - -> **Deprecated in v2.1** Please use `GET /pedigree?germplasmDbId={germplasmDbId}`. Github issue number #481 ->
Get the pedigree details of a specific Germplasm - - -##### `GET` /germplasm/{germplasmDbId}/progeny - -> **Deprecated in v2.1** Please use `GET /pedigree?germplasmDbId={germplasmDbId}`. Github issue number #481 ->
Get the progeny details of a specific Germplasm - - ##### `PUT` /images/{imageDbId}/imagecontent > Attach an image binary file to an existing image metadata record @@ -53,11 +41,6 @@ > Add new data members to a specific List -##### `POST` /lists/{listDbId}/items - -> Add Items to a specific List - - ##### `GET` /maps/{mapDbId}/linkagegroups > Get the Linkage Groups of a specific Genomic Map @@ -113,46 +96,6 @@ > Create new `VariantSet` based on search results -##### `GET` /vendor/orders - -> List current available orders - - -##### `POST` /vendor/orders - -> Submit New Order - - -##### `GET` /vendor/orders/{orderId}/plates - -> Get the Plates for a specific Order - - -##### `GET` /vendor/orders/{orderId}/results - -> Get the results of a specific Order - - -##### `GET` /vendor/orders/{orderId}/status - -> Get the status of a specific Order - - -##### `POST` /vendor/plates - -> Submit a new set of Sample data - - -##### `GET` /vendor/plates/{submissionId} - -> Get the data for a submitted set of plates - - -##### `GET` /vendor/specifications - -> Get the Vendor Specifications - - ##### `PUT` /calls > Update existing `Calls` with new genotype value or metadata @@ -173,11 +116,6 @@ > Update the details of existing Plates -##### `PUT` /samples/{sampleDbId} - -> Update the details of an existing Sample - - ##### `PUT` /observations/{observationDbId} > Update an existing Observation @@ -264,8 +202,11 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit + New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -382,8 +323,11 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit + New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -502,8 +446,11 @@ Changed response : **200 OK** * Changed property `result` (object) + > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit + New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -609,6 +556,7 @@ Changed content type : `application/json` New required properties: - `attributeDbId` +- `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -708,8 +656,11 @@ Changed response : **200 OK** * Changed property `result` (object) + > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit + New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -888,6 +839,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. + * Added property `attributePUI` (string) @@ -945,6 +898,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. + * Added property `attributePUI` (string) @@ -1006,6 +961,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. + * Added property `attributePUI` (string) @@ -1096,6 +1053,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. + * Added property `attributePUI` (string) @@ -1167,6 +1126,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The techniques and protocol used to produce a Cross or Germplasm + New required properties: - `abbreviation` @@ -1201,6 +1162,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -1212,6 +1175,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The techniques and protocol used to produce a Cross or Germplasm + New required properties: - `abbreviation` @@ -1304,6 +1269,10 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Call` represents the determination of genotype with respect to a particular `Variant`. + > + > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. + * Deleted property `genotype` (object) @@ -1435,6 +1404,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample + * Added property `sampleName` (string) @@ -1486,6 +1457,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -1497,6 +1470,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample + * Added property `sampleName` (string) @@ -1610,6 +1585,10 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Call` represents the determination of genotype with respect to a particular `Variant`. + > + > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. + * Deleted property `genotype` (object) @@ -1700,6 +1679,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented. + * Deleted property `crossingProjectDbId` (string) > The unique identifier for a crossing project @@ -1756,6 +1737,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented. + * Deleted property `crossingProjectDbId` (string) > The unique identifier for a crossing project @@ -1816,6 +1799,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented. + * Deleted property `crossingProjectDbId` (string) > The unique identifier for a crossing project @@ -1905,6 +1890,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented. + * Deleted property `crossingProjectDbId` (string) > The unique identifier for a crossing project @@ -1983,6 +1970,9 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. + >
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other + * Added property `studyPUI` (string) @@ -2137,6 +2127,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `sampleDbIds` (array) @@ -2277,6 +2269,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `sampleDbIds` (array) @@ -2409,6 +2403,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -2420,6 +2416,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `sampleDbIds` (array) @@ -2666,6 +2664,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -2677,6 +2677,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `sampleDbIds` (array) @@ -2866,6 +2868,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. + * Added property `personDbId` (string) @@ -2931,6 +2935,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. + * Added property `personDbId` (string) @@ -2988,6 +2994,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -2999,6 +3007,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. + * Added property `personDbId` (string) @@ -3104,6 +3114,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -3115,6 +3127,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. + * Added property `personDbId` (string) @@ -3220,6 +3234,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map. + New optional properties: - `mapName` @@ -3274,6 +3290,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -3285,6 +3303,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map. + New optional properties: - `mapName` @@ -3363,6 +3383,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. + * Added property `mapPUI` (string) @@ -3451,6 +3473,9 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A description of the way an Observation should be collected. