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bio-nexus-api / bioai-platform /backend /app

Commit History

Jul 17

10:03
fix: logging crash, md/function_predict ligand_smiles column fallback

Samad14

f062f79

Jul 16

20:29
Fix MD simulation: OpenMM fallback, PDB ID propagation, better error handling

Samad14

d9d71ff
20:19
Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

Samad14

99fb209
19:58
Phase 2: structured JSON logging, request ID middleware, enhanced health endpoint, Sentry breadcrumbs

Samad14

a38b802
19:46
Phase 1: harden rate limits — JWT-aware keys, per-endpoint caps, daily limits on all job types

Samad14

bd279b4

Jul 15

15:37
Phase 0c: offload large artifacts to Supabase Storage (docking, pipeline, sequencing)

Samad14

e47db42
15:26
Phase 0b: durable worker with FOR UPDATE SKIP LOCKED, per-type concurrency, separate container

Samad14

fee674e
15:11
Phase 0a: SSRF protection + auth on docking/sequencing, worker design doc

Samad14

89fd26d
12:45
Fix _TRP_RINGS -> _TRP_RING_ATOMS name error

Samad14

cd2115a
12:41
Docking viewer upgrade: Molstar GPU rendering, proper interaction geometry, 3D dashed-line rendering

Samad14

e86bafa
12:06
Fix KeyError: payload['smiles'] -> payload.get('ligand_smiles')

Samad14

9bf8068
11:59
Docking: minimal INSERT (only id/status/smiles), startup table check, migration SQL

Samad14

1c8e7f8
11:52
Fix docking INSERT: only use columns guaranteed to exist in Supabase

Samad14

15b7414
11:16
Major docking rewrite: match frontend contract (pdb_id+smiles input, nested poses/interactions output, PDB fetch from RCSB, auto grid center)

Samad14

8f9cafc
11:10
Fix docking route mismatches: GET /status/{id}, frontend pdb URL prefix

Samad14

e619a9b
11:02
Fix docking route: POST /api/docking/run to match frontend

Samad14

6c8b9a8
10:55
Fix docking: add pdb_to_pdbqt_receptor() for protein PDBQT conversion

Samad14

9125057
10:08
Fix unbounded _SESSION_EVENT_COUNTS dict leak (cap at 1000)

Samad14

e0f8f74
09:43
Use Dockerfile-installed Vina first, fall back to download

Samad14

dade2b6
09:31
Fix Settings attribute names: SUPABASE_URL, SUPABASE_SERVICE_ROLE_KEY

Samad14

2341dff
09:00
fix: undefined query_length variable in _run_blast

Samad14

3dd0c04
08:55
fix: Linux Vina binary, Open Babel PDBQT, pipeline_worker utcnow⁠

Samad14

fe05da9

Jul 14

16:08
test: reduce vina timeout to 10s for faster diagnostic

Samad14

4d3a2e8
15:54
fix: indentation error at line 610

Samad14

b100aa9
15:47
fix: revert to async subprocess (no thread pool to avoid import hang), keep --cpu 1

Samad14

2a4a790
15:29
fix: use ThreadPoolExecutor with subprocess.Popen (no asyncio subprocess), add --cpu 1 and stdin=/dev/null

Samad14

d242989
15:26
fix: use asyncio.create_subprocess_exec with file handles + asyncio.wait_for (no threads, no pipes)

Samad14

48bf0d7
15:17
fix: use poll() polling loop instead of proc.wait(timeout=N) to avoid Python 3.14 pidfd-wait hang

Samad14

4a1b691
15:16
fix: use Popen + wait(timeout=N) + killpg layered kill approach

Samad14

f381b03
15:10
fix: use /usr/bin/timeout OS-level command instead of Python subprocess timeout

Samad14

8329f93
15:03
fix: use subprocess.DEVNULL for Vina output — eliminates ALL I/O blocking

Samad14

3aeb8d2
14:58
fix: use dedicated ThreadPoolExecutor(max_workers=1) + subprocess.run(file handles, timeout=N)

Samad14

1242de8
14:38
fix: use asyncio.create_subprocess_exec with file descriptors + wait_for — no threads, no pipe buffer deadlock

Samad14

6c14e2d
14:14
fix: add vimontest timeout diagnostic with sleep test

Samad14

628b184
14:12
fix: set deployed commit hash

Samad14

19eb8d7
14:11
fix: update commit hash in vimontest

Samad14

951d3f5
14:11
chore: add deployed commit hash to vimontest for debugging

Samad14

e36a2bd
13:53
fix: use file handles instead of PIPE to avoid Vina pipe-buffer deadlock on Render

Samad14

88df0f4
11:56
test: vimontest runs Vina with 10s timeout to diagnose hangs

Samad14

583edb0
11:33
fix: use process group kill (killpg) for reliable Vina timeout

Samad14

32957ff
11:14
debug: set Vina timeout to 60s for testing timeout mechanism

Samad14

01cccda
10:45
fix: use subprocess.run(timeout=...) instead of asyncio subprocess for reliable Vina timeout

