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

Commit History

Jun 25

07:15
Move minimap2 download to runtime (avoids build failures on HF cpu-basic)

Samad14

0be08e1

Jun 24

20:02
Phase 3: Sequencing pipeline (FASTQ -> QC -> alignment -> variant calling -> report)⁠

Samad14

1cb972c
13:10
fix: load .env.deploy explicitly in config.py

Samad14

2224ea2
09:47
feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update⁠

Samad14

fb8c550

Jun 22

11:12
feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade

Samad14

305458b
10:09
fix: use valid EBI email (example.com), remove PhyML build from Docker

Samad14

87fe374
10:02
fix: remove PhyML source build from Docker (fails on HF), add graceful missing-binary error in phylo.py

Samad14

20cf1ce
09:32
feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

Samad14

07e58f6

Jun 21

10:18
feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

Samad14

990c867
09:15
fix: add logging to init_redis() so Redis failures are visible in server logs

Samad14

3edbe65

Jun 20

11:36
fix: Foldseek alignments are [dict] lists, parse target format

Samad14

5f521f2
11:35
fix: debug alignment structure types

Samad14

19208a9
11:33
fix: debug Foldseek result structure

Samad14

61dd06a
11:30
fix: Foldseek alignments are dicts, parse with .get() correctly

Samad14

7756be4
11:28
fix: debug Foldseek alignment format (list vs dict)

Samad14

758bd07
11:26
fix: add full traceback to Foldseek error

Samad14

106504c
11:24
fix: use aiohttp for Foldseek multipart upload

Samad14

feb3584
11:20
fix: debug Foldseek submit response type

Samad14

2058534
11:18
fix: use sync httpx in thread pool for Foldseek submit

Samad14

8dd7e6b
11:16
fix: restore nested alignments loop, remove debug raw

Samad14

e598246
11:14
fix: return raw Foldseek data for debugging

Samad14

36a7562
11:12
fix: Foldseek returns list directly, no alignments sub-key

Samad14

87455a5
11:10
fix: move fetch inside httpx async with block

Samad14

a55a85f
11:09
fix: manual multipart for Foldseek, add secrets import

Samad14

3b0a62a
11:07
fix: use sync httpx.Client for Foldseek multipart upload

Samad14

6f0c958
11:05
fix: add error detail to Foldseek, use bytes, longer timeout

Samad14

e368884
11:04
fix: simplify Foldseek integration, use full PDB, encode as bytes

Samad14

b4c387f
11:00
fix: primer error handling, interactions scores, structure comparison API⁠

Samad14

3030b52
10:13
fix: handle null name in InterPro domain response⁠

Samad14

76de492
09:48
feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation⁠

Samad14

bac1801

Jun 19

12:17
Fix KEGG search: use find/hsa with symbol matching + parse get/PATHWAY section

Samad14

28de608
12:09
Add Reactome diagrams, KEGG search, pathway enrichment (pipeline + standalone)

Samad14

8ce1e37
11:48
Security, crash fixes, demo prep, dead code removal⁠

Samad14

9a28cd0
10:31
Fix Reactome pathway search: correct param name and response parsing⁠

Samad14

2f3ea25

Jun 18

15:28
Add Render Blueprint, GitHub Actions auto-deploy, revert to CORS fix, local startup scripts

Samad14

3beb058
14:56
Fix structure viewer: correct PDB API URL (+/entry/), fix RCSB UniProt search attribute + payload format

Samad14

d721718
14:12
Fix MSA: use correct EBI result type 'fa' instead of 'aln-fasta' — confirmed via live API test

Samad14

7a98820
12:11
Fix MSA: dynamically discover EBI result types instead of hardcoding 'aln-fasta'

Samad14

4c0acd7
11:54
Fix MSA alignment: add Accept headers, result retry with delay, better error detail

Samad14

96668fa
11:45
Fix Phase 1 endpoints: resolve UniProt→PDB in structure viewer, use proper Reactome search, surface real backend errors in frontend

Samad14

13df1a1
11:14
Sprint 3-7: Alignment, Structure Viewer, Pathway Analysis, Utility Tools, analyze page fully live

Samad14

f0b48d6
11:11
Sprint 1-2: JWT auth middleware + UniProt dedicated page

Samad14

f8dfa58
09:54
full dark migration: CSS overrides for all legacy classes, framer-motion animations across every page/component, rebrand to Bio Nexus

