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Topic/change treatment backend

Open ryan-preble opened this issue 3 months ago • 1 comments

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/.
    • [ ] User-Facing Change
      • [ ] The user manual in /docs has been updated.
    • [ ] Any new Perl has been documented using perldoc.
    • [ ] Any new JavaScript has been documented using JSDoc.
    • [ ] Any new legacy JavaScript has been moved from /js to /js/source/legacy.

ryan-preble avatar Sep 18 '25 13:09 ryan-preble