Samad14

ab38821
09:59
fix: simplify vimontest to avoid Vina crash in request handler

Samad14

dc12ffd
09:55
fix: reliable Vina timeout via asyncio subprocess + cleanup vimontest

Samad14

ab9ad46
09:07
debug: check column positions in ATOM line

Samad14

c111908
09:04
fix: parse CACTUS API PDB-like ATOM records instead of V2000 SDF

Samad14

80b49f1
09:00
debug: show SDF and PDBQT content in vimontest

Samad14

63d6e0f
08:53
debug: step-by-step vimontest with short 10s timeout

Samad14

8d27657
08:50
fix: add urllib import to vimontest

Samad14

937dc91
08:49
debug: realistic vimontest with real PDB and SMILES

Samad14

c212267

Commit History

Jul 17

fix: logging crash, md/function_predict ligand_smiles column fallback

Jul 16

Fix MD simulation: OpenMM fallback, PDB ID propagation, better error handling

Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

Phase 2: structured JSON logging, request ID middleware, enhanced health endpoint, Sentry breadcrumbs

Phase 1: harden rate limits — JWT-aware keys, per-endpoint caps, daily limits on all job types

Jul 15

Phase 0c: offload large artifacts to Supabase Storage (docking, pipeline, sequencing)

Phase 0b: durable worker with FOR UPDATE SKIP LOCKED, per-type concurrency, separate container

Phase 0a: SSRF protection + auth on docking/sequencing, worker design doc

Fix _TRP_RINGS -> _TRP_RING_ATOMS name error

Docking viewer upgrade: Molstar GPU rendering, proper interaction geometry, 3D dashed-line rendering

Fix KeyError: payload['smiles'] -> payload.get('ligand_smiles')

Docking: minimal INSERT (only id/status/smiles), startup table check, migration SQL

Fix docking INSERT: only use columns guaranteed to exist in Supabase

Major docking rewrite: match frontend contract (pdb_id+smiles input, nested poses/interactions output, PDB fetch from RCSB, auto grid center)

Fix docking route mismatches: GET /status/{id}, frontend pdb URL prefix

Fix docking route: POST /api/docking/run to match frontend

Fix docking: add pdb_to_pdbqt_receptor() for protein PDBQT conversion

Fix unbounded _SESSION_EVENT_COUNTS dict leak (cap at 1000)

Use Dockerfile-installed Vina first, fall back to download

Fix Settings attribute names: SUPABASE_URL, SUPABASE_SERVICE_ROLE_KEY

fix: undefined query_length variable in _run_blast

fix: Linux Vina binary, Open Babel PDBQT, pipeline_worker utcnow⁠

Jul 14

test: reduce vina timeout to 10s for faster diagnostic

fix: indentation error at line 610

fix: revert to async subprocess (no thread pool to avoid import hang), keep --cpu 1

fix: use ThreadPoolExecutor with subprocess.Popen (no asyncio subprocess), add --cpu 1 and stdin=/dev/null

fix: use asyncio.create_subprocess_exec with file handles + asyncio.wait_for (no threads, no pipes)

fix: use poll() polling loop instead of proc.wait(timeout=N) to avoid Python 3.14 pidfd-wait hang

fix: use Popen + wait(timeout=N) + killpg layered kill approach

fix: use /usr/bin/timeout OS-level command instead of Python subprocess timeout

fix: use subprocess.DEVNULL for Vina output — eliminates ALL I/O blocking

fix: use dedicated ThreadPoolExecutor(max_workers=1) + subprocess.run(file handles, timeout=N)

fix: use asyncio.create_subprocess_exec with file descriptors + wait_for — no threads, no pipe buffer deadlock

fix: add vimontest timeout diagnostic with sleep test

fix: set deployed commit hash

fix: update commit hash in vimontest

chore: add deployed commit hash to vimontest for debugging

fix: use file handles instead of PIPE to avoid Vina pipe-buffer deadlock on Render

test: vimontest runs Vina with 10s timeout to diagnose hangs

fix: use process group kill (killpg) for reliable Vina timeout

debug: set Vina timeout to 60s for testing timeout mechanism

fix: use subprocess.run(timeout=...) instead of asyncio subprocess for reliable Vina timeout

fix: simplify vimontest to avoid Vina crash in request handler

fix: reliable Vina timeout via asyncio subprocess + cleanup vimontest

debug: check column positions in ATOM line

fix: parse CACTUS API PDB-like ATOM records instead of V2000 SDF

debug: show SDF and PDBQT content in vimontest

debug: step-by-step vimontest with short 10s timeout

fix: add urllib import to vimontest

debug: realistic vimontest with real PDB and SMILES