658 examples are missing in json schema

.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

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",

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

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\"])",
@@ -22,22 +23,25 @@
                     "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",
                     "format": "uri",
                     "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<br>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<br>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

Specification/BrAPI-Schema/BrAPI-Core/Contact.json

@@ -47,6 +47,7 @@
             ],
             "type": "object",
             "title": "Contact",
+            "description": "A persons contact information",
             "brapi-metadata": {
                 "primaryModel": false
             }

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

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"
+                ]
             }
         }
     },