fix: reuse the DuckDB connection across calls, fix a cache download race - #1
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connect() opened a brand new duckdb.connect() on every call, including from inside measurements(), chembl_bridge(), dti_pairs() and query(), re-running INSTALL/LOAD httpfs, re-creating the S3 secret, and re-registering all five core views every time. Measured: 8 repeat calls to measurements() went from 318s (39.8s/call) to 5.3s (0.66s/call, ~60x) after switching to a cursor() on a shared, lazily-created base connection per release, the same fix already shipped in scigantic-pubchem's bridge.py for the same reason. cache.py's atomic download used a temp filename derived only from the cache key, so two threads racing to fill the same key raced each other's os.replace() too; reproduced directly, 11/16 threads failed with FileNotFoundError in every trial. Fixed with a uuid-suffixed temp name per call, mirroring scigantic-pubchem's cache.py fix for the identical bug. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01L4ztUhMgoMFRicB8uiYx76
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Summary
connect()opened a brand newduckdb.connect()on every call frommeasurements(),chembl_bridge(),dti_pairs()andquery(), re-runningINSTALL/LOAD httpfs, re-creating the S3 secret, and re-registering all five core views every time. Now reuses a lazily-created, per-release base connection and hands out acursor()per call (thread-safe, verified). Measured: 8 repeat calls tomeasurements()went from 318s (39.8s/call) to 5.3s (0.66s/call), ~60x. Same fix already shipped inscigantic-pubchem'sbridge.py.cache.py's atomic download used a temp filename derived only from the cache key, so two threads racing to fill the same key raced each other'sos.replace()too. Reproduced directly: 11/16 threads failed withFileNotFoundErrorin every trial before the fix. Fixed with a uuid-suffixed temp name per call, mirroringscigantic-pubchem's cache.py fix for the identical bug.Test plan
pytest -q— 38 passedmypy src/scigantic_bindingdb(strict) — clean🤖 Generated with Claude Code
https://claude.ai/code/session_01L4ztUhMgoMFRicB8uiYx76