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Unify eFP schema + gene ID validation with combined_master.json - #328

Merged

asherpasha merged 38 commits into

BioAnalyticResource:devfrom

rmobmina:feature/reena-steven-integrated-endpoint

Aug 31, 2026

Commits on Jun 25, 2026
- Add eFP/ePlant gene ID validation, microarray probeset support, and master DB list
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  aa56b67
Commits on Jul 17, 2026
- Integrate Vincent's regex registry, fix master JSON species, refactor endpoints to use it
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  a577ee3
- Remove scratch CSVs, MDs, and one-off analysis files from repo root
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  afd8c63
Commits on Jul 23, 2026
Commits on Jul 27, 2026
Commits on Jul 28, 2026
- Clean up PR: drop local ePlant XML data, fold master_data_utils into bar_utils, and scope build-script exclusions to .git/info/exclude
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  f158077
Commits on Jul 30, 2026
- Add api/random_rows_json/ fallback dataset for local eFP seed queries
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  e7c5f96
Commits on Aug 5, 2026
Commits on Aug 6, 2026
- Address PR 328 review: simplify regex validation, drop bootstrap/fallback scaffolding
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  b31f367
Commits on Aug 7, 2026
- Replace per-species is_XXX_gene_valid() wrappers with direct is_efp_gene_valid() calls
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  6047eef
Commits on Aug 10, 2026
- Fix flake8 E302 in test_efp_data.py
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  3050b4c
- Fix cacao gene ID validation bypass and simplify eFP query service
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  7f420a0
Commits on Aug 13, 2026
- Restore per-species gene ID validators for non-eFP endpoints
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  5215f57
- Revert mfinder_utils.py to use is_arabidopsis_gene_valid
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  5d4681e
Commits on Aug 18, 2026
- cleaning up
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  f34219e
- fix test assertion for updated invalid-gene error message
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  e824146
Commits on Aug 20, 2026
- additional cleaning up
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  4ae2bfd
Commits on Aug 24, 2026
- Simplify eFP gene expression querying with dynamic per-database models
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  3dc939b
Commits on Aug 25, 2026
- Fix CI: test light_series dump isn't in the seeded test set, use arabidopsis_ecotypes instead
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  2465233
- Replace f-strings with .format() to match project convention
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  c010801
Commits on Aug 28, 2026
- revert efp_utils
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  38dcb4e
- Remove EFP_PROJECT_REGEXES and is_efp_gene_valid, use 1:1 gene_id_patterns lookups
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  374d01e
Commits on Aug 30, 2026
- DRY gene ID validation into BARUtils.is_valid_gene_id
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  d50f959