bttoxin-pipeline/@fix_plan.md

BtToxin Pipeline 开发任务清单

当前阶段: CRISPR-Cas 模块开发 (P0)

Phase 1: 基础设施与检测

• C1.1: 创建 crispr_cas 目录结构 (scripts, docs, tests)
• C1.2: 激活 pixi.toml 中的 [feature.crispr] 环境依赖
• C1.3: 实现 crispr_cas/scripts/detect_crispr.py (CRISPRCasFinder 包装器)
• C1.4: 编写检测模块单元测试 tests/test_detect_crispr.py

Phase 2: 融合分析 (Fusion Analysis)

• C2.1: 实现 crispr_cas/scripts/fusion_analysis.py (Spacer-Toxin 关联)
• C2.2: 实现基因组位置映射逻辑
• C2.3: 编写融合分析测试 tests/test_fusion_analysis.py

Phase 3: 整合与可视化

• C3.1: 修改 bttoxin_shoter.py 集成 CRISPR 评分参数
• C3.2: 更新 plot_shotter.py 添加 CRISPR 可视化面板
• C3.3: 更新 API 支持 CRISPR 参数输入 (Backend updated)

已完成 (上一阶段)

• 2025-01-14: Docker 部署修复与上线 (Traefik/Postgres/Redis)
• 2025-01-14: 后端国际化 (i18n)
• 2025-01-14: 文档更新 (AGENTS.md, DOCKER_DEPLOYMENT.md)
• 2025-01-14: 基础功能 (F1-F5, B1-B3)

参考文档

参考文档

• Shotter 算法原理: docs/shotter_math_full_zh_typora.md
• CRISPR 实现计划: docs/CRISPR_IMPLEMENTATION_PLAN.md
• UI/UX 设计计划: docs/UI_UX_DESIGN_PLAN.md
• 现有前端代码: frontend/src/
• Pixi 环境配置: pixi.toml

部署状态

当前状态 (2025-01-14)

• Traefik: ✅ Running (traefik:v3.5.3)
• Domain: ✅ Configured (bttiaw.hzau.edu.cn)
• SSL/HTTPS: ✅ Working (self-signed cert)
• Routing: ✅ Traefik routing to domain OK
• Docker Build: ✅ SUCCESS - Image built and service running
• Health Check: ✅ Passed (internal curl test)

部署问题 (已解决)

Fixed:

• Docker registry 401 error: Switched to docker.m.daocloud.io
• Frontend build errors: Fixed missing icons and types
• Backend dependencies: Added missing python packages
• Import errors: Fixed missing classes in backend models

部署步骤

Standard Deployment

# Build and start services
docker compose -f docker/compose/docker-compose.traefik.yml up -d --build

# View logs
docker logs -f bttoxin-pipeline

完整部署流程

Once registry issue is resolved:

1. Build production image: docker build -f docker/dockerfiles/Dockerfile.traefik -t bttoxin-prod .
2. Deploy with docker-compose: docker-compose -f docker/compose/docker-compose.traefik.yml up -d
3. Verify deployment: curl -k https://bttiaw.hzau.edu.cn
4. Check logs: docker logs bttoxin-pipeline