Auto-sync on project open

.claude/skills/agent-log.md

@@ -8,9 +8,11 @@ This file tracks all work done by Claude sessions on this project.
 
 ### Session Start
 - **Task**: Plan and implement web application + database for the splicing model
-- **Status**: Planning phase complete - awaiting user approval
+- **Status**: Phase 1 Core Infrastructure COMPLETE
 
 ### Work Completed
+
+#### Planning Phase
 1. Explored entire codebase structure
 2. Read all documentation files (01-10)
 3. Understood model architecture:
@@ -19,8 +21,18 @@ This file tracks all work done by Claude sessions on this project.
    - Output: PSI value (0-1)
    - Model size: ~10k parameters, ~263KB
 4. Reviewed NAR Web Server requirements from doc 08
-5. Attempted to get design inspiration from RRMScorer website
-6. Gathered comprehensive requirements through Q&A session
+5. Gathered comprehensive requirements through Q&A session
+
+#### Implementation Phase 1 - Core Infrastructure
+1. Created webapp/ directory structure
+2. Created requirements.txt with all dependencies
+3. Created Makefile for single-command startup
+4. Set up SQLite database with SQLAlchemy
+5. Created model loading service (predictor.py)
+6. Implemented FastAPI application with all API endpoints
+7. Created Pydantic schemas for API validation
+8. Extracted example sequences from test data
+9. Created initial test file
 
 ### Decisions Made (User Confirmed)
 
@@ -48,21 +60,82 @@ This file tracks all work done by Claude sessions on this project.
 | **Dev Setup** | Single command startup (Makefile) |
 | **Timeline** | Feature complete before deployment |
 
-### Key Findings
-- Pre-trained model available at: `output/custom_adjacency_regularizer_20210731_124_step3.h5`
-- Requires ViennaRNA for structure prediction (~0.5-1s per sequence)
-- No GPU required for inference
-- Custom TensorFlow layers need to be registered when loading model
-- Test data available for creating example sequences
+### Files Created
+
+```
+webapp/
+├── app/
+│   ├── __init__.py
+│   ├── config.py          # Configuration settings
+│   ├── database.py        # SQLite + SQLAlchemy
+│   ├── main.py            # FastAPI app with HTML pages
+│   ├── api/
+│   │   ├── __init__.py
+│   │   ├── routes.py      # API endpoints
+│   │   └── schemas.py     # Pydantic schemas
+│   ├── models/
+│   │   ├── __init__.py
+│   │   └── job.py         # Job model
+│   ├── services/
+│   │   ├── __init__.py
+│   │   └── predictor.py   # Model wrapper
+│   └── ui/
+│       ├── __init__.py
+│       ├── components/__init__.py
+│       └── pages/__init__.py
+├── static/
+│   ├── css/
+│   ├── js/
+│   └── examples.json      # Extracted example sequences
+├── templates/
+├── tests/
+│   ├── __init__.py
+│   └── test_api.py
+├── scripts/
+│   └── extract_examples.py
+├── Makefile
+├── requirements.txt
+└── README.md
+```
+
+### API Endpoints Implemented
+
+| Method | Endpoint | Status |
+|--------|----------|--------|
+| GET | `/` | Implemented |
+| GET | `/result/{job_id}` | Implemented |
+| GET | `/help` | Implemented |
+| GET | `/tutorial` | Implemented |
+| GET | `/methodology` | Implemented |
+| POST | `/api/predict` | Implemented |
+| POST | `/api/batch` | Implemented |
+| GET | `/api/status/{job_id}` | Implemented |
+| GET | `/api/result/{job_id}` | Implemented |
+| GET | `/api/example` | Implemented |
+| GET | `/api/export/{job_id}/{format}` | Implemented |
+| GET | `/api/health` | Implemented |
+| GET | `/docs` | Implemented (FastAPI auto-docs) |
+
+### How to Run
+
+```bash
+cd webapp
+make install   # Install dependencies
+make dev       # Run development server
+# Open http://localhost:8000
+```
 
 ### Plan File
 See: `/Users/sachin/.claude/plans/tingly-sauteeing-bengio.md`
 
-### Next Steps
-- [ ] Awaiting user approval of plan
-- [ ] Create webapp/ directory structure
-- [ ] Set up Python dependencies
-- [ ] Begin Phase 1 implementation
+### Next Steps (Future Sessions)
+- [ ] Add PyShiny + shiny.react frontend (Phase 3)
+- [ ] Implement proper HTML templates
+- [ ] Add email notification service
+- [ ] Create PDF export
+- [ ] Write comprehensive tests
+- [ ] Add Docker configuration
+- [ ] Set up deployment scripts
 
 ---