Robustify pathway search and visualization (SCP-5990)

[eweitz]

This refines new pathway exploration functionality before it is launched.

Overview

Previously, per #2206, the search box in study pages had a new way to search and visualize biological pathway diagrams. It's a big new feature, but had some inefficiencies and bugs:

• The loading icon often did not appear when it should have.
• Pathways don't yet work for mouse, because homology-converted pathways aren't yet integrated. This broke study gene search for mouse.
• Pathways should not have shown for numeric annotations. Such annotations have continuous values, and nodes are colored by expression in discrete group labels.
• A couple of useless Morpheus / dot plot SCP API requests were sent upon searching a pathway, slowing the UI and adding unnecessary server load

Now that's refined and fixed.

Video

Here's how it looks!

Robustify_pathway_search_and_visualization__SCP_2025-05-05.mov

Tests

A new automated test helps verify these changes work. To optionally manually test:

1. Set pathway_expression_overlay feature flag to true
2. Go to "Cellular and transcriptional diversity over the course of human lactation" study
3. In search box, type "lac"
4. Confirm suggestions appear in "Genes" and "Pathways" groups in autocomplete
5. Select first pathway suggestion
6. Confirm "Loading expression..." appears, then "Mammary gland development: pregnancy and lactation - stage 3 of 4" pathway nodes are filled with color
7. Click "Reset view"
8. Switch annotation to "time_post_partum_days"
9. Search "PTEN"
10. Gene only genes are suggestion, and no pathways are suggested
11. Go to an initialized mouse study
12. Search a gene
13. Confirm expression scatter plot is shown

This satisfies SCP-5990.

[codecov]

Codecov Report

Attention: Patch coverage is 85.36585% with 6 lines in your changes missing coverage. Please review.

Project coverage is 71.13%. Comparing base (8c3913c) to head (def2112).
Report is 11 commits behind head on development.

Files with missing lines	Patch %	Lines
app/javascript/lib/pathway-expression.js	42.85%	3 Missing and 1 partial ⚠️
...p/javascript/components/explore/StudyGeneField.jsx	90.90%	2 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development    #2248      +/-   ##
===============================================
- Coverage        71.16%   71.13%   -0.03%     
===============================================
  Files              335      335              
  Lines            28672    28671       -1     
  Branches          2520     2522       +2     
===============================================
- Hits             20404    20395       -9     
- Misses            8126     8134       +8     
  Partials           142      142              

Files with missing lines	Coverage Δ
.../components/explore/ExploreDisplayPanelManager.jsx	62.03% <100.00%> (+0.17%)	⬆️
...vascript/components/explore/ExploreDisplayTabs.jsx	64.70% <100.00%> (-0.06%)	⬇️
...pp/javascript/components/visualization/Pathway.jsx	68.29% <100.00%> (+0.39%)	⬆️
app/javascript/lib/search-utils.js	90.16% <100.00%> (-0.67%)	⬇️
...p/javascript/components/explore/StudyGeneField.jsx	59.47% <90.90%> (+0.65%)	⬆️
app/javascript/lib/pathway-expression.js	53.72% <42.85%> (-0.29%)	⬇️

... and 4 files with indirect coverage changes

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[bistline]

Looks good!