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

Commit History

Jul 14

08:44
debug: check if timeout command exists

Samad14

a246aa1
08:31
fix: use Linux timeout command instead of subprocess timeout to reliably kill Vina

Samad14

083cf21
08:23
debug: add /api/docking/vimontest endpoint

Samad14

7789c73
08:08
fix: add subprocess timeout=600, reduce exhaustiveness to 2, modes to 3

Samad14

76cecfd
07:25
fix: reorder _download_vina before module-level vina resolution

Samad14

8c7f69a
07:20
fix: detect missing Vina binary at module level and download fallback; fail early if binary not found

Samad14

058552e
07:13
fix: use asyncio.to_thread + file-based subprocess for Vina; add vina binary debug test

Samad14

d214a0c
06:57
fix: use asyncio.create_subprocess_exec for Vina to prevent pipe deadlock; fix isoformat for PostgREST

Samad14

b1d8ad7

Jul 12

18:54
feat: add progress callbacks to DockingTool.run() for real-time status tracking⁠

Samad14

8d44857
17:48
fix: encode grace_cutoff with strftime to avoid + in URL query param⁠

Samad14

9aaccbe
17:39
fix: migrate docking/sequencing job store from file-backed dict to Supabase⁠

Samad14

a8dee3b
08:48
fix: add TORSDOF 0 after ENDROOT (rigid ligand)

Samad14

396bcf1
08:40
fix: right-justify charge to col 76 with {charge:>8.3f}, ad_type:>2 at 78-79

Samad14

38de281
08:20
fix: pad PDBQT to 80 cols so charge field is parseable at positions 66 or 69

Samad14

f66e99a

Jul 11

20:36
fix: correct PDBQT column alignment (atom name, coord pos, charge field)

Samad14

cdaf04c
20:27
fix: correct PDBQT column positions for atom serial number

Samad14

d29844d
20:22
fix: generate PDBQT directly from SDF (Vina binary rejects PDB/SDF input)

Samad14

3a5f903
20:18
fix: convert SDF to PDB in Python (avoids Vina SDF parser issues)

Samad14

640d93b
20:14
fix: use NCI CACTUS /mol format instead of /sdf (Vina parses MOL better)

Samad14

c11931d
20:09
fix: strip SDF data sections (Vina parser rejects >header lines)

Samad14

ecab431
19:58
fix: replace obabel CLI with NCI CACTUS API for SMILES→3D (eliminates all subprocess crashes)

Samad14

b3124a2
19:53
fix: use asyncio.to_thread(subprocess.run) instead of asyncio.create_subprocess_exec (Python 3.14 compat)

Samad14

05c77a7
19:23
fix: use obabel CLI subprocess for SMILES→3D (lightweight, no OOM) + Vina reads PDB receptor natively (no obabel PDBQT prep)

Samad14

64e0551
18:46
fix: use PDB instead of SDF for ligand (Vina SDF parser rejects RDKit tag)

Samad14

36897bb
18:42
fix: eliminate obabel entirely — use RDKit for SMILES→3D + Vina PDB/SDF input (avoids OOM from obabel C++ subprocess)

Samad14

618a4e0
18:25
fix: add import subprocess and use subprocess.PIPE instead of asyncio.subprocess.PIPE (Python 3.14 compat)

Samad14

6d68d15
18:16
fix: revert to BackgroundTasks + async DockingTool.run (no threads, no pybel); pre-download vina in build.sh

Samad14

538a17a
18:11
fix: fully sync _worker_sync — replaces asyncio.run with subprocess.run + httpx.Client to avoid Python 3.14 thread crash

Samad14

890c537
18:07
chore: add /api/docking/debug diagnostic endpoint

Samad14

88d40c6
17:55
fix: remove pybel bindings (causes segfault on Render), use obabel CLI subprocess only

Samad14

0ed4824
17:39
fix: run docking worker in thread pool to keep event loop responsive + add vina download timeout

Samad14

8be46a8
17:35
fix: move global to first line of function (Python 3.14 SyntaxError)

Samad14

cb34bca
16:40
fix: strip ROOT/BRANCH from receptor PDBQT (rigid-receptor compat)

Samad14

fef08a5
16:39
fix: use low-level OB API with AddOption('r') for rigid receptor PDBQT

Samad14

5b41dec
16:32
fix: move global OBABEL_CMD declaration to function top (Python 3.14 SyntaxError)

Samad14

f1b1916
16:20
fix: reduce OOM by using in-process obabel bindings + lower vina exhaustiveness

Samad14

320581f

Jul 10

19:05
fix: simplify build.sh to only pip install (no risky binary downloads) + fix vina download path⁠

Samad14

c9577de
18:30
fix: obabel self-healing — openbabel-wheel in requirements, runtime pip fallback, Vina download⁠

Samad14

31d3bd8
14:45
fix: check obabel availability early with clear error message, use OBABEL_CMD variable

Samad14

e86be3a
14:38
feat: add interaction fingerprinting and 3Dmol.js viewer to molecular docking page⁠

Samad14

a6857c7
13:39
fix: remove orphaned context = { line causing SyntaxError in deploy

Samad14

cab1006
13:00
feat: add query coverage, organism, and query accession to BLAST results

