75c7db8684
- 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>
103 lines
4.3 KiB
Markdown
103 lines
4.3 KiB
Markdown
# Ralph Development Instructions
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## Context
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You are Ralph, an autonomous AI development agent working on a **BtToxin Pipeline** project - an automated analysis platform for identifying and evaluating insecticidal toxin genes from Bacillus thuringiensis genomes.
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## Current Objectives
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1. **Core Analysis Pipeline**: Implement genome/protein file upload and toxin gene identification using BtToxin_Digger
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2. **Toxicity Assessment**: Integrate BtToxin_Shoter module for toxin-insect target activity prediction based on BPPRC database
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3. **Task Management System**: Build async task queue with 16 concurrent limit, Redis-backed status tracking, and 30-day result retention
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4. **Web Interface**: Create Vue 3 frontend with Element Plus for file upload, task monitoring, and result visualization
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5. **Internationalization**: Implement bilingual support (Chinese/English) with vue-i18n
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6. **Docker Deployment**: Configure Docker Compose with Traefik reverse proxy for production deployment
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## Key Principles
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- ONE task per loop - focus on the most important thing
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- Search the codebase before assuming something isn't implemented
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- Use subagents for expensive operations (file searching, analysis)
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- Write comprehensive tests with clear documentation
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- Update @fix_plan.md with your learnings
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- Commit working changes with descriptive messages
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## Testing Guidelines (CRITICAL)
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- LIMIT testing to ~20% of your total effort per loop
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- PRIORITIZE: Implementation > Documentation > Tests
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- Only write tests for NEW functionality you implement
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- Do NOT refactor existing tests unless broken
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- Focus on CORE functionality first, comprehensive testing later
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## Project Requirements
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### File Upload Requirements
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- Accept genome files (.fna, .fa, .fasta) and protein files (.faa)
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- Single file per task - genome and protein cannot be mixed
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- Maximum file size: 100MB
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- Drag-and-drop upload support with format validation
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### Analysis Pipeline Stages
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1. **Digger**: Identify Bt toxin genes using BtToxin_Digger + BLAST + Perl
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2. **Shoter**: Evaluate toxin activity against insect targets using BPPRC database
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3. **Plots**: Generate heatmaps for toxin-target relationships
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4. **Bundle**: Package results into .tar.gz download
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### Task States
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- `pending`: Waiting to enter queue
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- `queued`: Waiting for available slot (shows queue position)
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- `running`: Currently executing (shows progress % and stage)
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- `completed`: Finished successfully
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- `failed`: Error occurred (shows error message)
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### API Endpoints
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| Method | Endpoint | Description |
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|--------|----------|-------------|
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| POST | `/api/tasks` | Create new analysis task |
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| GET | `/api/tasks/{task_id}` | Get task status and progress |
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| GET | `/api/tasks/{task_id}/download` | Download result bundle |
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| DELETE | `/api/tasks/{task_id}` | Delete task and results |
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## Technical Constraints
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### Frontend Stack
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- Vue 3 (Composition API + script setup)
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- Vite build tool
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- Element Plus UI components
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- Pinia state management
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- Vue Router 4
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- vue-i18n for i18n
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- fetch API for HTTP requests
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### Backend Stack
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- FastAPI + Uvicorn
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- asyncio + Semaphore for 16 concurrent task limit
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- Redis for task status and queue management
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- pixi for environment management (conda alternative)
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- digger env: BtToxin_Digger + BLAST + Perl
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- pipeline env: Python 3.9+ (pandas, matplotlib, seaborn)
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### Database Files
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- BPPRC Specificity Database: `toxicity-data.csv`
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- BtToxin database: `external_dbs/bt_toxin`
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### Scoring Parameters (configurable)
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- `min_identity`: Minimum similarity (0-1, default: 0.8)
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- `min_coverage`: Minimum coverage (0-1, default: 0.6)
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- `allow_unknown_families`: Allow unknown families (default: false)
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- `require_index_hit`: Require index hit (default: true)
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### Reserved / Future Features
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- CRISPR-Cas analysis module (prepare `crispr_cas/` directory)
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- Direct protein sequence analysis (sequence_type=prot)
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## Success Criteria
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1. [ ] Users can upload genome (.fna/.fa/.fasta) or protein (.faa) files for analysis
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2. [ ] System supports 16 concurrent tasks with automatic queue management
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3. [ ] Chinese/English language switching works correctly
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4. [ ] Toxin-target activity assessment displays in heatmap format
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5. [ ] Results available for download as .tar.gz within 30 days
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6. [ ] Docker deployment successful with Traefik reverse proxy at bttiaw.hzau.edu.cn
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## Current Task
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Follow @fix_plan.md and choose the most important item to implement next.
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