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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: download pre-compiled PhyML binary from bioconda instead of source build
aad6f8e -
fix: remove PhyML source build from Docker (fails on HF), add graceful missing-binary error in phylo.py
20cf1ce -
fix: add libtool + ca-certificates to PhyML build, remove -j for low-mem environments
e9f3afa -
fix: PhyML build — disable -march=native, split RUN steps, remove -q from wget
428cddb -
feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign
07e58f6
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fix: make primer3-py optional (separate install step, router handles missing import gracefully)
2572d7f
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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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Fix Reactome pathway search: correct param name and response parsing
- Changed 'q' to 'query' in search/query params (Reactome API rejects 'q') - Fixed response parsing: Reactome returns grouped JSON (results[N].entries) not a flat list — added _extract_entries() helper - Updated Dockerfile port from 8000 to 7860 for HF Spaces compatibility2f3ea25
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Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow
76fb273