Samad14

2f67ecf

Jun 17

15:24
design.md + rules.md compliance: dark theme, teal palette, pulsing dot, Pydantic models, api.ts routing, config fixes, db/max_hits threading, Supabase migration 004

Samad14

f42f5a6
14:53
Fix PostgREST in() filter: quote status values in startup hook

Samad14

9d6a43d
14:48
Add RefSeq->UniProt mapping step in pipeline + demo uniprot_accession

Samad14

c080f36
14:20
Add startup resume hook for stuck jobs + persist NCBI RID

Samad14

94ca7cd
13:06
fix: extract user UUID from JWT for rate limiter, skip anon

Samad14

c14f4eb
11:19
fix: logger.exception instead of stderr, fail job on thread crash

Samad14

be02b10
11:15
fix: move first _set_step into try block + stderr fallback in run_pipeline_sync

Samad14

2cb3e54

Commit History

Jun 25

Move minimap2 download to runtime (avoids build failures on HF cpu-basic)

Jun 24

Phase 3: Sequencing pipeline (FASTQ -> QC -> alignment -> variant calling -> report)⁠

fix: load .env.deploy explicitly in config.py

feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update⁠

Jun 22

feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade

fix: use valid EBI email (example.com), remove PhyML build from Docker

fix: remove PhyML source build from Docker (fails on HF), add graceful missing-binary error in phylo.py

feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

Jun 21

feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

fix: add logging to init_redis() so Redis failures are visible in server logs

Jun 20

fix: Foldseek alignments are [dict] lists, parse target format

fix: debug alignment structure types

fix: debug Foldseek result structure

fix: Foldseek alignments are dicts, parse with .get() correctly

fix: debug Foldseek alignment format (list vs dict)

fix: add full traceback to Foldseek error

fix: use aiohttp for Foldseek multipart upload

fix: debug Foldseek submit response type

fix: use sync httpx in thread pool for Foldseek submit

fix: restore nested alignments loop, remove debug raw

fix: return raw Foldseek data for debugging

fix: Foldseek returns list directly, no alignments sub-key

fix: move fetch inside httpx async with block

fix: manual multipart for Foldseek, add secrets import

fix: use sync httpx.Client for Foldseek multipart upload

fix: add error detail to Foldseek, use bytes, longer timeout

fix: simplify Foldseek integration, use full PDB, encode as bytes

fix: primer error handling, interactions scores, structure comparison API⁠

fix: handle null name in InterPro domain response⁠

feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation⁠

Jun 19

Fix KEGG search: use find/hsa with symbol matching + parse get/PATHWAY section

Add Reactome diagrams, KEGG search, pathway enrichment (pipeline + standalone)

Security, crash fixes, demo prep, dead code removal⁠

Fix Reactome pathway search: correct param name and response parsing⁠

Jun 18

Add Render Blueprint, GitHub Actions auto-deploy, revert to CORS fix, local startup scripts

Fix structure viewer: correct PDB API URL (+/entry/), fix RCSB UniProt search attribute + payload format

Fix MSA: use correct EBI result type 'fa' instead of 'aln-fasta' — confirmed via live API test

Fix MSA: dynamically discover EBI result types instead of hardcoding 'aln-fasta'

Fix MSA alignment: add Accept headers, result retry with delay, better error detail

Fix Phase 1 endpoints: resolve UniProt→PDB in structure viewer, use proper Reactome search, surface real backend errors in frontend

Sprint 3-7: Alignment, Structure Viewer, Pathway Analysis, Utility Tools, analyze page fully live

Sprint 1-2: JWT auth middleware + UniProt dedicated page

full dark migration: CSS overrides for all legacy classes, framer-motion animations across every page/component, rebrand to Bio Nexus

Jun 17

design.md + rules.md compliance: dark theme, teal palette, pulsing dot, Pydantic models, api.ts routing, config fixes, db/max_hits threading, Supabase migration 004

Fix PostgREST in() filter: quote status values in startup hook

Add RefSeq->UniProt mapping step in pipeline + demo uniprot_accession

Add startup resume hook for stuck jobs + persist NCBI RID

fix: extract user UUID from JWT for rate limiter, skip anon

fix: logger.exception instead of stderr, fail job on thread crash

fix: move first _set_step into try block + stderr fallback in run_pipeline_sync