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DDOS-6057: feat: timeout for files upload #567

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Merged
sg-s merged 2 commits into from
Jun 4, 2026
Merged

DDOS-6057: feat: timeout for files upload #567

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41b9f9a
feat: timout for files upload
sg-s Jun 4, 2026
8936b3a
chore: drop unrelated notebook and VERSION changes from timeout PR
sg-s Jun 4, 2026
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14 changes: 4 additions & 10 deletions docs/notebooks/clean/constrained-docking.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -163,15 +163,9 @@
"metadata": {},
"outputs": [],
"source": [
"repo_root = next(\n",
" p\n",
" for p in (Path.cwd(), *Path.cwd().parents)\n",
" if (p / \"tests/fixtures/files/pocketfinder/pocket_1.pdb\").exists()\n",
")\n",
"pocket = Pocket.from_pdb_file(\n",
" repo_root / \"tests/fixtures/files/pocketfinder/pocket_1.pdb\"\n",
")\n",
"protein.show(pockets=[pocket])"
"pf = PocketFinder(protein=protein, pocket_count=1)\n",
"pockets = pf.run()\n",
"protein.show(pockets=pockets)"
Comment on lines +166 to +168
]
},
{
Expand All @@ -194,7 +188,7 @@
"source": [
"cd = ConstrainedDocking(\n",
" protein=protein,\n",
" pocket=pocket,\n",
" pocket=pockets[0],\n",
" ligand=query_ligand,\n",
" reference=reference_pose,\n",
" effort=5,\n",
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2 changes: 1 addition & 1 deletion src/VERSION
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@@ -1 +1 @@
0.0.0.dev0
0.0.0.dev0
11 changes: 10 additions & 1 deletion src/platform/files.py
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Expand Up @@ -22,6 +22,15 @@

_MISSING_URL_FIELD = "Signed URL response missing 'url' field"

# Signed-URL PUTs upload full file bodies; default httpx read timeout (5s) is too
# short under concurrent upload_tree workers waiting on S3.
_SIGNED_URL_UPLOAD_TIMEOUT = httpx.Timeout(
connect=10.0,
read=120.0,
write=300.0,
pool=10.0,
)


class FileStream:
"""Streaming wrapper around an HTTP download response.
Expand Down Expand Up @@ -325,7 +334,7 @@ def _put_to_signed_url(
last_exc: Exception | None = None
for attempt in range(max_retries + 1):
try:
with httpx.Client() as upload_client:
with httpx.Client(timeout=_SIGNED_URL_UPLOAD_TIMEOUT) as upload_client:
resp = upload_client.put(
signed_url,
content=file_content,
Expand Down
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