lingyuzeng/bttoxin-pipeline
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452e15c8062f382df4f79b14dbd5627e8f8d7398
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7 Commits

Author SHA1 Message Date
zly
c75c85c53b Refactor: Unified pipeline execution, simplified UI, and fixed Docker config 
- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency.
- Backend: Changed output format to ZIP and added auto-cleanup of intermediate files.
- Backend: Fixed language parameter passing in API and tasks.
- Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views.
- Frontend: Implemented simulated progress bar for better UX.
- Frontend: Restored One-click load button and added result file structure documentation.
- Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml.
- Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.
 2026-01-20 20:25:25 +08:00
zly
c9be0694ab Update shotter math documentation with Logit Prior algorithm 2026-01-18 20:34:03 +08:00
zly
9835b6e341 feat(deploy): fix docker deployment and add backend i18n 
- Docker Deployment Fixes:
  - Switch base images to docker.m.daocloud.io to resolve registry 401 errors
  - Add Postgres and Redis services to docker-compose.traefik.yml
  - Fix frontend build: replace missing icons (Globe->Location, Chart->TrendCharts)
  - Fix frontend build: resolve pnpm CI/TTY issues and frozen lockfile errors
  - Add missing backend dependencies (sqlalchemy, psycopg2, redis-py, celery, docker-py) in pixi.toml
  - Ensure database tables are created on startup (lifespan event)

- Backend Internationalization (i18n):
  - Add backend/app/core/i18n.py for locale handling
  - Update API endpoints (jobs, tasks, uploads, results) to return localized messages
  - Support 'Accept-Language' header (en/zh)

- Documentation:
  - Update DOCKER_DEPLOYMENT.md with new architecture and troubleshooting
  - Update AGENTS.md with latest stack details and deployment steps
  - Update @fix_plan.md status

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-14 12:38:54 +08:00
zly
89ed5cfa1a feat(crispr): reserve CRISPR-Cas module infrastructure for future implementation\n\n- Add [feature.crispr] environment to pixi.toml (commented, ready to activate)\n- Create comprehensive CRISPR implementation plan document\n- Document 4-phase implementation roadmap:\n * Phase 1: CRISPR detection using CRISPRCasFinder\n * Phase 2: Spacer-toxin gene association analysis\n * Phase 3: Integration with shoter scoring (reserved parameters)\n * Phase 4: Enhanced visualization\n- Define data structures, API contracts, and usage examples\n- Document scientific background and testing strategy\n\nStatus: RESERVED - not yet implemented, all infrastructure prepared for future activation.\n\nCo-Authored-By: Claude <noreply@anthropic.com> 2026-01-13 23:55:12 +08:00
hotwa
3fc41a2924 docs: add mathematical formulation and algorithmic principles for BtToxin_Shotter toxicity prediction 2025-12-01 09:43:35 +08:00
hotwa
b80939f0ca add math description 2025-11-22 10:09:35 +08:00
hotwa
82cfb13e50 add usage markdown file 2025-11-21 20:23:15 +08:00