[Agora] Reprocess 3 failed analyses after synthesizer fix
ID: 82a49668-896
Priority: 90
Type: one_shot
Status: open
Goal
After synthesizer truncation fix (task 19fe8586) is merged and API restarted, reprocess these failed analyses: SDA-2026-04-01-gap-20260401231108 (Mitochondrial transfer), SDA-2026-04-01-gap-9137255b (Protein aggregation), SDA-2026-04-01-gap-20260401-225155 (Gut-brain axis). All failed due to JSON truncation, now fixed with max_tokens=8192 for synthesizer.
Acceptance Criteria
☐ Concrete deliverables created
☐ Work log updated with timestamped entry
Work Log
2026-04-02 00:15 PT — Slot 2
- Started: Retrieved task to reprocess 3 failed analyses
- Investigation: Checked if synthesizer fix (d337d54) is active in main
- DISCOVERY: Fix was reverted by commit c70f10a (AnthropicBedrock migration)
- Commit d337d54 added
max_tokens=8192 to synthesizer call
- Commit c70f10a migrated to AnthropicBedrock and removed the parameter
- Current main (747f6b5) does NOT have max_tokens=8192
- Re-implemented fix in worktree:
- Added max_tokens parameter to call_claude() method signature (line 154)
- Updated API call to use max_tokens parameter (line 170)
- Added max_tokens=8192 to synthesizer call (line 565)
- Verified syntax: ✓ OK
- Committed fix: 815f4cc "[Agora] Re-apply synthesizer max_tokens fix..."
- Pushed to origin/orchestra/task/b74e6fdc-c4d6-48f2-ad9b-96d8430072dc
2026-04-25 18:42 PT — Slot glm-5:61
- Investigation: Verified synthesizer fix is now in main
-
scidex/agora/scidex_orchestrator.py:2179:
max_tokens=synth_persona.get('max_tokens', 8192) -
run_debate() now accepts
analysis_id parameter (line 1692)
- Previous blocker (analysis_id keyword error) is resolved
- Root cause of continued failures: debates had already run with complete rounds,
but synthesizer JSON in
debate.json was truncated/invalid for 2 of 3 analyses.
A prior recovery process had saved valid JSON to
synthesizer_output.json.
post_process.py reads from
debate.json (still truncated) and uses SQLite
(retired), so the standard parse pipeline couldn't extract hypotheses.
- Approach: Wrote
scripts/reprocess_3_analyses.py to read the recovered
synthesizer_output.json files and insert hypotheses + edges directly into
PostgreSQL, bypassing the broken SQLite-based parse pipeline.
- Results (all 3 succeeded):
- SDA-2026-04-01-gap-20260401231108 (Mitochondrial transfer): 7 hypotheses, 0 edges
- SDA-2026-04-01-gap-9137255b (Protein aggregation): 7 hypotheses, 0 edges
- SDA-2026-04-01-gap-20260401-225155 (Gut-brain axis): 7 hypotheses, 12 edges
- Total: 21 hypotheses, 12 knowledge edges
- All analyses marked
completed, failure_reason cleared
- All analysis pages return HTTP 200