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Commit History
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fix: default import PhyloTreeViewer in alignment, report, and PipelineResults
fe5ce87
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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
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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 -
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 -
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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Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1)
5a0e691