Retry Foldseek search fetches through a reset connection - #91
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foldseek-search and foldseek-multimer-search each reuse one session across a submit POST, several poll_until_complete GETs, and a post-poll result-archive GET against search.foldseek.com -- the same reuse pattern that let a pooled connection reset go unretried in uniprot-fetch: urllib3's adapter-level Retry doesn't cover a ConnectionResetError raised while sending on a connection the server already closed, which surfaces as requests.exceptions.ConnectionError above the adapter rather than through it. foldseek-multimer-search imports _submit from foldseek_search.py rather than defining its own, so fixing it there covers both tools; multimer's own result-archive GET needed its own fix. poll_until_complete's internal GETs already retry ConnectionError/Timeout against a wall-clock deadline and are unaffected. Depends on the request_with_retry helper added in the uniprot-fetch fix (fix/uniprot-connection-reset-retry) -- this branch is based on it.
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Superseded by #93, which combines this and the other sibling fixes into one PR. |
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Summary
foldseek-searchandfoldseek-multimer-searcheach reuse one session across a submit POST, severalpoll_until_completeGETs, and a post-poll result-archive GET againstsearch.foldseek.com— the same reuse pattern that let a pooled-connection reset go unretried inuniprot-fetch.foldseek-multimer-searchimports_submitfromfoldseek_search.pyrather than defining its own, so fixing it there covers both tools; multimer's own result-archive GET needed its own separate fix.poll_until_complete's internal GETs already retryConnectionError/Timeoutagainst a wall-clock deadline and are unaffected.Depends on #84 (
fix/uniprot-connection-reset-retry) for therequest_with_retryhelper — this PR is based on that branch and should be reviewed/merged after it (or rebased ontomainonce #84 lands).Test plan
pytest tests/structure_alignment_tests/test_foldseek_search.py tests/structure_alignment_tests/test_foldseek_multimer_search.py -q -m "not integration"— 15 passed, 2 skipped (unrelated slow tests), including a new regression test on the shared_submit(covers both tools) reproducing the reused-connection failure directly.--integration(livesearch.foldseek.comremote submit-and-poll, including a real multimer search finding PDL1 complex neighbors) — 19 passed, 0 failed, 2 skipped.ruff check/ruff format --checkclean.mypy— no new errors.test_docstring_style.py) — clean.Opened as a draft for review before merging.