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Topic/change treatment backend #5723

ryan-preble wants to merge 122 commits into from
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@ryan-preble ryan-preble commented Sep 18, 2025 •
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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 added 30 commits July 16, 2025 14:50
@ryan-preble
Touch files for creating backend
5a1c1ae
@ryan-preble
Rename and create field management regime dbpatch
86025f3
@ryan-preble
Create treatment CV dbpatch
f05b6e4
@ryan-preble
Suppress single trial upload
f4cfb81
@ryan-preble
Add design subsection for field management regime
af57a2b
@ryan-preble
Add skeleton field management regime UI
a2a4516
@ryan-preble
Merge branch 'master' into topic/change_treatment_backend
6e6ce89
@ryan-preble
Fixing display issue on plant dialogs and adding a bit more to field …
df5f918 
…management UI
@ryan-preble
Convert add management factor dialog to modal
cf74815
@ryan-preble
UI improvements. Tweaking treatments and management factors in trial …
98c1497 
…uploads
@ryan-preble
Rename dbpatch and move around
b2e35ea
@ryan-preble
Tweak to UI and changing get_treatments function
c0e7ee2
@ryan-preble
Adding spreadsheet treatment upload
64ac5f2
@ryan-preble
Add back old treatment project function and start conversion script
e6b15a8
@ryan-preble
First draft of treatment project conversion script
30772d1
@ryan-preble
Fixing conversion script
cbd36cc
@ryan-preble
More fixes to conversion script
6faf2a7
@ryan-preble
Change trait search page title
6291bb4
@ryan-preble
Starting management factor backend
1a22b3b
@ryan-preble
Enable adding management factors through trial detail page
10f39ee
@ryan-preble
Finish management regime on trial detail page
8b888b6
@ryan-preble
Rename treatment cv to experiment_treatment
5719e23
@ryan-preble
Add completions records to management factors
9cab160
@ryan-preble
Add edit button
5abab73
@ryan-preble
Enable editing management factors and adding completion records
4b06dca
@ryan-preble
Fix pesky newline issue
f8d1881
@ryan-preble
Fix dbpatch and script to have proper cvterm relationships
dd62c2b
@ryan-preble
First working version of dbpatch and script
3252ced
@ryan-preble
Revert trait search page to master
08d7c9b
@ryan-preble
Change conversion script to allow substocks to inherit treatments
c7dc15c
ryan-preble and others added 17 commits September 26, 2025 15:37
@ryan-preble
Add a fixture cleanup in test before failing test
a1c983c
update bookdown docs
fed19bf
@ryan-preble
Try to fix tests again
ed0dd39
@ryan-preble
Merge branch 'topic/change_treatment_backend' of github.com:solgenomi…
5a36f7a 
…cs/sgn into topic/change_treatment_backend
update bookdown docs
0d5e7c9
@ryan-preble
Fix selenium test
5fa7e5e
@ryan-preble
Merge branch 'topic/change_treatment_backend' of github.com:solgenomi…
7deb37d 
…cs/sgn into topic/change_treatment_backend
update bookdown docs
4e2d2c2
@ryan-preble
testing different dbh statements
7f27c4d
@ryan-preble
Change dbh create statement
0f21751
update bookdown docs
0f2441c
@ryan-preble
change timing of label_designer selenium test
701a731
update bookdown docs
e5e9976
@ryan-preble
Do a single storephenotypes instead of one per trial
5962642
update bookdown docs
cd42042
@ryan-preble
Do long sleep again like master branch
bb62d76
update bookdown docs
33f4788
lukasmueller
lukasmueller approved these changes Oct 16, 2025
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:-) :-) :-)

@afpowell afpowell mentioned this pull request Oct 24, 2025
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afpowell
afpowell approved these changes Oct 27, 2025
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👍

@afpowell afpowell mentioned this pull request Nov 24, 2025
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lukasmueller commented Dec 18, 2025

waiting on comments from Thomas

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Convert treatments to use ontologies Treatment improvements

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