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + * Added property `ontologyReferenceDbId` (string) @@ -3508,6 +3533,9 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A description of the way an Observation should be collected. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + * Added property `ontologyReferenceDbId` (string) @@ -3559,6 +3587,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -3570,6 +3600,9 @@ Changed response : **200 OK** * Changed property `result` (object) + > A description of the way an Observation should be collected. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + * Added property `ontologyReferenceDbId` (string) @@ -3619,6 +3652,8 @@ Changed content type : `application/json` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -3630,6 +3665,9 @@ Changed response : **200 OK** * Changed property `result` (object) + > A description of the way an Observation should be collected. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + * Added property `ontologyReferenceDbId` (string) @@ -3820,6 +3858,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. + * Added property `germplasmPUI` (string) @@ -3965,6 +4005,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. + * Added property `germplasmPUI` (string) @@ -4060,6 +4102,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. + * Added property `germplasmPUI` (string) @@ -4159,6 +4203,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. + * Added property `germplasmPUI` (string) @@ -4262,6 +4308,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifier and metadata needed to reference an external controlled vocabulary + * Deleted property `ontologyDbId` (string) > Ontology database unique identifier @@ -4313,6 +4361,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifier and metadata needed to reference an external controlled vocabulary + * Deleted property `ontologyDbId` (string) > Ontology database unique identifier @@ -4370,6 +4420,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The identifier and metadata needed to reference an external controlled vocabulary + * Deleted property `ontologyDbId` (string) > Ontology database unique identifier @@ -4451,6 +4503,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The identifier and metadata needed to reference an external controlled vocabulary + * Deleted property `ontologyDbId` (string) > Ontology database unique identifier @@ -4604,6 +4658,8 @@ Changed: `germplasmPUI` in `query` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -4619,6 +4675,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances. + New required properties: - `germplasmPUI` @@ -4688,6 +4746,8 @@ Changed content type : `application/json` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -4703,6 +4763,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances. + New required properties: - `germplasmPUI` @@ -4834,6 +4896,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -4891,6 +4955,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -4942,6 +5008,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -4953,6 +5021,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -5034,6 +5104,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -5045,6 +5117,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -5178,6 +5252,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. + * Added property `programName` (string) @@ -5247,6 +5323,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. + * Added property `programName` (string) @@ -5310,6 +5388,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -5321,6 +5401,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. + * Added property `programName` (string) @@ -5432,6 +5514,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. + * Added property `personDbId` (string) @@ -5501,6 +5585,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. + * Added property `personDbId` (string) @@ -5574,6 +5660,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. + * Added property `personDbId` (string) @@ -5689,6 +5777,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. + * Added property `personDbId` (string) @@ -5818,6 +5908,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). + New required properties: - `sampleDbId` @@ -5974,6 +6066,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -5989,6 +6083,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). + New required properties: - `sampleDbId` @@ -6091,6 +6187,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). + New required properties: - `sampleDbId` @@ -6185,6 +6283,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -6196,6 +6296,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). + New required properties: - `sampleDbId` @@ -6309,6 +6411,8 @@ Changed response : **200 OK** * Added property `data` (array) Items (object): + > The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier. + * Property `callSetDbIds` (array) @@ -6398,6 +6502,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -6489,8 +6595,11 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit + New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -6623,7 +6732,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -6639,8 +6752,11 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit + New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -6763,6 +6879,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. + * Added property `attributePUI` (string) @@ -6838,7 +6956,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -6854,6 +6976,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. + * Added property `attributePUI` (string) @@ -6935,6 +7059,10 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Call` represents the determination of genotype with respect to a particular `Variant`. + > + > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. + * Deleted property `genotype` (object) @@ -7021,6 +7149,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -7052,6 +7182,10 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Call` represents the determination of genotype with respect to a particular `Variant`. + > + > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. + * Deleted property `genotype` (object) @@ -7122,6 +7256,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample + * Added property `sampleName` (string) @@ -7197,6 +7333,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -7212,6 +7350,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample + * Added property `sampleName` (string) @@ -7275,6 +7415,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `sampleDbIds` (array) @@ -7433,7 +7575,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -7449,6 +7595,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `sampleDbIds` (array) @@ -7597,6 +7745,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. + * Added property `personDbId` (string) @@ -7680,6 +7830,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -7695,6 +7847,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. + * Added property `personDbId` (string) @@ -7768,6 +7922,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. + * Added property `mapPUI` (string) @@ -7836,6 +7992,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -7851,6 +8009,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. + * Added property `mapPUI` (string) @@ -7909,6 +8069,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. + * Added property `germplasmPUI` (string) @@ -8022,7 +8184,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -8038,6 +8204,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. + * Added property `germplasmPUI` (string) @@ -8141,6 +8309,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances. + New required properties: - `germplasmPUI` @@ -8242,7 +8412,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -8258,6 +8432,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances. + New required properties: - `germplasmPUI` @@ -8349,6 +8525,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -8424,6 +8602,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -8439,6 +8619,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -8504,6 +8686,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. + * Added property `programName` (string) @@ -8591,7 +8775,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -8607,6 +8795,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. + * Added property `programName` (string) @@ -8684,6 +8874,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. + * Added property `personDbId` (string) @@ -8771,7 +8963,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -8787,6 +8983,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. + * Added property `personDbId` (string) @@ -8864,6 +9062,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). + New required properties: - `sampleDbId` @@ -8984,7 +9184,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -9000,6 +9204,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). + New required properties: - `sampleDbId` @@ -9112,6 +9318,7 @@ Changed response : **200 OK** Changed items (object): New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -9240,7 +9447,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -9258,6 +9469,7 @@ Changed response : **200 OK** Changed items (object): New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -9376,6 +9588,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. + * Added property `variantSetName` (string) @@ -9496,6 +9710,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -9511,6 +9727,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. + * Added property `variantSetName` (string) @@ -9615,6 +9833,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A VariantSet is a collection of variants and variant calls intended to be analyzed together. + * Added property `analysiDbIds` (array) @@ -9703,6 +9923,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -9718,6 +9940,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A VariantSet is a collection of variants and variant calls intended to be analyzed together. + * Added property `analysiDbIds` (array) @@ -9802,6 +10026,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like "Spring" or "Summer", or this term could be a month, like "May" or "June", or this could be an arbitrary season name which is meaningful to the breeding Program like "PlantingTime_3" or "Season E". + * Changed property `seasonDbId` (string) @@ -9835,6 +10061,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like "Spring" or "Summer", or this term could be a month, like "May" or "June", or this could be an arbitrary season name which is meaningful to the breeding Program like "PlantingTime_3" or "Season E". + * Changed property `seasonDbId` (string) @@ -9872,6 +10100,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like "Spring" or "Summer", or this term could be a month, like "May" or "June", or this could be an arbitrary season name which is meaningful to the breeding Program like "PlantingTime_3" or "Season E". + * Changed property `seasonDbId` (string) @@ -9913,6 +10143,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like "Spring" or "Summer", or this term could be a month, like "May" or "June", or this could be an arbitrary season name which is meaningful to the breeding Program like "PlantingTime_3" or "Season E". + * Changed property `seasonDbId` (string) @@ -9974,6 +10206,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program. + * Deleted property `contentMixture` (array) > The mixture of germplasm present in the seed lot. @@ -10051,6 +10285,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program. + * Deleted property `contentMixture` (array) > The mixture of germplasm present in the seed lot. @@ -10122,6 +10358,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -10133,6 +10371,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program. + * Deleted property `contentMixture` (array) > The mixture of germplasm present in the seed lot. @@ -10254,6 +10494,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -10265,6 +10507,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program. + * Deleted property `contentMixture` (array) > The mixture of germplasm present in the seed lot. @@ -10376,6 +10620,9 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Trait describes what property is being observed. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + * Added property `ontologyReferenceDbId` (string) @@ -10449,6 +10696,9 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Trait describes what property is being observed. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + * Added property `ontologyReferenceDbId` (string) @@ -10514,6 +10764,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -10525,6 +10777,9 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Trait describes what property is being observed. