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

Commit History

Jun 24

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

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

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

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
09:08
fix: remove current_step_label and error_message refs — columns missing from jobs table

Samad14

e5d75ff

Jun 12

13:44
Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow

Samad14

76fb273

Jun 11

08:52
Core pipeline testability: progress callback, rate limiter 429, history table⁠

Samad14

88aa370
07:24
Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1)

Samad14

5a0e691

Commit History

Jun 24

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

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

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

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: remove current_step_label and error_message refs — columns missing from jobs table

Jun 12

Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow

Jun 11

Core pipeline testability: progress callback, rate limiter 429, history table⁠

Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1)