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bio-nexus-api / bioai-platform

Commit History

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
11:50
Fix: alignment sample sequences, reverse complement tool, BLAST program filtering, sample buttons on structure/pathway pages

Samad14

aa498ec
11:45
Fix Phase 1 endpoints: resolve UniProt→PDB in structure viewer, use proper Reactome search, surface real backend errors in frontend

Samad14

13df1a1
11:22
Polish: restyle blast/dashboard/jobs/history/results pages to dark theme, fix Loader2 icons, update result components

Samad14

2a12412
11:16
Guest upgrade, DB migration, settings functional, full Phase 1 feature set

Samad14

90b88af
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
10:34
fix: remove Lenis SmoothScrollProvider - blocks native scroll in dashboard layout

Samad14

7bd015b
10:18
fix: animate='visible' -> animate='show' to match fadeUp variant

Samad14

b008d9f
10:14
fix: rename lucide-react icons (LoaderCircle, CircleCheck), remove unused imports, replace Set.isSubsetOf

Samad14

5242ec8
10:02
fix: dark input/textarea/select backgrounds and focus border override

Samad14

2fe4d4c
09:54
full dark migration: CSS overrides for all legacy classes, framer-motion animations across every page/component, rebrand to Bio Nexus

Samad14

2f67ecf
09:31
redesign: BioFlow AI void-dark theme — new landing page, dashboard, Three.js DNA helix, Lenis smooth scroll

Samad14

627ac39
09:19
dark mode: add missing CSS overrides (gradients, forms, badges, hover, bg-opacity, teal variants) + ThemeToggle on landing, auth, callback, shared pages

Samad14

076e8f2
08:53
settings: mark notifications & danger zone as coming-soon, clean up unused state/imports

Samad14

28efc96
08:48
named exports, any->unknown, theme toggle (light/dark), dark mode fixes, error extractor, deleted pipline/ typo dir

Samad14

973dd4c

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
10:59
fix: Analyze button on retrieve page + sessionStorage handoff to blast wizard

Samad14

6c461b6
10:56
fix: UniProt API sequence key is value not sequence -- confirmed via API response

Samad14

627b3e0
10:49
fix: UniprotTool missing sequence field — empty sequence in fetchSequence for UniProt accessions

Samad14

f1b67a7
10:43
fix: E-value underflow, AlphaFold step, steps_completed append, UniProt always runs

Samad14

3154548
09:08
fix: remove current_step_label and error_message refs — columns missing from jobs table

Samad14

e5d75ff
09:03
debug: expose real error in 500 response

Samad14

0e26ec1
08:45
fix: use Array.from instead of Set spread for TS compatibility

Samad14

3bc04b9
08:44
fix: FASTA header text bleeding into sequence validation, add IUPAC codes U O B Z X J

Samad14

57fa457

Jun 15

08:21
Simplify vercel.json — remove @-ref env vars (set via dashboard instead)

Samad14

8d8e1c0

Jun 12

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

Samad14

76fb273
10:26
Re-enable OAuth: restore auth pages, Providers wrapper, dashboard auth guard, landing page CTA

Samad14

dc1f75e

Jun 11

09:12
AlphaFold 3D viewer via 3Dmol.js — pLDDT confidence coloring, style selector, spin toggle⁠

Samad14

ffe46cc
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 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: alignment sample sequences, reverse complement tool, BLAST program filtering, sample buttons on structure/pathway pages

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

Polish: restyle blast/dashboard/jobs/history/results pages to dark theme, fix Loader2 icons, update result components

Guest upgrade, DB migration, settings functional, full Phase 1 feature set

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

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

fix: remove Lenis SmoothScrollProvider - blocks native scroll in dashboard layout

fix: animate='visible' -> animate='show' to match fadeUp variant

fix: rename lucide-react icons (LoaderCircle, CircleCheck), remove unused imports, replace Set.isSubsetOf

fix: dark input/textarea/select backgrounds and focus border override

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

redesign: BioFlow AI void-dark theme — new landing page, dashboard, Three.js DNA helix, Lenis smooth scroll

dark mode: add missing CSS overrides (gradients, forms, badges, hover, bg-opacity, teal variants) + ThemeToggle on landing, auth, callback, shared pages

settings: mark notifications & danger zone as coming-soon, clean up unused state/imports

named exports, any->unknown, theme toggle (light/dark), dark mode fixes, error extractor, deleted pipline/ typo dir

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

fix: Analyze button on retrieve page + sessionStorage handoff to blast wizard

fix: UniProt API sequence key is value not sequence -- confirmed via API response

fix: UniprotTool missing sequence field — empty sequence in fetchSequence for UniProt accessions

fix: E-value underflow, AlphaFold step, steps_completed append, UniProt always runs

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

debug: expose real error in 500 response

fix: use Array.from instead of Set spread for TS compatibility

fix: FASTA header text bleeding into sequence validation, add IUPAC codes U O B Z X J

Jun 15

Simplify vercel.json — remove @-ref env vars (set via dashboard instead)

Jun 12

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

Re-enable OAuth: restore auth pages, Providers wrapper, dashboard auth guard, landing page CTA

Jun 11

AlphaFold 3D viewer via 3Dmol.js — pLDDT confidence coloring, style selector, spin toggle⁠

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

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