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + * Added property `ontologyReferenceDbId` (string) @@ -10590,6 +10845,8 @@ Changed content type : `application/json` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -10601,6 +10858,9 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Trait describes what property is being observed. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + * Added property `ontologyReferenceDbId` (string) @@ -10781,6 +11041,7 @@ Changed response : **200 OK** Changed items (object): New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -10893,6 +11154,7 @@ Changed response : **200 OK** Changed items (object): New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -10997,6 +11259,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -11010,6 +11274,7 @@ Changed response : **200 OK** * Changed property `result` (object) New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -11110,6 +11375,7 @@ Deleted: `observationVariableDbId` in `path` Changed content type : `application/json` New required properties: +- `methodDbId` - `methodName` - `observationVariableDbId` - `observationVariableDbId` @@ -11195,6 +11461,8 @@ New optional properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -11208,6 +11476,7 @@ Changed response : **200 OK** * Changed property `result` (object) New required properties: + - `methodDbId` - `methodName` - `scaleDbId` - `scaleName` @@ -11399,6 +11668,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. + * Added property `variantSetName` (string) @@ -11489,6 +11760,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -11500,6 +11773,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. + * Added property `variantSetName` (string) @@ -11652,6 +11927,10 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Call` represents the determination of genotype with respect to a particular `Variant`. + > + > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. + * Deleted property `genotype` (object) @@ -11775,6 +12054,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A VariantSet is a collection of variants and variant calls intended to be analyzed together. + * Added property `analysiDbIds` (array) @@ -11839,6 +12120,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -11850,6 +12133,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A VariantSet is a collection of variants and variant calls intended to be analyzed together. + * Added property `analysiDbIds` (array) @@ -11976,6 +12261,10 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Call` represents the determination of genotype with respect to a particular `Variant`. + > + > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. + * Deleted property `genotype` (object) @@ -12119,6 +12408,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample + * Added property `sampleName` (string) @@ -12269,6 +12560,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. + * Added property `variantSetName` (string) @@ -12385,6 +12678,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present. + * Deleted property `crossAttributes` (array) > Set of custom attributes associated with a cross @@ -12428,8 +12723,12 @@ Changed response : **200 OK** * Changed property `plannedCrossName` (string) * Changed property `parent1` (object) + > The identifying information gor the parent material of a cross. + * Added property `germplasm` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Property `accessionNumber` (string) @@ -12592,8 +12891,12 @@ New required properties: * Added property `crossingProjectName` (string) * Added property `parent1` (object) + > The identifying information gor the parent material of a cross. + * Property `germplasm` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Property `observationUnitDbId` (string) @@ -12613,6 +12916,8 @@ New required properties: * `POPULATION` * `CLONAL` * Added property `parent2` (object) + > The identifying information gor the parent material of a cross. + * Added property `plannedCrossDbId` (string) @@ -12635,6 +12940,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present. + * Deleted property `crossAttributes` (array) > Set of custom attributes associated with a cross @@ -12678,8 +12985,12 @@ Changed response : **200 OK** * Changed property `plannedCrossName` (string) * Changed property `parent1` (object) + > The identifying information gor the parent material of a cross. + * Added property `germplasm` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `observationUnitPUI` (string) @@ -12728,6 +13039,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present. + * Deleted property `crossAttributes` (array) > Set of custom attributes associated with a cross @@ -12771,8 +13084,12 @@ Changed response : **200 OK** * Changed property `plannedCrossName` (string) * Changed property `parent1` (object) + > The identifying information gor the parent material of a cross. + * Added property `germplasm` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `observationUnitPUI` (string) @@ -12841,6 +13158,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -12869,8 +13188,12 @@ Changed response : **200 OK** * Changed property `parent1` (object) + > The identifying information gor the parent material of a cross. + * Added property `germplasm` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `observationUnitPUI` (string) @@ -12918,8 +13241,12 @@ New required properties: * Added property `crossingProjectName` (string) * Added property `parent1` (object) + > The identifying information gor the parent material of a cross. + * Added property `parent2` (object) + > The identifying information gor the parent material of a cross. + * Added property `plannedCrossDbId` (string) @@ -12951,6 +13278,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -12979,8 +13308,12 @@ Changed response : **200 OK** * Changed property `parent1` (object) + > The identifying information gor the parent material of a cross. + * Added property `germplasm` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `observationUnitPUI` (string) @@ -13029,6 +13362,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field. + * Deleted property `externalReferences` (array) > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. @@ -13057,8 +13392,12 @@ Changed response : **200 OK** * Changed property `parent1` (object) + > The identifying information gor the parent material of a cross. + * Added property `germplasm` (object) + > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. + * Added property `observationUnitPUI` (string) @@ -13180,6 +13519,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable. + * Added property `sourceGermplasmDbIds` (array) @@ -13222,6 +13563,8 @@ Changed response : **200 OK** * Changed property `sourceURI` (string) * Changed property `species` (object) + > A pointer to an ontology used by a genomic reference + * Changed property `term` (string) @@ -13247,6 +13590,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -13258,6 +13603,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable. + * Added property `sourceGermplasmDbIds` (array) @@ -13300,6 +13647,8 @@ Changed response : **200 OK** * Changed property `sourceURI` (string) * Changed property `species` (object) + > A pointer to an ontology used by a genomic reference + * Changed property `term` (string) @@ -13384,6 +13733,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data. + * Added property `referenceDbId` (string) @@ -13430,6 +13781,8 @@ Changed response : **200 OK** * Changed property `sourceURI` (string) * Changed property `species` (object) + > A pointer to an ontology used by a genomic reference + * Changed property `term` (string) @@ -13468,6 +13821,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data. + * Added property `referenceDbId` (string) @@ -13514,6 +13869,8 @@ Changed response : **200 OK** * Changed property `sourceURI` (string) * Changed property `species` (object) + > A pointer to an ontology used by a genomic reference + * Changed property `term` (string) @@ -13579,6 +13936,9 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Scale describes the units and acceptable values for an ObservationVariable. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + * Added property `ontologyReferenceDbId` (string) @@ -13618,6 +13978,8 @@ Changed response : **200 OK** * Changed property `units` (string) * Changed property `validValues` (object) + > Metadata describing the acceptable values for this Scale + * Added property `scaleDbId` (string) @@ -13669,6 +14031,9 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Scale describes the units and acceptable values for an ObservationVariable. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + * Added property `ontologyReferenceDbId` (string) @@ -13708,6 +14073,8 @@ Changed response : **200 OK** * Changed property `units` (string) * Changed property `validValues` (object) + > Metadata describing the acceptable values for this Scale + * Added property `scaleDbId` (string) @@ -13751,6 +14118,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -13762,6 +14131,9 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Scale describes the units and acceptable values for an ObservationVariable. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + * Added property `ontologyReferenceDbId` (string) @@ -13801,6 +14173,8 @@ Changed response : **200 OK** * Changed property `units` (string) * Changed property `validValues` (object) + > Metadata describing the acceptable values for this Scale + * Added property `scaleDbId` (string) @@ -13844,6 +14218,8 @@ Changed content type : `application/json` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -13855,6 +14231,9 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Scale describes the units and acceptable values for an ObservationVariable. + >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + * Added property `ontologyReferenceDbId` (string) @@ -13894,6 +14273,8 @@ Changed response : **200 OK** * Changed property `units` (string) * Changed property `validValues` (object) + > Metadata describing the acceptable values for this Scale + * Added property `scaleDbId` (string) @@ -13963,6 +14344,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable. + * Added property `sourceGermplasmDbIds` (array) @@ -14005,6 +14388,8 @@ Changed response : **200 OK** * Changed property `sourceURI` (string) * Changed property `species` (object) + > A pointer to an ontology used by a genomic reference + * Changed property `term` (string) @@ -14044,6 +14429,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -14059,6 +14446,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable. + * Added property `sourceGermplasmDbIds` (array) @@ -14101,6 +14490,8 @@ Changed response : **200 OK** * Changed property `sourceURI` (string) * Changed property `species` (object) + > A pointer to an ontology used by a genomic reference + * Changed property `term` (string) @@ -14150,6 +14541,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data. + * Added property `referenceDbId` (string) @@ -14196,6 +14589,8 @@ Changed response : **200 OK** * Changed property `sourceURI` (string) * Changed property `species` (object) + > A pointer to an ontology used by a genomic reference + * Changed property `term` (string) @@ -14235,6 +14630,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -14250,6 +14647,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data. + * Added property `referenceDbId` (string) @@ -14296,6 +14695,8 @@ Changed response : **200 OK** * Changed property `sourceURI` (string) * Changed property `species` (object) + > A pointer to an ontology used by a genomic reference + * Changed property `term` (string) @@ -14345,13 +14746,15 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - * Added property `contactDbIds` (array) - * Added property `environmentParameterDbIds` (array) + * Added property `contactDbIds` (array) * Added property `lastUpdateDbId` (string) + * Added property `observationLevelDbIds` (array) + * Added property `trialPUI` (string) * Deleted property `contacts` (array) @@ -14431,6 +14834,8 @@ Changed response : **200 OK** * Changed property `trialName` (string) * Changed property `experimentalDesign` (object) + > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + * Added property `studyDbId` (string) @@ -14443,6 +14848,8 @@ Changed response : **200 OK** * Changed property `description` (string) * Changed property `growthFacility` (object) + > Short description of the facility in which the study was carried out. + * Added property `studyDbId` (string) @@ -14488,7 +14895,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -14504,13 +14915,15 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - * Added property `contactDbIds` (array) - * Added property `environmentParameterDbIds` (array) + * Added property `contactDbIds` (array) * Added property `lastUpdateDbId` (string) + * Added property `observationLevelDbIds` (array) + * Added property `trialPUI` (string) * Deleted property `contacts` (array) @@ -14590,6 +15003,8 @@ Changed response : **200 OK** * Changed property `trialName` (string) * Changed property `experimentalDesign` (object) + > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + * Added property `studyDbId` (string) @@ -14602,6 +15017,8 @@ Changed response : **200 OK** * Changed property `description` (string) * Changed property `growthFacility` (object) + > Short description of the facility in which the study was carried out. + * Added property `studyDbId` (string) @@ -14657,6 +15074,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + * Added property `studyDbIds` (array) @@ -14707,6 +15126,8 @@ Changed response : **200 OK** * Changed property `contacts` (array) Changed items (object): + > A persons contact information + * Changed property `contactDbId` (string) @@ -14754,7 +15175,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -14770,6 +15195,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + * Added property `studyDbIds` (array) @@ -14820,6 +15247,8 @@ Changed response : **200 OK** * Changed property `contacts` (array) Changed items (object): + > A persons contact information + * Changed property `contactDbId` (string) @@ -14955,13 +15384,15 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - * Added property `contactDbIds` (array) - * Added property `environmentParameterDbIds` (array) + * Added property `contactDbIds` (array) * Added property `lastUpdateDbId` (string) + * Added property `observationLevelDbIds` (array) + * Added property `trialPUI` (string) * Deleted property `contacts` (array) @@ -15041,6 +15472,8 @@ Changed response : **200 OK** * Changed property `trialName` (string) * Changed property `experimentalDesign` (object) + > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + * Added property `studyDbId` (string) @@ -15053,6 +15486,8 @@ Changed response : **200 OK** * Changed property `description` (string) * Changed property `growthFacility` (object) + > Short description of the facility in which the study was carried out. + * Added property `studyDbId` (string) @@ -15090,13 +15525,15 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - * Added property `contactDbIds` (array) - * Added property `environmentParameterDbIds` (array) + * Added property `contactDbIds` (array) * Added property `lastUpdateDbId` (string) + * Added property `observationLevelDbIds` (array) + * Added property `trialPUI` (string) * Deleted property `contacts` (array) @@ -15176,6 +15613,8 @@ Changed response : **200 OK** * Changed property `trialName` (string) * Changed property `experimentalDesign` (object) + > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + * Added property `studyDbId` (string) @@ -15188,6 +15627,8 @@ Changed response : **200 OK** * Changed property `description` (string) * Changed property `growthFacility` (object) + > Short description of the facility in which the study was carried out. + * Added property `studyDbId` (string) @@ -15219,6 +15660,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -15230,13 +15673,15 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - * Added property `contactDbIds` (array) - * Added property `environmentParameterDbIds` (array) + * Added property `contactDbIds` (array) * Added property `lastUpdateDbId` (string) + * Added property `observationLevelDbIds` (array) + * Added property `trialPUI` (string) * Deleted property `contacts` (array) @@ -15316,6 +15761,8 @@ Changed response : **200 OK** * Changed property `trialName` (string) * Changed property `experimentalDesign` (object) + > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + * Added property `studyDbId` (string) @@ -15328,6 +15775,8 @@ Changed response : **200 OK** * Changed property `description` (string) * Changed property `growthFacility` (object) + > Short description of the facility in which the study was carried out. + * Added property `studyDbId` (string) @@ -15360,10 +15809,10 @@ New required properties: * Added property `contactDbIds` (array) -* Added property `environmentParameterDbIds` (array) - * Added property `lastUpdateDbId` (string) +* Added property `observationLevelDbIds` (array) + * Added property `studyDbId` (string) * Added property `trialPUI` (string) @@ -15439,6 +15888,8 @@ New required properties: * Changed property `trialName` (string) * Changed property `experimentalDesign` (object) + > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + * Added property `studyDbId` (string) @@ -15451,6 +15902,8 @@ New required properties: * Changed property `description` (string) * Changed property `growthFacility` (object) + > Short description of the facility in which the study was carried out. + * Added property `studyDbId` (string) @@ -15465,6 +15918,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -15476,13 +15931,15 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - * Added property `contactDbIds` (array) - * Added property `environmentParameterDbIds` (array) + * Added property `contactDbIds` (array) * Added property `lastUpdateDbId` (string) + * Added property `observationLevelDbIds` (array) + * Added property `trialPUI` (string) * Deleted property `contacts` (array) @@ -15562,6 +16019,8 @@ Changed response : **200 OK** * Changed property `trialName` (string) * Changed property `experimentalDesign` (object) + > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + * Added property `studyDbId` (string) @@ -15574,6 +16033,8 @@ Changed response : **200 OK** * Changed property `description` (string) * Changed property `growthFacility` (object) + > Short description of the facility in which the study was carried out. + * Added property `studyDbId` (string) @@ -15719,6 +16180,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + * Added property `studyDbIds` (array) @@ -15769,6 +16232,8 @@ Changed response : **200 OK** * Changed property `contacts` (array) Changed items (object): + > A persons contact information + * Changed property `contactDbId` (string) @@ -15808,6 +16273,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + * Added property `studyDbIds` (array) @@ -15858,6 +16325,8 @@ Changed response : **200 OK** * Changed property `contacts` (array) Changed items (object): + > A persons contact information + * Changed property `contactDbId` (string) @@ -15889,6 +16358,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -15900,6 +16371,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + * Added property `studyDbIds` (array) @@ -15950,6 +16423,8 @@ Changed response : **200 OK** * Changed property `contacts` (array) Changed items (object): + > A persons contact information + * Changed property `contactDbId` (string) @@ -16027,6 +16502,8 @@ New required properties: * Changed