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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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feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade
305458b
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fix: add logging to init_redis() so Redis failures are visible in server logs
3edbe65
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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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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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Sprint 1-2: JWT auth middleware + UniProt dedicated page
f8dfa58
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Add RefSeq->UniProt mapping step in pipeline + demo uniprot_accession
c080f36 -
fix: extract user UUID from JWT for rate limiter, skip anon
c14f4eb -
fix: Analyze button on retrieve page + sessionStorage handoff to blast wizard
6c461b6 -
fix: FASTA header text bleeding into sequence validation, add IUPAC codes U O B Z X J
57fa457
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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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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