Paused after 50 exit-0 runs with no commits on branch=(none); stale worktree deleted
h-var-*) is from 2026-04-07T14:05:08. Recent analyses show status='completed' but have 0 hypotheses associated.The earlier diagnosis (broken venv python path) was wrong. Verified:
/home/ubuntu/scidex/venv/bin/python3 exists as a symlink to /usr/bin/python3 (Python 3.12.3)anthropic 0.88.0, neo4j 6.1.0, event_bus, exchange, market_dynamics)scidex-agent.service has been running healthily for 1h+ using the venv pathPostgreSQL continuously:post_process.py opens many sub-module connections (exchange.compute_allocation_weight, event_bus.publish, market_dynamics.*) — each opens its own sqlite3.connect().event_bus.publish had a 30-second busy_timeout that wasn't enough headroom; it raised sqlite3.OperationalError: database is locked.parse_all_analyses() and crashed the entire post_process.py batch on the FIRST contended publish.Reproducible failure trace:
[1] Parsing analysis transcripts → DB
✗ FAIL evidence_gate [h-e12109e3]: No evidence citations
✓ PASS score_gate [h-e12109e3]: Valid score: 0.601
→ Could not assign missions: database is locked ← caught
Traceback ...
File ".../event_bus.py", line 67, in publish
cursor = db.execute(...)
sqlite3.OperationalError: database is locked ← uncaught, killed batchTwo-part fix in event_bus.py and post_process.py:
_BUSY_TIMEOUT). Gives WAL writers more headroom under heavy contention.event_bus.publish call sites in post_process.py with try/except sqlite3.OperationalError. A transient lock no longer crashes the whole batch — it logs and continues to the next hypothesis.These prevent the immediate crash. Verified post-patch: post_process.py no longer dies on the first contended publish; it now runs through the iteration loop.
The patch fixes the crash, but post_process.py is still slow under contention because every sub-module opens its own connection without coordinated busy_timeout:
exchange.compute_allocation_weight(db_path=...) — opens new connectionexchange.create_hypothesis_gap(db_path=...) — opens new connectionupdate_/insert_ helpers that may open their own_BUSY_TIMEOUT constant across exchange.py, market_dynamics.py, database.py so all helpers respect 120s. That's a larger follow-up.SELECT MAX(created_at) FROM hypotheses WHERE id LIKE 'h-var-%' should advance past 2026-04-07T14:05:08)/home/ubuntu/scidex/venv/bin/python3 → /home/ubuntu/miniconda3/bin/python3/home/ubuntu/scidex/venv/bin/python3 exists (symlink → /usr/bin/python3),post_process.py and saw it crash with sqlite3.OperationalError: database
is locked at event_bus.py:67 inside event_bus.publish(). The error waslsof showsevent_bus.py: bumped busy_timeout 30s → 120s (extracted as_BUSY_TIMEOUT constant), applied to all 4 sqlite3.connect call sitespost_process.py: wrapped all 3 event_bus.publish() call sites intry/except sqlite3.OperationalError so a transient lock logs-and-exchange.compute_allocation_weight() which has the same shape (opensorchestra/task/c487964b-... branch with the{
"requirements": {
"coding": 8,
"analysis": 8,
"reasoning": 8,
"safety": 7
},
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"completion_shas_checked_at": "2026-04-11T13:17:58.383044+00:00",
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"_stall_requeued_by": "pro_allen",
"_stall_requeued_at": "2026-04-15 21:46:22",
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"_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",
"_watchdog_repair_task_id": "46717e70-de02-4329-95cc-4f38a1cb9149",
"_watchdog_repair_created_at": "2026-04-18T19:02:36.825691+00:00"
}