lingyuzeng/bttoxin-pipeline
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Author SHA1 Message Date
zly
c0f2de02ca docs: update fix_plan.md - mark CRISPR-Cas tasks complete 2026-01-14 09:49:08 +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
029e49bf6a docs: update fix_plan.md with Docker deployment tasks 2026-01-13 23:50:06 +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
af83b5fba8 docs: update fix_plan.md - mark B3.3 protein support as complete 2026-01-13 23:45:55 +08:00
zly
80e7d1ffb6 feat(scripts): add protein file (.faa) support to pipeline\n\n- Add detect_sequence_type() function for automatic file type detection\n- Rename run_single_fna_pipeline() to run_single_file_pipeline()\n- Add backward compatibility alias for existing callers\n- Add --input CLI argument (preferred over --fna)\n- Support .faa protein files alongside .fna/.fa/.fasta genome files\n- Auto-detect sequence type and pass correct suffix to BtToxin_Digger\n- Update documentation with protein file examples\n\nCo-Authored-By: Claude <noreply@anthropic.com> 2026-01-13 23:45:34 +08:00
zly
7379c98fac docs: update fix_plan.md with completed backend tasks 2026-01-13 23:41:45 +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
zly
1df699b338 docs: add ralph-runner Claude Skill 
- SKILL.md: Complete documentation for Ralph automation
- scripts/status.sh: Check project and Ralph status
- scripts/start.sh: Start Ralph loop with options
- scripts/commit.sh: Git commit helper
- README.md: Skill usage guide

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-13 17:31:51 +08:00
zly
75c7db8684 docs: add Ralph project structure 
- PROMPT.md: Ralph development instructions with BtToxin Pipeline specifics
- specs/requirements.md: Technical specifications (API, file formats, concurrency)
- @AGENT.md: Build, test, and deployment commands

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-13 17:26:23 +08:00
zly
547328ad44 feat(frontend): add i18n support and navigation 
- Install vue-i18n and configure locales (zh/en)
- Add complete navigation bar with 5 items: Home, About, Submit, Status, Tool Guide
- Add language switcher (中文/EN) with localStorage persistence
- Create HomeView with hero section, features, and quick links
- Create AboutView with features and usage guide
- Create ToolInfoView explaining BtToxin_Shoter principles (no formulas, no Digger)
- Update TaskSubmitForm: single file upload, genome/protein toggle, tooltips
- Update TaskMonitorView: i18n, queue status display
- Add queue_position field to TaskStatusResponse type

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-13 16:57:03 +08:00
zly
e19f51c660 docs: add @fix_plan.md task list 
- Add high/medium/low priority tasks
- Cover frontend i18n, upload, status pages
- Cover backend FastAPI, concurrency, multi-format support
- Include CRISPR-Cas design预留

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-13 16:50:44 +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
4c9a7d0978 docs: 添加中文文档，新增前端和后端代码 
- 新增 README_CN.md 中文文档
- 新增 frontend/ Vue 3 前端项目
- 新增 web/ FastAPI 后端项目

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

Co-Authored-By: Claude <noreply@anthropic.com>
 2026-01-08 22:31:06 +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
665506e1a5 docs: add pipeline architecture diagrams 
- Add bttoxin-pipeline.png and .svg workflow diagrams
 2026-01-08 17:00:14 +08:00
hotwa
a5cb891d0e chore: clean up obsolete test data files 
- Remove ncbi_dataset download files
- Remove outdated test documentation
 2026-01-08 16:59:42 +08:00
hotwa
8d11216481 docs: update README and add pixi-based tests 
- Add property-based tests for PixiRunner
- Add HAN055.fna test data file
- Update README with pixi installation and usage guide
- Update .gitignore for pixi and test artifacts
- Update CLI to remove Docker-related arguments
 2026-01-08 16:59:17 +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
hotwa
5883e13c56 feat(shotter): 实现 Shotter v1 活性评估与单 FNA 流程，新增 API/CLI/绘图与报告 
- 新增 scripts/bttoxin_shoter.py：从 BPPRC 正样本 CSV 构建 name/亚家族/家族特异性索引，
  解析 BtToxin_Digger All_Toxins.txt，计算 per-hit 权重并以 noisy-OR 合成菌株×目标目/物种分数，
  输出 TSV/JSON；含 HMM 加成与配对毒素规则（Vip1/Vip2，Vpa/Vpb），other/unknown 桶。
- 新增端到端工具链：
  - scripts/run_single_fna_pipeline.py：Digger → Shotter → Plot → 打包
  - scripts/plot_shotter.py：绘制热图并生成论文式/摘要式报告
  - scripts/bttoxin_api.py 与 bttoxin/api.py：纯 Python API；bttoxin/cli.py 暴露 bttoxin-run
  - pyproject.toml：项目打包与 CLI 入口
- docs(README): 增加输入文件格式与结果解读，补充单目录写入方案
- chore(gitignore): 忽略 runs/ 与 tests/output
- ci: 移除 .woodpecker/test.yml
 2025-12-01 10:11:26 +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
6b923ae567 add test data 2025-12-01 09:41:39 +08:00
hotwa
b80939f0ca add math description 2025-11-22 10:09:35 +08:00
hotwa
06c5cb7448 compare data 2025-11-21 20:29:03 +08:00
hotwa
82cfb13e50 add usage markdown file 2025-11-21 20:23:15 +08:00
lingyuzeng
50a901c167 修改测试案例 2025-10-13 22:10:36 +08:00
lingyuzeng
675bce4b5a 运行时候 docker 内的路径与权限问题解决方案 2025-10-13 22:08:22 +08:00
lingyuzeng
0b904cd69b add uv use 2025-10-13 21:08:44 +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