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Commit History
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feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update
- Molecular docking tool via AutoDock Vina (free, CPU-based, local binary) - Dockerfile: openbabel apt install + vina binary from GitHub releases - Backend: DockingTool (PDB fetch, obabel PDBQT conversion, vina subprocess, pose parser) - Backend: POST /api/docking/run + GET /api/docking/status/{job_id} - Frontend: analyze/docking/page.tsx — PDB ID + SMILES input, auto-detect binding pocket, results table with affinity color-coding, PDBe structure viewer - Frontend: docking card with 'New' badge added to analyze/page.tsx - Documentation site: /learn pages (10 topics + glossary), LearnPopover inline help, TutorialWalkthrough onboarding modal - Sentry error monitoring: sentry.client.config.ts, sentry.server.config.ts, next.config.js withSentryConfig, backend sentry_sdk init in main.py - Cache stats tracking: _cache_stats counters, from_cache flag, /api/admin/cache-stats endpoint, @ttl_cache on ncbi_service.search_by_name and pathway_enrichment - All .md docs (MASTER_PL…fb8c550
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fix: default import PhyloTreeViewer in alignment, report, and PipelineResults
fe5ce87 -
feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign
07e58f6 -
fix: accurate phylogenetic tree visualization — proportional branch lengths, scale bar, bootstrap labels, circular layout mode
9e11dca
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feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes
990c867 -
fix: convert AlignmentView.tsx light-theme classes to dark void theme tokens
312665c -
feat: add PNG/TSV/JSON/CSV/FASTA export to all 8 tool components
- Shared export utility (export-utils.ts): downloadTsv, downloadJson, copyText, exportSvgPng - DomainArchitecture: Export PNG (SVG canvas), Export TSV (domain table) - PhyloTreeViewer: Export PNG - ConservationTrack: Export PNG - StructureComparison: Export PNG (TM-score bars), Export TSV (metrics) - UniProt page: Export JSON, Export CSV (header fields) - PrimerDesigner: Export TSV (all primer pairs) - PathwayEnrichment: Copy links, Export TSV (pathway table) - BlastPanel: Export CSV (hit table), Export FASTA (sequences)342fa92 -
fix: use STRING-DB image API for accurate PPI diagram, add PNG/TSV/copy export buttons
c1c07f1
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fix: primer error handling, interactions scores, structure comparison API
- PrimerDesigner: handle array-type d.detail from Pydantic validation errors preventing '[object Object]' display - interactions: remove /1000 divisor — STRING-DB v12 returns scores in 0-1 range - structure_analysis: replace defunct PDBeFold REST API with Foldseek (async job-based, returns TM-score, seq identity, alignment length)3030b52 -
fix: forward backend error detail in 4 components
DomainArchitecture, StringDBViewer, RamachandranPlot, SecondaryStructure now parse the response body's 'detail' field on error, showing the actual API message instead of a generic status code.5b7a343 -
fix: handle non-200 responses in domains, interactions, ramachandran, SS components
Add res.ok checks and error state to DomainArchitecture, StringDBViewer, RamachandranPlot, and SecondaryStructureViewer. Prevents 'can't access property map of undefined' crash when API returns 404/502.9fc8479 -
feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation
- Add backend routers: domains (InterPro), interactions (STRING-DB), primers (Primer3), structure_analysis (Ramachandran, SS pred, comparison) - Add frontend components: AnalysisWizard, PhyloTreeViewer, DomainArchitecture, StringDBViewer, PrimerDesigner, RamachandranPlot, SecondaryStructureViewer, StructureComparison, ConservationTrack - Add pages: /wizard, /analyze/domains, /analyze/interactions, /analyze/primers, /analyze/compare - Update analyze hub: 10 operations in 3 groups + wizard CTA - Update alignment page: visual phylo tree + conservation track - Update job results: Advanced Analysis tabs panel - Register all routers in main.py; add primer3-py to requirements; fix CORS & profilebac1801
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Fix invisible fonts in Reactome DiagramJs: isolate widget from dark-theme CSS overrides
59495c0 -
Add Reactome diagrams, KEGG search, pathway enrichment (pipeline + standalone)
8ce1e37 -
Security, crash fixes, demo prep, dead code removal
- Auth guard: GET/DELETE /api/jobs/{id} now verify ownership (403 on mismatch) - Streaming auth: interpretStream() injects Supabase Bearer token - DELETE 404: return 404 if job never existed - JobProgress: fixed active step to show next pending step - Step names unified: worker → definition → frontend all match - Null-guards: BlastPanel, ScoreBars, UniprotPanel handle undefined/null data - ErrorBoundary: new class component wrapping dashboard layout - Silent catches: replaced .catch(noop) with user-visible error banner - Demo data: filled alignment strings for all hits; added hemoglobin + BRCA1 - History page: linked in sidebar nav (was orphaned) - pipeline_type default fixed: blast → protein_analysis - Axios timeout: added 30s timeout to api client - Dead code: removed 8 files (engine.py, results/export/waitlist routers, celery_app, redis service, registration tool, StructureViewer component) and 4 unused api.ts functions9a28cd0
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Polish: restyle blast/dashboard/jobs/history/results pages to dark theme, fix Loader2 icons, update result components
2a12412 -
Guest upgrade, DB migration, settings functional, full Phase 1 feature set
90b88af -
fix: animate='visible' -> animate='show' to match fadeUp variant
b008d9f -
full dark migration: CSS overrides for all legacy classes, framer-motion animations across every page/component, rebrand to Bio Nexus
2f67ecf -
redesign: BioFlow AI void-dark theme — new landing page, dashboard, Three.js DNA helix, Lenis smooth scroll
627ac39 -
named exports, any->unknown, theme toggle (light/dark), dark mode fixes, error extractor, deleted pipline/ typo dir
973dd4c
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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
f42f5a6 -
fix: Analyze button on retrieve page + sessionStorage handoff to blast wizard
6c461b6 -
fix: E-value underflow, AlphaFold step, steps_completed append, UniProt always runs
3154548
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Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow
76fb273
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AlphaFold 3D viewer via 3Dmol.js — pLDDT confidence coloring, style selector, spin toggle
- Self-contained AlphaFoldViewer component (client-only, global namespace) - Loads 3Dmol-min.js on demand via <script> - Colors structure by per-residue pLDDT (B-factor column) using AF DB standard scheme - 4 display modes: cartoon·pLDDT, cartoon·spectrum, surface·pLDDT, stick·pLDDT - pLDDT confidence legend in footer - Wired into /results/[jobId] and /shared/[token]ffe46cc -
Core pipeline testability: progress callback, rate limiter 429, history table
- Pipeline engine: progress_callback fires after BLAST/UniProt/AlphaFold, Pydantic models normalized to plain dict (fixes 'runs but no result') - Worker: async Supabase REST PATCH for real-time step progress - Rate limiter: raises HTTP 429 with Content-Range parsing, fail-open - History: table layout with clickable rows -> /results/[jobId] - BLAST: add stype param, fix email (EBI rejects invalid domains) - Celery: Redis ping check so fallback to sync thread works - UI: progress bar + percentage in JobProgress, nav link fixes - Auth: removed for testing (will re-enable in Phase 1) - Status: changed pending -> queued to match DB check constraint88aa370 -
Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1)
5a0e691