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DDOS-6057: feat: timeout for files upload - #567
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Pull request overview
This PR primarily updates the Files platform client to use a longer httpx timeout when uploading file bodies to signed URLs, reducing spurious timeouts during concurrent upload_tree operations. It also includes a documentation notebook update that changes how binding pockets are obtained.
Changes:
- Extend signed-URL upload timeouts in
Files._put_to_signed_url()by configuring an explicithttpx.Timeout. - Update the constrained docking notebook to run
PocketFinderand usepockets[0]for docking. - Minor/no-op change to
src/VERSIONcontent/formatting.
Reviewed changes
Copilot reviewed 2 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| src/VERSION | No functional version bump; appears to be a formatting/no-op change. |
| src/platform/files.py | Introduces a longer, explicit httpx timeout for signed-URL PUT uploads. |
| docs/notebooks/clean/constrained-docking.ipynb | Switches pocket selection from fixture-based loading to running PocketFinder and using the first returned pocket. |
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Comment on lines
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| "pf = PocketFinder(protein=protein, pocket_count=1)\n", | ||
| "pockets = pf.run()\n", | ||
| "protein.show(pockets=pockets)" |
| "cd = ConstrainedDocking(\n", | ||
| " protein=protein,\n", | ||
| " pocket=pocket,\n", | ||
| " pocket=pockets[0],\n", |
Keep PR scoped to signed-URL upload timeout fix in files.py only. Co-authored-by: Cursor <cursoragent@cursor.com>
sg-s
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Summary
Increase httpx timeouts for signed-URL file uploads in
Files._put_to_signed_url. The default 5s read timeout was causing intermittent upload failures under concurrentupload_treeworkloads (e.g. RBFE finalize uploading hundreds of execution artifacts to S3).Timeout values: connect 10s, read 120s, write 300s, pool 10s.
Test plan
functionality-testspass (unit/integration, no live API)level-1-tests— dev env currently fails on main too (test_organizations.pyAPI shape drift); unrelated to this changedeeporigin-sdkafter merge so toolbox PR can pin5.0.1