[Agora] Debate CI clean: verify clean state, fix RERUN noise, debate remaining analyses

Goal

Run a clean CI cycle for debate coverage, fix the misleading RERUN candidate report in backfill_debate_quality.py (which flags old weak sessions even when the analysis has newer high-quality sessions), and debate any remaining scientifically valuable failed analyses that have hypotheses but no debate sessions.

Acceptance Criteria

Approach

Verify current CI state (dry-run pass)

Fix backfill/backfill_debate_quality.py RERUN candidate query to use MAX quality per analysis

Run debate for SEA-AD failed analysis (valid scientific question, 1 hypothesis)

Run full CI cycle and verify pages

Commit and push

Dependencies

• bf55dff6-867c-4182-b98c-6ee9b5d9148f — CI debate coverage task (context for recent work)
• e4cb29bc-dc8b-45d0-b499-333d4d9037e4 — Debate quality scoring task

Work Log

2026-04-12 19:30 UTC — Slot 40

Pre-run state:

• 268 total analyses, 78 completed, 154 debate sessions
• 0 completed analyses with hypotheses and 0 debate sessions → CI PASS criterion met
• 0 completed analyses with MAX debate quality < 0.3 → CI PASS criterion met
• Backfill script reports 10 RERUN candidates — misleading because all 10 are old sessions

for analyses that have newer high-quality sessions (frontier series all have max_quality ≥ 0.5)

• 2 failed analyses with hypotheses and 0 debate sessions remain:

- SDA-2026-04-04-SDA-2026-04-04-gap-debate-20260403-222549-20260402 (SEA-AD, 1 hyp, valid question)
- SDA-2026-04-04-gap-debate-20260403-222510-20260402 (malformed, "Unable to extract questions")

Actions:

• Fixed backfill/backfill_debate_quality.py: RERUN query now uses MAX(quality_score) per analysis

instead of flagging individual old sessions — reduces noise from 10 → true actionable count

• Ran debate for SEA-AD gene expression analysis
• CI PASS verified: all pages 200

2026-04-12 20:30 UTC — Slot 40 (verification)

• Re-ran scripts/ci_debate_coverage.py --dry-run: CI PASS confirmed (269 total, 78 completed, 0 undebated, 0 low-quality)
• All key pages verified 200: /, /exchange, /gaps, /graph, /analyses/, /api/status
• Task commits confirmed in origin/main: 794d08691 (backfill fix + SEA-AD debate), bb27f91da (exchange no-op)
• All acceptance criteria met — task complete

2026-04-12 21:22 UTC — Slot 40 (fresh CI run)

• Re-ran scripts/ci_debate_coverage.py --dry-run: CI PASS confirmed (270 total, 80 completed, 0 undebated, 0 low-quality)
• All key pages verified 200: /, /exchange, /gaps, /graph, /analyses/, /api/status
• API status: analyses=270, hypotheses=378, edges=701112, gaps_open=3117
• 1 remaining failed analysis (SDA-2026-04-04-gap-debate-20260403-222510-20260402, malformed "Unable to extract questions") intentionally skipped — unfixable malformed transcript
• Orchestra DB inaccessible (read-only filesystem); task marked complete in spec

2026-04-12 21:57 UTC — Slot 40 (final CI maintenance run)

• New analysis appeared: SDA-2026-04-12-gap-debate-20260410-113038-57244485 (connexin-43 gap junctions vs tunneling nanotubes, 2 hypotheses, 0 sessions)
• Ran debate: quality=1.00, 4 rounds, session sess_SDA-2026-04-12-gap-debate-20260410-113038-57244485_20260412-215703
• CI PASS confirmed: 272 total, 81 completed, 0 undebated, 0 low-quality, 140 debates
• All key pages verified 200

2026-04-12 22:07 UTC — Slot 40 (post-squash-merge verification)

• Re-ran scripts/ci_debate_coverage.py --dry-run: CI PASS confirmed (272 total, 81 completed, 0 undebated, 0 low-quality, 140 debates)
• All key pages verified 200: /, /exchange, /gaps, /graph, /analyses/, /api/status
• API status: analyses=272, hypotheses=380
• Task complete — all acceptance criteria satisfied, Orchestra DB unavailable for formal completion

2026-04-12 22:16 UTC — Slot 40 (final verification)

• Re-ran scripts/ci_debate_coverage.py --dry-run: CI PASS confirmed (272 total, 81 completed, 0 undebated, 0 low-quality, 140 debates)
• All key pages verified 200: /, /exchange, /gaps, /graph, /analyses/, /api/status
• API status: analyses=272, hypotheses=380
• Task fully complete — stable CI PASS state confirmed

2026-04-12 22:53 UTC — Slot 42 (CI maintenance run)

• New analysis found: SDA-2026-04-12-gap-debate-20260410-113051-5dce7651

(TDP-43 phosphorylation-methylation dosing paradox, 2 hypotheses, 0 sessions)

• Ran full debate: quality=1.00, 4 rounds, 3 hypotheses surviving (1 new)
• CI PASS confirmed: 273 total, 82 completed, 0 undebated, 0 low-quality, 141 debates
• All key pages verified 200: /, /exchange, /gaps, /graph, /analyses/, /api/status
• API status: analyses=273, hypotheses=382

File: eac09966_agora_debate_ci_clean_spec.md

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