fix(pubchem): add thread safety to cache and rate limiter#379
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fix(pubchem): add thread safety to cache and rate limiter#379robotlearning123 wants to merge 6 commits intomainfrom
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…m, extractor, email_intake Wave 1 of test coverage improvements for lab-manager: - test_email_poller.py (NEW): 28 tests for IMAP polling, error handling, shutdown - test_documents_route_coverage.py: +48 tests for background tasks, CRUD, review, upload - test_litellm_client.py: +4 tests for load_litellm_config - test_pubchem.py: expanded test coverage - test_extractor_coverage.py: expanded test coverage - test_email_intake.py: expanded test coverage Unit test count: 1406 → 1444 (+38 net new) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- test_api_validation.py (NEW): 58 tests for email validation (74% → 96%) - test_more_ocr_coverage.py (NEW): 68 tests for OCR providers (59% → 100%) - test_extractor_coverage.py: +12 tests for intake/extractor (82% → 98%) - test_pubchem.py: +6 tests for pubchem service (90% → 100%) - test_litellm_client.py: +18 tests for litellm client (68% → 100%) - test_email_poller.py: +31 tests for email poller (78% → 99%) - test_email_intake.py: +9 tests for email intake (90% → 100%) - test_documents_route_coverage.py: clean 56 tests (removed isolation-broken classes) Unit test count: 1406 → 1626 (+220 net new) All 1626 pass, 0 failures. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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The locked_until field from SQLite may be offset-naive, causing TypeError when compared with datetime.now(timezone.utc). Add tz normalization. Also add access_expires_at check during login. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
PATCH could set status to approved/rejected/deleted, bypassing the review workflow. Now raises 422 for review statuses and deleted. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Route handlers should use flush() to let the session middleware handle commits. Direct commit() can cause issues with nested sessions. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- receive_items: use SELECT FOR UPDATE to prevent double-receive race - transfer: reject disposed/depleted/deleted/expired items - Fix status error message formatting Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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| staff_role_level = 4 | ||
| staff_active = False | ||
| staff_locked_until = None | ||
| staff_access_expires_at = None |
| get_settings.cache_clear() | ||
| from lab_manager.api.app import create_app | ||
|
|
||
| app = create_app() |
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Closing: cascading test file conflicts make rebase impractical. Will re-apply the fix as a clean PR from main. |
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## Summary - Add `threading.Lock` protecting `_CACHE`, `_cache_put`, and `_rate_limit` - Prevents data races in concurrent PubChem enrichment calls Replaces #379 ## Test plan - [x] `tests/test_pubchem_safety.py` verifies lock exists and concurrent cache writes succeed Co-authored-by: Cong <72737794+robolearning123@users.noreply.github.com> Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Bug
The PubChem service used module-level mutable state (
_CACHEdict and_last_request_timefloat) without threading locks. Under concurrent FastAPI requests (sync endpoints run in thread pool), this could:_last_request_timesimultaneouslyRoot Cause
No thread synchronization on shared mutable state. FastAPI runs sync endpoints in a thread pool, so concurrent requests can race.
Fix
Added
threading.Lockfor both the cache (_CACHE_LOCK) and rate limiter (_rate_limit_lock). Cache reads, writes, and evictions are all protected. Rate limiter serializes sleep+update atomically.Test
5 tests: lock existence, concurrent cache writes, eviction under concurrency, cache hit behavior.
🤖 Found and fixed by bug-hunter autonomous loop.