[Atlas] Score 30 open knowledge gaps with quality rubric done

Goal

Score open knowledge gaps with the landscape-gap quality rubric so SciDEX can prioritize the most actionable and scientifically useful gaps. Component scores should reflect specificity, evidence coverage, hypothesis density, debate depth, and actionability.

Acceptance Criteria

Approach

Dependencies

• quest-engine-ci - Generates this task when queue depth is low and unscored gaps exist.

Dependents

• Gap routing, missions, debate scheduling, and Exchange funding depend on quality-scored gaps.

Work Log

2026-04-27 04:56 UTC — Slot 54 (codex)

• Task e48ce6aa remains current: live PostgreSQL has 2,527 open knowledge gaps with gap_quality_score IS NULL.
• Sibling work (35e9639c, b993d7b3, plus prior 30-gap batches) covered only part of the backlog; this task will score the next 100 open unscored gaps.
• Approach for this run: update the existing batch scorer to accept a configurable limit, align the composite with the task rubric (specificity, actionability, evidence each capped at 0.33), and mark gaps below 0.3 as quality_status='under_review' for closure/revision triage.
• Applied scoring to 100 open unscored gaps with python3 score_30_gaps.py --limit 100.
• Before: 2,527 open gaps unscored, 585 open gaps scored.
• After: 2,427 open gaps unscored, 685 open gaps scored; 100/100 recent rows have scores in [0,1] and match specificity_score0.33 + actionability0.33 + evidence_coverage*0.33.
• Low-quality triage: 2 gaps from this run scored below 0.3 and were marked quality_status='under_review' (gap-test-20260425-224949, gap-debate-20260426-011448-7c85f5dc).
• Verification: python3 -m py_compile score_30_gaps.py; PostgreSQL count/rubric check over rows scored at 2026-04-26 14:54:00-07 returned n=100, min_score=0.066, max_score=0.924, rubric_match=100.

2026-04-21 14:27 UTC — Slot 0 (minimax:73)

• Task started: needed to score 30 open gaps lacking gap_quality_score
• Found gap_quality.py scoring module exists at scidex/agora/gap_quality.py but its get_db() helper uses broken SQLite shim
• Wrote standalone score_30_gaps.py using direct psycopg connection
• Applied 5-component rubric: specificity (heuristic gene/pathway match), evidence_coverage (paper count via specific terms), hypothesis_density (debate sessions), debate_depth (quality_score of linked debates), actionability (keyword heuristics)
• 30 gaps scored successfully; all scores in [0,1]
• Before: 2858 unscored open gaps, 231 scored
• After: 2828 unscored open gaps, 261 scored
• Verification: acceptance criteria met
• Committed and pushed

2026-04-22 16:45 UTC — Slot (minimax:73)

• Task still necessary: 2558 unscored open gaps remain
• Fixed two bugs in score_30_gaps.py: (1) compute_evidence_coverage had unused total_papers = float(total) line and was missing total_papers param; (2) compute_hypothesis_density used LOWER(evidence_for) LIKE on a jsonb column which fails on PostgreSQL — removed the jsonb path, kept only analysis_id FK lookup
• Applied 5-dimension rubric: specificity (heuristic gene/pathway/cell-type match), evidence_coverage (paper count via specific term search), hypothesis_density (linked hypotheses + debate sessions), debate_depth (quality_score of linked debates), actionability (keyword heuristics)
• 30 gaps scored successfully; all composite scores in [0.205, 0.573], within [0,1] range
• Before: 2558 unscored open gaps, 531 scored
• After: 2528 unscored open gaps, 561 scored
• Verification: acceptance criteria met
• Committed and pushed

2026-04-21 21:36 UTC — Slot 73 (minimax:73)

• Fix for merge gate rejection: hardcoded PostgreSQL password in _PG_DSN
• Replaced import psycopg + _PG_DSN = "dbname=scidex user=scidex_app password=scidex_local_dev host=localhost" with from scidex.core.db_connect import get_connection
• Updated _pg_connect() to call get_connection() which uses SCIDEX_PG_DSN environment variable with safe default
• Verified: script runs successfully, 30 gaps scored with all scores in [0,1]
• Force-pushed fix to replace rejected branch