lingyuzeng/bttoxin-pipeline
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  • d66abf1596 refactor(docker): rename postgres service to avoid DNS conflicts main zly 2026-01-28 21:04:36 +08:00
  • 41a6fa976c chore: remove .claude/ from git tracking zly 2026-01-28 20:33:37 +08:00
  • 8e0deb1691 feat: add base_prokka tool and CRISPR-Cas analysis source code zly 2026-01-28 20:31:00 +08:00
  • ef09a1c5d5 chore: add .claude/ to gitignore zly 2026-01-28 20:26:47 +08:00
  • 963215de2d Fix(pipeline): prevent nested zip packaging and update CRISPR dependencies zly 2026-01-28 20:06:41 +08:00
  • e44692600c Fix(pipeline): optimize docker build, fix zip structure, and update UI zly 2026-01-21 20:43:28 +08:00
  • 452e15c806 Fix(docker): optimize pnpm build and explicitly set image tag zly 2026-01-21 00:40:34 +08:00
  • c75c85c53b Refactor: Unified pipeline execution, simplified UI, and fixed Docker config zly 2026-01-20 20:25:25 +08:00
  • 5067169b0b update location zly 2026-01-18 22:37:19 +08:00
  • c9be0694ab Update shotter math documentation with Logit Prior algorithm zly 2026-01-18 20:34:03 +08:00
  • e23731f6ca Update docs with new directory structure zly 2026-01-17 13:13:31 +08:00
  • 166af50219 Move digger reproduction env to tools/reproduction/ zly 2026-01-17 13:11:16 +08:00
  • 33f44e2df0 Remove Motia dependencies and references from frontend zly 2026-01-17 13:06:17 +08:00
  • 194f4d2fcb Remove motia-backend module zly 2026-01-17 13:02:47 +08:00
  • 3ed9558bac docs: add AGENTS.md for BtToxin_Digger reproduction guide zly 2026-01-17 12:38:24 +08:00
  • 700bdb8307 feat(digger): containerize BtToxin_Digger with v5 database integration zly 2026-01-17 12:14:39 +08:00
  • 6f2365981d chore: update pixi lockfile with new dependencies zly 2026-01-14 15:59:29 +08:00
  • 59d7f8e051 feat(worker): integrate CRISPR-Cas pipeline execution logic zly 2026-01-14 15:57:12 +08:00
  • 92b01b408f feat(frontend): integrate CRISPR controls and fix i18n zly 2026-01-14 15:55:41 +08:00
  • e652c0975b docs: add frontend crispr integration tasks to plan zly 2026-01-14 15:48:45 +08:00
  • 7090676f46 feat(backend): implement CRISPR-Cas API parameters and database schema zly 2026-01-14 15:47:35 +08:00
  • 74ca20707c feat(crispr): implement CRISPR-Cas detection and fusion analysis module zly 2026-01-14 15:34:45 +08:00
  • a43269be50 feat: enable swagger ui at /api/docs zly 2026-01-14 15:25:31 +08:00
  • e3c524c351 feat(deploy): enable automatic lets encrypt certificates zly 2026-01-14 15:18:00 +08:00
  • 29bedcbe94 chore: update .gitignore to exclude ralph agent state files zly 2026-01-14 14:58:20 +08:00
  • 96598b9d25 fix(backend): serve frontend at root path and move meta info to /api/meta zly 2026-01-14 14:57:11 +08:00
  • 39765e4782 docs: update fix plan with network configuration fix zly 2026-01-14 14:42:27 +08:00
  • 65ba1d938d refactor(docker): standardize docker network name to 'frontend' zly 2026-01-14 14:39:57 +08:00
  • 9835b6e341 feat(deploy): fix docker deployment and add backend i18n zly 2026-01-14 12:38:54 +08:00
  • c0f2de02ca docs: update fix_plan.md - mark CRISPR-Cas tasks complete zly 2026-01-14 09:49:08 +08:00
  • 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> zly 2026-01-13 23:55:12 +08:00
  • 029e49bf6a docs: update fix_plan.md with Docker deployment tasks zly 2026-01-13 23:50:06 +08:00
  • 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> zly 2026-01-13 23:49:19 +08:00
  • af83b5fba8 docs: update fix_plan.md - mark B3.3 protein support as complete zly 2026-01-13 23:45:55 +08:00
  • 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> zly 2026-01-13 23:45:34 +08:00
  • 7379c98fac docs: update fix_plan.md with completed backend tasks zly 2026-01-13 23:41:45 +08:00
  • 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> zly 2026-01-13 23:41:15 +08:00
  • 1df699b338 docs: add ralph-runner Claude Skill zly 2026-01-13 17:31:51 +08:00
  • 75c7db8684 docs: add Ralph project structure zly 2026-01-13 17:26:23 +08:00
  • 547328ad44 feat(frontend): add i18n support and navigation zly 2026-01-13 16:57:03 +08:00
  • e19f51c660 docs: add @fix_plan.md task list zly 2026-01-13 16:50:44 +08:00
  • fe353fc0bc chore: 初始版本提交 - 简化架构 + 轮询改造 zly 2026-01-13 16:50:09 +08:00
  • 4c9a7d0978 docs: 添加中文文档，新增前端和后端代码 hotwa 2026-01-08 22:31:06 +08:00
  • 4267bda227 feat: 添加 frontend 和 webbackend 开发环境配置 hotwa 2026-01-08 22:29:37 +08:00
  • 665506e1a5 docs: add pipeline architecture diagrams hotwa 2026-01-08 17:00:14 +08:00
  • a5cb891d0e chore: clean up obsolete test data files hotwa 2026-01-08 16:59:42 +08:00
  • 8d11216481 docs: update README and add pixi-based tests hotwa 2026-01-08 16:59:17 +08:00
  • ae4c6351d9 feat: migrate from Docker to pixi for BtToxin_Digger execution hotwa 2026-01-08 16:58:45 +08:00
  • 1c0e8f90a5 feat: 支持绑定外部 bt_toxin 数据库 (2025-11-04 更新) hotwa 2026-01-04 14:37:49 +08:00
  • 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 hotwa 2025-12-01 10:11:26 +08:00
  • 3fc41a2924 docs: add mathematical formulation and algorithmic principles for BtToxin_Shotter toxicity prediction hotwa 2025-12-01 09:43:35 +08:00
  • 6b923ae567 add test data hotwa 2025-12-01 09:41:39 +08:00
  • b80939f0ca add math description hotwa 2025-11-22 10:09:35 +08:00
  • 06c5cb7448 compare data hotwa 2025-11-21 20:29:03 +08:00
  • 82cfb13e50 add usage markdown file hotwa 2025-11-21 20:23:15 +08:00
  • 50a901c167 修改测试案例 lingyuzeng 2025-10-13 22:10:36 +08:00
  • 675bce4b5a 运行时候 docker 内的路径与权限问题解决方案 lingyuzeng 2025-10-13 22:08:22 +08:00
  • 0b904cd69b add uv use lingyuzeng 2025-10-13 21:08:44 +08:00
  • d71163df00 first add lingyuzeng 2025-10-13 21:05:00 +08:00
  • c7744836e9 Initial commit: BtToxin Pipeline project structure lingyuzeng 2025-10-13 19:22:56 +08:00