lingyuzeng/bttoxin-pipeline
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452e15c8062f382df4f79b14dbd5627e8f8d7398
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13 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
59d7f8e051 feat(worker): integrate CRISPR-Cas pipeline execution logic 2026-01-14 15:57:12 +08:00
zly
7090676f46 feat(backend): implement CRISPR-Cas API parameters and database schema 2026-01-14 15:47:35 +08:00
zly
a43269be50 feat: enable swagger ui at /api/docs 2026-01-14 15:25:31 +08:00
zly
96598b9d25 fix(backend): serve frontend at root path and move meta info to /api/meta 2026-01-14 14:57:11 +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
1a1ba71777 feat(docker): add SPA static file serving and fix Dockerfile paths\n\n- Add backend/app/main_spa.py with FastAPI static file serving for SPA\n- Fix Dockerfile.traefik to use correct backend path (backend.app.main_spa)\n- Remove web/ references (project has backend/ at root)\n- Frontend dist files served from /app/frontend/dist\n- Health check endpoint at /health\n- Supports Traefik reverse proxy at bttiaw.hzau.edu.cn\n\nCo-Authored-By: Claude <noreply@anthropic.com> 2026-01-13 23:49:19 +08:00
zly
d4f0e27af8 feat(backend): add missing API endpoints, concurrency control, and queue management\n\n- Add /api/v1/tasks router for task management\n- Add DELETE endpoint for task deletion\n- Add GET /download endpoint for result bundling (tar.gz)\n- Add GET /queue endpoint for queue position queries\n- Create ConcurrencyManager service with Redis Semaphore (16 concurrent limit)\n- Add QUEUED status to JobStatus enum\n- Update Job model with queue_position, current_stage, progress_percent fields\n- Add scoring parameters (min_identity, min_coverage, etc.) to jobs API\n- Implement pipeline stages: digger -> shoter -> plots -> bundle\n- Add update_queue_positions Celery task for periodic queue updates\n- Clean up duplicate code in main.py\n\nCo-Authored-By: Claude <noreply@anthropic.com> 2026-01-13 23:41:15 +08:00
hotwa
ae4c6351d9 feat: migrate from Docker to pixi for BtToxin_Digger execution 
- Add pixi.toml with digger and pipeline environments
- Implement PixiRunner class replacing DockerContainerManager
- Add run_digger_stage.py for standalone digger execution
- Update run_single_fna_pipeline.py to use PixiRunner
- Remove docker dependency from pyproject.toml
- Delete docker_client.py (no longer needed)

BREAKING CHANGE: Docker is no longer required. Use 'pixi install' instead.
 2026-01-08 16:58:45 +08:00
hotwa
1c0e8f90a5 feat: 支持绑定外部 bt_toxin 数据库 (2025-11-04 更新) 
- docker_client.py: run_bttoxin_digger() 新增 bttoxin_db_dir 参数，支持挂载外部数据库
- run_single_fna_pipeline.py: 新增 --bttoxin_db_dir 参数，自动检测 external_dbs/bt_toxin
- README.md: 添加 bttoxin_db 更新说明和 Docker 绑定文档
- external_dbs/bt_toxin: 添加 2025-11-04 版本数据库文件

测试验证: HAN055 样本毒素命名版本号变化 (Cry2Aa9→22, Cry2Ab35→41, Cry1Ia40→42, Vip3Aa7→79)
 2026-01-04 14:37:49 +08:00
lingyuzeng
50a901c167 修改测试案例 2025-10-13 22:10:36 +08:00
lingyuzeng
d71163df00 first add 2025-10-13 21:05:00 +08:00
lingyuzeng
c7744836e9 Initial commit: BtToxin Pipeline project structure 2025-10-13 19:22:56 +08:00