property `contacts` (array) Changed items (object): + > A persons contact information + * Changed property `contactDbId` (string) @@ -16043,6 +16520,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -16054,6 +16533,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + * Added property `studyDbIds` (array) @@ -16104,6 +16585,8 @@ Changed response : **200 OK** * Changed property `contacts` (array) Changed items (object): + > A persons contact information + * Changed property `contactDbId` (string) @@ -16225,6 +16708,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The metadata for an image file that is connected to some phenotypic observation data. + * Added property `observationUnitName` (string) @@ -16311,6 +16796,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The metadata for an image file that is connected to some phenotypic observation data. + * Added property `observationUnitName` (string) @@ -16391,6 +16878,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -16402,6 +16891,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The metadata for an image file that is connected to some phenotypic observation data. + * Added property `observationUnitName` (string) @@ -16541,6 +17032,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -16552,6 +17045,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > The metadata for an image file that is connected to some phenotypic observation data. + * Added property `observationUnitName` (string) @@ -16700,6 +17195,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + * Added property `childLocationDbIds` (array) @@ -16796,6 +17293,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + * Added property `childLocationDbIds` (array) @@ -16884,6 +17383,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -16895,6 +17396,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + * Added property `childLocationDbIds` (array) @@ -17054,6 +17557,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -17065,6 +17570,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + * Added property `childLocationDbIds` (array) @@ -17294,6 +17801,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + * Added property `germplasmPUI` (string) @@ -17447,6 +17956,8 @@ New required properties: ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -17462,6 +17973,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + * Added property `germplasmPUI` (string) @@ -17540,6 +18053,8 @@ Changed content type : `application/json` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -17555,6 +18070,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + * Added property `germplasmPUI` (string) @@ -17641,6 +18158,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -17652,6 +18171,8 @@ Changed response : **200 OK** * Changed property `result` (object) + > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + * Added property `germplasmPUI` (string) @@ -17762,6 +18283,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The metadata for an image file that is connected to some phenotypic observation data. + * Added property `observationUnitName` (string) @@ -17856,7 +18379,11 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Deleted response : **404 Not Found** +> Not Found + Changed response : **200 OK** > OK @@ -17872,6 +18399,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > The metadata for an image file that is connected to some phenotypic observation data. + * Added property `observationUnitName` (string) @@ -17976,6 +18505,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + * Added property `childLocationDbIds` (array) @@ -18080,6 +18611,8 @@ Deleted: `Authorization` in `header` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -18095,6 +18628,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + * Added property `childLocationDbIds` (array) @@ -18209,6 +18744,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + * Added property `germplasmPUI` (string) @@ -18313,6 +18850,8 @@ Deleted: `pageSize` in `query` ###### Return Type: Deleted response : **202 Accepted** +> Accepted + Changed response : **200 OK** > OK @@ -18328,6 +18867,8 @@ Changed response : **200 OK** * Changed property `data` (array) Changed items (object): + > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + * Added property `germplasmPUI` (string) diff --git a/docs/requirements.txt b/docs/requirements.txt index 702146a7..ed785985 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,4 @@ # Defining the exact version will make sure things don't break sphinx==5.3.0 sphinx_rtd_theme==1.3.0 -readthedocs-sphinx-search==0.3.1 \ No newline at end of file +readthedocs-sphinx-search==0.3.2 \ No newline at end of file diff --git a/generator/build.gradle b/generator/build.gradle index b89d8e89..b0e4e8d9 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,16 +4,17 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.31.0-SNAPSHOT' + brapiSchemaToolsVersion = '0.37.0' } repositories { mavenCentral() + maven {url 'https://central.sonatype.com/repository/maven-snapshots/'} maven {url 'https://s01.oss.sonatype.org/content/repositories/snapshots/'} } dependencies { - implementation "org.brapi:brapi-schema-tools-cli:$brapiSchemaToolsVersion" + implementation "org.brapi.brapi-schema-tools:brapi-schema-tools-cli:$brapiSchemaToolsVersion" } tasks.register('copyOpenApi', Copy) { @@ -46,24 +47,48 @@ tasks.register("generateGraphQL", JavaExec) { '-l', 'GRAPHQL', '-f', filename, '-x', - '-s'] + '-t'] } tasks.register("generateOpenAPI", JavaExec) { group = 'BrAPI' - description = 'Generate OpenAPI schema from the Json Schema' + description = 'Generate YAML OpenAPI schema per module from the Json Schema' classpath = sourceSets.main.runtimeClasspath mainClass = javaMainClass workingDir = '../' - def filename = "Specification/Generated/brapi_generated.json" + def filename = "Specification/Generated" + def optionfilename = "generator/openapi-options.yaml" + def metadatafilename = "generator/openapi-metadata.yaml" args = ['generate', 'Specification/BrAPI-Schema', '-l', 'OPEN_API', '-f', filename, + '-o', optionfilename, + '-m', metadatafilename, '-c', 'Specification/OpenAPI-Components', '-x', - '-s'] + '-t'] } +tasks.register("generateOpenAPIJSON", JavaExec) { + group = 'BrAPI' + description = 'Generate Single JSON OpenAPI schema from the Json Schema' + classpath = sourceSets.main.runtimeClasspath + mainClass = javaMainClass + workingDir = '../' + def filename = "Specification/Generated/brapi_generated.json" + def optionfilename = "generator/openapi-single-file-options.yaml" + def