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Topic/change treatment backend
Description
- adds ontologies for experiment treatments and composed experiment treatments
- adds script for converting treatment projects to treatment cvterms and storing entries on phenotype table
- adds server config keys (allow_trait_edits and allow_treatment_edits) that enable creation/modification/deletion of trait and treatment cvterms respectively
- adds trait and treatment designer pages, accessible to curators on sites with those features enabled
- adds field management regimes as a projectprop, accessible from trial detail page
- adds treatments and field management regimes to label designer
- adds treatments to field map viewer
- updates splitplot trial design to use treatment ontology
- updates treatments on trial upload to require trait-style identifiers
- adds treatment upload to experimental design section of trial detail page
- treatments are inherited by substocks (plot->subplot->plant->tissue sample) on treatment upload or on substock creation
- adds treatments as a group-by option on phenotype summary statistics
- adds treatment search page
- adds treatment composition page
Important things to test:
- is is possible to upload treatments that are not successfully inherited by child stocks? (the answer should be no)
- is it possible to create substocks in such a way that they do not inherit the treatments of their parents? (the answer should be no)
- does the treatment conversion dbpatch/script work on reasonably large datasets?
- do treatments work as expected on trial upload? If uploading trials and adding plants, do these plants inherit treatments as expected?
Fixes #5552 Fixes #5578
Checklist
- [ ] Refactoring only
- [ ] Documentation only
- [ ] Fixture update only
- [ ] Bug fix
- [ ] The relevant issue has been closed.
- [ ] Further work is required.
- [ ] New feature
- [ ] Relevant tests have been created and run.
- [ ] Data was added to the fixture
- [ ] Data was added via a patch in
/t/data/fixture/patches/.
- [ ] Data was added via a patch in
- [ ] User-Facing Change
- [ ] The user manual in
/docshas been updated.
- [ ] The user manual in
- [ ] Any new Perl has been documented using perldoc.
- [ ] Any new JavaScript has been documented using JSDoc.
- [ ] Any new legacy JavaScript has been moved from
/jsto/js/source/legacy.