[pull] develop from solgenomics:master #29
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…r detection tool; upgrade fieldmap to d3 v4; add back missing generic message function; show non-numeric traits and raw trait data on trait detail page; other improvements.
…e BTI logo in footer.
…h, the genotyping plate loading script, seed transaction loading and management, and new reporting pages.
…eing one present.
…sted in alphabetical order, and planting date has been made optional again. The multiple trial fieldmap view now overlays phenotypic data correctly on all the trials. Fixed population requirement for stock loading script. BrAPI observations query fixed to not use materialized views. In the Cview repo, includes fixes for Cview IL map.
…n the accession detail page. Fixes issue with entrypoint.sh and how database are loaded automatically.
…olgenomics repo (not GMOD).
…lInfo for germplasm; require genotype protocol and warn of too large datasets for wizard genotype download; add script that downloads accessions for seedlot names.
…m trial using plot names; add new R libraries.
…ool; add dihaploid_induction as a new cross_type; fix issue with BrAPI observation values of 0; fix genotype download issue without protocol; fix download from project detail page; other improvements.
…pe dihaploid_induction; fix blast db related script; allow synonyms in accession upload to be replaced or appended; add new rtb logo; allow download of cached vcf files that were uploaded; other improvements.
…t data when creating seedlots from trial; add related stocks to vector page to see transformed accessions.
…ebugging alert in fieldbook file generator; improve related stocks section for vectors; add dumping script for ontologies to .obo files; fix issue with raw data phenotype section; plot order download: include correct name (harvest or planting order); create a file-based annotation search page.
…notyping page issues; additions to annotation page from file; allow protocol edits; show empty plots on geofieldmap and view only mode; implement marker validation for markersets; update certain brapi calls to 2.1 version; add new stability tool; add breeding_program type for breeding program folder.
…it input on Fieldbook); include entry number in trial download; add entry numbers to label designer; improve population related function on accession detail page; limit stock property autocomplete to 100 in stock search to prevent page crashes in large databases; flexible headers and entry numbers in single and multi trial upload; tweak GPCP tool for non-dioecious plants; run test on ubuntu-latest.
…field trial section; fix add accessions from a list; add show password check box to login page.
…wn coordinates and arrangement within the plot; make headers in the fieldbook file upload more flexible which should allow for easier image upload if other data has been transferred by BrAPI; tool compatibility feature improvements; make sure plants are added to subplots when they are present and not to plots.
…clty retrieve error conditions. When replacing accessions in plots, accession assignments are changed for all objects inheriting from that plot, such as subplot, plant and tissue_sample; improve tool compatibility checker; rename management factors to treatment factors (management factors to be implemented later); add a script to update stockprops in bulk.
…deleted when updating stock attributes; allow both point and polygon coordinates for plot geolocation information; remove a link to a specific analysis on the image_analysis tool page; improve error messages during the observation upload; improvements for the composed trait submission, including possibility to refresh lists without reloading the page; implement upload for historical tranformation data and sort transformant tables with natural sort; link to the correct label designer tool from the trial detail page; allow images to be searched by associated accessions.
…ta upload; fix polygon created when there are more than three points on geo field map; obsolete multiple transformants at once; indicate if marker found in multiple protocols; add ontology terms for time ontology; fix a couple of issues with phenotype upload.
…d cross and family name info using progeny list; add dbpatch to add missing cvterms in materialized_stockprop to fix vector search.
Update R apt source
…ssues; fix geoCoordinates to float instead of string to improve BrAPI compatibility; remove ghost image rows in trial detail page image section after images are deleted; add a script to fix tissue sample / plot associations; improve delete stock script; add new functionalities to lists.
…nsertions in transformants; edits to the manual; fix in the GCPC tool link to the selection index tool.
…ldbook files based on observation unit ids in addition to observation unit names.
…with observation units; tweak phenotype upload - do not apply checks to values that are undef, emtpy string, . or NA; fix tissue_sample count; add subplot data dimension to the wizard.
…ector detail pages; adds ability to run multiple image analyses on one image with the Image Analysis tool; allows searching with stock_id in stock search and wizard and display stock ids in result pages; adds libreoffice document format support for uploads; fixes an issue with authentication in the brapi observation call; improves loading speed of image section on trial detail pages; adds a list comparison tool.
…eenhouse design even after the trial has been created; adds a tool to view all the accessions and the genotyping protocols they were genotyped with in a table format; adds a list comparison tool with downloadable diffs between lists; fixes an issue with changing accessions in a trial using a file upload; adds the ability to scan barcodes in images containing observation unit information, with options to associate the image automatically with that observation unit; do not check the trait constraints for trait values that are not defined; adds a vector viewer on the vector construct detail pages; improve label writer features - display dimensions in either S.I. units or inches, adds options to left align or center align label texts, fixes an issue with barcode fuzzyness by moving internal barcode image creation from jpg to png; adds .ods file format support for all uploads; fixes an issue with authentication in the observation brapi call; adds ability to run image analysis for analyses that detect mulitple sub-objects and report multiple values, creates a new tissue sample for each sub-image; speeds up image section on trial detail page; adds a feature that stores marker names associated with each marker in a genotyping protocol, can assign specific names for markers in an alias column; adds improved logging for pca tool; fixes how the wizard download handles tempfiles; fixes a bug in the spatial correction tool.
…etter deal with web downloads.
…es in-silico PCR tool; fix an issue with the vector viewer css import; return ids in the same order as the names in the accession transform utility; add the new CASS logo; fix an issue with start and end date in the phenotype download; enable COMP trait variable uploads; fix an issue with CXGN::Jobs; in label designer tool, store the selected units (cm or inches) so that it is retrieved correctly when it is opened later; other improvements to label designer.
…es on trial detail page; adds a trend line to repetitive measurement graph with linear regression; fixes an issue with genotyping download; adds the ability to create new accessions from other accessions, plots, plants or tissue_samples; adds BrAPI NIRS endpoints.
…ot information on the accession detail page; fixes issues with the motif finder tool.
…adds support for Synonym Search Tool auth client; fixes aspects of the find genotypes by accession feature and allow filtering by genotyping projects; adds study create date to additional info for BrAPI call (needs to be added to the spec!).
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