metadatafilename = "generator/openapi-metadata.yaml" + args = ['generate', 'Specification/BrAPI-Schema', + '-l', 'OPEN_API_JSON', + '-f', filename, + '-o', optionfilename, + '-m', metadatafilename, + '-c', 'Specification/OpenAPI-Components', + '-x', + '-t'] +} + + tasks.register("generateOWL", JavaExec) { group = 'BrAPI' description = 'Generate OWL schema from the Json Schema' @@ -76,12 +101,13 @@ tasks.register("generateOWL", JavaExec) { '-f', filename, '-m', 'generator/ont-model-metadata.yaml', '-x', - '-s'] + '-t'] } tasks.register("generateAll") { dependsOn generateGraphQL dependsOn generateOpenAPI + dependsOn generateOpenAPIJSON dependsOn generateOWL } @@ -99,7 +125,7 @@ tasks.register("compareOpenAPI", JavaExec) { '-f', filename, '-w', 'MARKDOWN', '-x', - '-s'] + '-t'] } tasks.register("compareAll") { diff --git a/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml b/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml new file mode 100644 index 00000000..f55f9428 --- /dev/null +++ b/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml @@ -0,0 +1,175 @@ +info: + title: BrAPI + version: '' +openapi: 3.0.0 +paths: + /serverinfo: + get: + description: |- + Implementation Notes + + Having a consistent structure for the path string of each call is very + important for teams to be able to connect and find errors. Read more on Github. + + Here are the rules for the path of each call that should be returned + + Every word in the call path should match the documentation exactly, both in + spelling and capitalization. Note that path strings are all lower case, but + path parameters are camel case. + + Each path should start relative to \"/\" and therefore should not include \"/\" + + No leading or trailing slashes (\"/\") + + Path parameters are wrapped in curly braces (\"{}\"). The name of the path parameter + should be spelled exactly as it is specified in the documentation. + + Examples + + GOOD "call": "germplasm/{germplasmDbId}/pedigree" + + BAD "call": "germplasm/{id}/pedigree" + + BAD "call": "germplasm/{germplasmDBid}/pedigree" + + BAD "call": "brapi/v2/germplasm/{germplasmDbId}/pedigree" + + BAD "call": "/germplasm/{germplasmDbId}/pedigree/" + + BAD "call": "germplasm//pedigree" + parameters: + - description: Filter the list of endpoints based on the response content type. + in: query + name: contentType + required: false + schema: + $ref: '#/components/schemas/ContentTypes' + - description: |- + **Deprecated in v2.1** Please use `contentType`. Github issue number #443 +
The data format supported by the call. + deprecated: true + in: query + name: dataType + required: false + schema: + $ref: '#/components/schemas/ContentTypes' + - $ref: '#/components/parameters/authorizationHeader' + responses: + '200': + content: + application/json: + schema: + properties: + '@context': + $ref: '#/components/schemas/Context' + metadata: + $ref: '#/components/schemas/metadata' + result: + $ref: '#/components/schemas/ServerInfo' + required: + - metadata + - result + title: ServerInfoResponse + type: object + description: OK + headers: {} + '400': + $ref: '#/components/responses/400BadRequest' + '401': + $ref: '#/components/responses/401Unauthorized' + '403': + $ref: '#/components/responses/403Forbidden' + summary: Get the list of implemented Calls + tags: + - Server Info +components: + schemas: + Service: + type: object + required: + - service + - versions + - methods + properties: + service: + description: The name of the available call as recorded in the documentation + type: string + example: germplasm/{germplasmDbId}/pedigree + contentTypes: + description: The possible content types returned by the service endpoint + items: + $ref: '#/components/schemas/ContentTypes' + type: array + example: ['application/json'] + dataTypes: + description: |- + **Deprecated in v2.1** Please use `contentTypes`. Github issue number #443 +
The possible data formats returned by the available call + deprecated: true + items: + $ref: '#/components/schemas/ContentTypes' + type: array + example: ['application/json'] + methods: + description: The possible HTTP Methods to be used with the available call + items: + enum: + - GET + - POST + - PUT + - DELETE + type: string + type: array + example: ['GET', 'POST'] + versions: + description: The supported versions of a particular call + items: + enum: + - '2.0' + - '2.1' + - '2.2' + type: string + type: array + example: ['2.0', '2.1'] + ServerInfo: + type: object + required: + - calls + properties: + contactEmail: + description: A contact email address for this server management + type: string + example: contact@institute.org + documentationURL: + description: A URL to the human readable documentation of an object + type: string + example: institute.org/server + organizationURL: + description: The URL of the organization that manages this server and data + type: string + example: institute.org/home + organizationName: + description: The name of the organization that manages this server and data + type: string + example: The Institute + serverName: + description: The name of this server + type: string + example: The BrAPI Test Server + serverDescription: + description: A description of this server + type: string + example: |- + The BrAPI Test Server + Web Server - Apache Tomcat 7.0.32 + Database - Postgres 10 + Supported BrAPI Version - V2.0 + location: + description: Physical location of this server (ie. City, Country) + type: string + example: USA + calls: + description: Array of available calls on this server + items: + $ref: '#/components/schemas/Service' + type: array diff --git a/generator/openapi-metadata.yaml b/generator/openapi-metadata.yaml new file mode 100644 index 00000000..f4ba2f9d --- /dev/null +++ b/generator/openapi-metadata.yaml @@ -0,0 +1,2 @@ +title: BrAPI +version: 2.1 \ No newline at end of file diff --git a/generator/openapi-options.yaml b/generator/openapi-options.yaml new file mode 100644 index 00000000..5b5d386d --- /dev/null +++ b/generator/openapi-options.yaml @@ -0,0 +1,2 @@ +supplementalSpecificationFor: + BrAPI-Core: generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml \ No newline at end of file diff --git a/generator/openapi-single-file-options.yaml b/generator/openapi-single-file-options.yaml new file mode 100644 index 00000000..04e17b3a --- /dev/null +++ b/generator/openapi-single-file-options.yaml @@ -0,0 +1,3 @@ +separateByModule: false +supplementalSpecificationFor: + BrAPI-Core: generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml \ No newline at end of file