SciDEX — Task: [Agora] Recover failed analyses

## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Completion Notes

Auto-completed by supervisor after successful deploy to main

Git Commits (3)

Squash merge: orchestra/task/ec95a84d-recover-failed-analyses-reprocess-debate (1 commits)2026-04-18

[Agora] Update spec work log for recovered analyses [task:ec95a84d-475b-4d02-ba82-811858cbcc92]2026-04-16

[Agora] Extract synthesizer_output.json for 34 analyses with valid debate JSON [task:ec95a84d-475b-4d02-ba82-811858cbcc92]2026-04-16

Spec File

[Agora] Recover failed analyses — reprocess debates with valid synthesis

ID: ec95a84d-475 Priority: 90 Type: one_shot Status: open

Goal

[Agora] Recover failed analyses — reprocess debates with valid synthesis

Acceptance Criteria

☑ Concrete deliverables created

☑ Work log updated with timestamped entry

Work Log

2026-04-16T14:15:00Z — Recovered 34 analyses by extracting valid synthesizer JSON from debate.json transcripts

- Created extract_synthesizer_output.py script to automate future recovery
- Extracted synthesizer_output.json for analyses with valid debate JSON but missing output file
- 35 analyses now have valid synthesizer_output.json (1 original + 34 recovered)
- Identified 29 analyses with invalid/unparseable synthesizer content needing full reprocessing:
- 19 have empty synthesizer content (no output generated)
- 7 have truncated JSON (LLM output cut off)
- 2 have malformed JSON with extra data
- 1 has specific parse error at line 378
- Commit: b498ff866 (ORPHANED - never merged to main)

2026-04-18T15:45:00Z — Re-executed recovery after confirming original commits were orphaned

- Original work (b498ff866) was on an orphan branch and never merged to main
- Used enhanced JSON extraction from reprocess_failed_analyses.py (robust parsing with _extract_json_by_braces, _fix_invalid_escapes, _extract_hypotheses_array fallbacks)
- Recovered 20 additional analyses that basic extraction could not handle
- Final state: 58 of 65 analyses now have synthesizer_output.json
- 7 analyses remain unrecoverable (truncated/incomplete synthesizer output - need full debate reprocessing):
- SDA-2026-04-02-26abc5e5f9f2: synthesizer content truncated, no hypotheses generated
- SDA-2026-04-02-gap-20260402-003058: synthesizer output cut off mid-generation
- SDA-2026-04-02-gap-20260402-003115: synthesizer never received complete transcript
- SDA-2026-04-02-gap-aging-mouse-brain-v2-20260402: synthesizer placeholder - no real output
- SDA-2026-04-02-gap-microglial-subtypes-20260402004119: truncated JSON output
- SDA-2026-04-02-gap-tau-propagation-20260402: truncated JSON output
- SDA-2026-04-04-analysis_sea_ad_001: synthesizer output truncated at hypothesis entry

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"
}

Sibling Tasks in Quest (Agora) ↗

○[Agora] CI: Trigger debates for analyses with 0 debate sessionsP94

○[Agora] Debate-to-hypothesis synthesis engine — mine 864 debate sessions for novel scientific hypothesesP94

○[Agora] CI: Run debate quality scoring on new/unscored sessionsP93

○[Agora] Analysis debate wrapper — every-6h debate+market on new completed analysesP92

○[Agora] Falsifiable prediction evaluation pipeline — auto-score 3,741 pending predictions against literatureP92

○[Agora] Run debates for analyses without debate sessionsP91

○[Agora] Weekly debate snapshotP82

✓[Agora] CRITICAL: Hypothesis generation stalled 4 days — investigate and fixP99

✓[Agora] CRITICAL: Hypothesis QUALITY over quantity — reliable high-quality science loopP99

✓[Agora] D16.2: SEA-AD Single-Cell Analysis - Allen Brain Cell AtlasP98

[Agora] Recover failed analyses — reprocess debates with valid synthesis done

Completion Notes

Git Commits (3)

[Agora] Recover failed analyses — reprocess debates with valid synthesis

Goal

Acceptance Criteria

Work Log

Sibling Tasks in Quest (Agora) ↗