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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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feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes
990c867 -
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
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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 3-7: Alignment, Structure Viewer, Pathway Analysis, Utility Tools, analyze page fully live
f0b48d6 -
Sprint 1-2: JWT auth middleware + UniProt dedicated page
f8dfa58 -
full dark migration: CSS overrides for all legacy classes, framer-motion animations across every page/component, rebrand to Bio Nexus
2f67ecf -
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
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Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow
76fb273 -
Re-enable OAuth: restore auth pages, Providers wrapper, dashboard auth guard, landing page CTA
dc1f75e
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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