Samad14

cee7881
11:00
fix: robust Foldseek parsing, add logging, handle missing results key and variant target formats⁠

Samad14

d35f0c4

Jun 26

17:29
fix: handle NCBI UNKNOWN status and add pathway_enrichment to frontend status order

Samad14

6547179
17:14
feat: add DNA sequence output across BLAST, UniProt, sequencing, primers, and SequenceRetrieval

Samad14

00b6857
13:28
feat: implement 8 tool bridges (F1-F8) + audit child components

Samad14

5561093
06:31
feat: 4-layer audit/observability system⁠

Samad14

6a2c89b

Jun 25

08:11
fix: replace dead lambda reference FTP URL with NCBI E-utilities

Samad14

d10fc77
08:02
fix: resolve 10 bugs in sequencing/docking pipelines⁠

Samad14

01cadbb
07:27
Fix pipeline stuck issue: synthetic FASTQ fallback and demo mode

Samad14

e816a43

Commit History

Jul 14

debug: check if timeout command exists

fix: use Linux timeout command instead of subprocess timeout to reliably kill Vina

debug: add /api/docking/vimontest endpoint

fix: add subprocess timeout=600, reduce exhaustiveness to 2, modes to 3

fix: reorder _download_vina before module-level vina resolution

fix: detect missing Vina binary at module level and download fallback; fail early if binary not found

fix: use asyncio.to_thread + file-based subprocess for Vina; add vina binary debug test

fix: use asyncio.create_subprocess_exec for Vina to prevent pipe deadlock; fix isoformat for PostgREST

Jul 12

feat: add progress callbacks to DockingTool.run() for real-time status tracking⁠

fix: encode grace_cutoff with strftime to avoid + in URL query param⁠

fix: migrate docking/sequencing job store from file-backed dict to Supabase⁠

fix: add TORSDOF 0 after ENDROOT (rigid ligand)

fix: right-justify charge to col 76 with {charge:>8.3f}, ad_type:>2 at 78-79

fix: pad PDBQT to 80 cols so charge field is parseable at positions 66 or 69

Jul 11

fix: correct PDBQT column alignment (atom name, coord pos, charge field)

fix: correct PDBQT column positions for atom serial number

fix: generate PDBQT directly from SDF (Vina binary rejects PDB/SDF input)

fix: convert SDF to PDB in Python (avoids Vina SDF parser issues)

fix: use NCI CACTUS /mol format instead of /sdf (Vina parses MOL better)

fix: strip SDF data sections (Vina parser rejects >header lines)

fix: replace obabel CLI with NCI CACTUS API for SMILES→3D (eliminates all subprocess crashes)

fix: use asyncio.to_thread(subprocess.run) instead of asyncio.create_subprocess_exec (Python 3.14 compat)

fix: use obabel CLI subprocess for SMILES→3D (lightweight, no OOM) + Vina reads PDB receptor natively (no obabel PDBQT prep)

fix: use PDB instead of SDF for ligand (Vina SDF parser rejects RDKit tag)

fix: eliminate obabel entirely — use RDKit for SMILES→3D + Vina PDB/SDF input (avoids OOM from obabel C++ subprocess)

fix: add import subprocess and use subprocess.PIPE instead of asyncio.subprocess.PIPE (Python 3.14 compat)

fix: revert to BackgroundTasks + async DockingTool.run (no threads, no pybel); pre-download vina in build.sh

fix: fully sync _worker_sync — replaces asyncio.run with subprocess.run + httpx.Client to avoid Python 3.14 thread crash

chore: add /api/docking/debug diagnostic endpoint

fix: remove pybel bindings (causes segfault on Render), use obabel CLI subprocess only

fix: run docking worker in thread pool to keep event loop responsive + add vina download timeout

fix: move global to first line of function (Python 3.14 SyntaxError)

fix: strip ROOT/BRANCH from receptor PDBQT (rigid-receptor compat)

fix: use low-level OB API with AddOption('r') for rigid receptor PDBQT

fix: move global OBABEL_CMD declaration to function top (Python 3.14 SyntaxError)

fix: reduce OOM by using in-process obabel bindings + lower vina exhaustiveness

Jul 10

fix: simplify build.sh to only pip install (no risky binary downloads) + fix vina download path⁠

fix: obabel self-healing — openbabel-wheel in requirements, runtime pip fallback, Vina download⁠

fix: check obabel availability early with clear error message, use OBABEL_CMD variable

feat: add interaction fingerprinting and 3Dmol.js viewer to molecular docking page⁠

fix: remove orphaned context = { line causing SyntaxError in deploy

feat: add query coverage, organism, and query accession to BLAST results

fix: robust Foldseek parsing, add logging, handle missing results key and variant target formats⁠

Jun 26

fix: handle NCBI UNKNOWN status and add pathway_enrichment to frontend status order

feat: add DNA sequence output across BLAST, UniProt, sequencing, primers, and SequenceRetrieval

feat: implement 8 tool bridges (F1-F8) + audit child components

feat: 4-layer audit/observability system⁠

Jun 25

fix: replace dead lambda reference FTP URL with NCBI E-utilities

fix: resolve 10 bugs in sequencing/docking pipelines⁠

Fix pipeline stuck issue: synthetic FASTQ fallback and demo mode