lingyuzeng/bttoxin-pipeline
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9 Commits

Author SHA1 Message Date
zly
963215de2d Fix(pipeline): prevent nested zip packaging and update CRISPR dependencies 
- Add filter to skip .zip and .tar.gz files when creating result archive
- Update CRISPR feature with CASFinder dependencies (hmmer, blast, vmatch, etc.)
- Add install-casfinder task for macsydata installation
- Remove obsolete CRISPR test files

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-28 20:06:41 +08:00
zly
e44692600c Fix(pipeline): optimize docker build, fix zip structure, and update UI 
- Docker:
  - Explicitly install pixi environments (digger, pipeline, webbackend) during build to prevent runtime network/DNS failures.
  - Optimize pnpm config (copy method) to fix EAGAIN errors.
- Backend:
  - Refactor ZIP bundling: use flat semantic directories (1_Toxin_Mining, etc.).
  - Fix "nested zip" issue by cleaning existing archives before bundling.
  - Exclude raw 'context' directory from final download.
- Frontend:
  - Update TutorialView documentation to match new result structure.
  - Improve TaskMonitor progress bar precision (1 decimal place).
  - Update i18n (en/zh) for new file descriptions.

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-21 20:43:28 +08:00
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
74ca20707c feat(crispr): implement CRISPR-Cas detection and fusion analysis module 2026-01-14 15:34:45 +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
zly
fe353fc0bc chore: 初始版本提交 - 简化架构 + 轮询改造 
- 移除 Motia Streams 实时通信，改用 3 秒轮询
- 简化前端代码，移除冗余组件
- 简化后端架构，准备 FastAPI 重构
- 更新 pixi.toml 环境配置
- 保留 bttoxin_digger_v5_repro 作为参考文档

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-13 16:50:09 +08:00
hotwa
4267bda227 feat: 添加 frontend 和 webbackend 开发环境配置 
- 新增 frontend 环境：Vue 3 + Vite + Element Plus
- 新增 webbackend 环境：FastAPI
- 更新 README 开发文档

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-08 22:29:37 +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