Continuing gene_expression_context enrichment. 118 hypotheses still missing. Batch 2 covers next 30 by composite_score.
## REOPENED TASK — CRITICAL CONTEXT
This task was previously marked 'done' but the audit could not verify
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different priorities), close the task with reason "obsolete: "
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Completion Notes
Cannot verify or re-execute: local DB corrupted (database disk image is malformed), and batch2 script was migrated to deprecated/ by PG migration (aec879a68). Original work commits (1ed142fb5 etc.) never merged to main — only on orphan task branches. Task requires database access which is currently unavailable.
Git Commits (1)
[Exchange] Work log: batch 2 gene_expression_context backfill complete [task:fa89d516-0a71-458f-a2b8-4498627ec68c]2026-04-16
Spec File
[Exchange] Backfill gene_expression_context batch 2 — next 30 hypotheses
ID: fa89d516-0a7
Priority: 85
Type: one_shot
Status: open
Goal
Continuing gene_expression_context enrichment. 118 hypotheses still missing. Batch 2 covers next 30 by composite_score.
Acceptance Criteria
☐ Concrete deliverables created
☐ Work log updated with timestamped entry
Work Log
2026-04-16 13:31 PT — Slot 71 (minimax:71)
Verified task still necessary: 267 hypotheses missing gene_expression_context on main (362 enriched, 601 total)
Batch 1 covered top ~59 hypotheses (top score tier); batch 2 covers next 30 by composite_score
Created backfill/backfill_gex_batch2_fa89d516.py with curated Allen Brain Atlas + SEA-AD + GTEx data for 36 genes
28/30 hypotheses updated; 2 skipped (CYP450 enzymes is drug-target category not single gene; TREM2 and C3 is composite)
Result: 362 total hypotheses now have gene_expression_context (was 334)
Committed as b1c806933 and pushed to orchestra/task/fa89d516-backfill-gene-expression-context-batch-2
2 hypotheses still missing: h-0aecd2de (CYP450 enzymes, transporters, drug targets), h-3616325a (TREM2 and C3)
Status: complete
Payload JSON
{
"_reset_note": "This task was reset after a database incident on 2026-04-17.\n\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\ncorruption. Some work done during Apr 16-17 may have been lost.\n\n**Before starting work:**\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\n\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\nSCIDEX_DB_BACKEND=postgres env var.",
"_reset_at": "2026-04-18T06:29:22.046013+00:00",
"_reset_from_status": "done"
}