Add eFP/ePlant gene ID validation, microarray probeset support, and m…#324
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rmobmina wants to merge 3 commits into
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Add eFP/ePlant gene ID validation, microarray probeset support, and m…#324rmobmina wants to merge 3 commits into
rmobmina wants to merge 3 commits into
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…aster DB list Adds per-eFP-project regex validation (EFP_PROJECT_REGEXES, is_efp_gene_valid) covering both canonical gene IDs and microarray probeset IDs, with a database-to-project mapping (DATABASE_EFP_PROJECT) so gene_expression.py can validate against the right format per database. Adds the eFP+ePlant discovery/validation pipeline: - scrape_view_databases.py / scrape_species_view_info.py: live-discover every eFP and ePlant view across 55 sites, tagging eFP-only vs ePlant-only vs both - build_proj_id_view_mapping.py: resolves multi-paper databases (e.g. atgenexp_*) to per-view proj_id breakdowns - validate_db_regex_coverage.py: tests every database's real sample IDs against production validation, including legacy databases no longer linked from a live dropdown - build_master_db_list.py: rolls everything up by species, tagging source (efp/eplant/both/legacy) and platform (microarray/rna_seq) 193 databases validated, 0 unexplained failures.
… endpoints to use it - Merge heterodera_schachtii into arabidopsis (it's an Arabidopsis-gene-ID database, not a separate species); fix brassica/lupin/triticale scientific names per professor's review comments - Load EFP_PROJECT_REGEXES and DATABASE_EFP_PROJECT from Vincent's regex_master_list_efp_eplant registry (58 grouped project patterns instead of 193 per-database ones), embedded into combined_master.json at build time; empirically verify every regex_project assignment against real sample dumps before trusting it, demoting 3 unverified species-fallback guesses and fixing 2 misassigned projects (maize_lipid_map, tomato_trait) - Add a general injection checker (BARUtils.is_injection_attempt) that runs before the probeset-shape check in /gene_expression, closing a bypass where any string ending in "_at" skipped format validation entirely - Derive schema_variants directly from real sample_data column dumps instead of a coarse rna_seq/microarray platform split, so every one of the 193 databases is schema_verified against its own real columns (was 146/193) - Refactor /microarray_gene_expression/<species>/databases and .../<species>/<view>/samples to read from combined_master.json instead of a hardcoded dict and a since-deleted JSON file (the latter was broken on this branch); add test coverage for both - Add api/utils/master_data_utils.py as the shared combined_master.json loader used across bar_utils, gene_id_utils, and the refactored resource
These were leftover exploratory outputs (regex audit dumps, coverage CSVs, speed benchmark plots, old email drafts) not consumed by any script in the active build pipeline. db_regex_coverage_report.csv is kept since build_master_db_list.py reads it as an input.
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