Longevity Biomarker Tracking System

Database system for tracking biomarkers and calculating biological age based on NHANES data.

NOT for medical diagnostic purposes.

Quick Start

### First-time setup (Mac/Linux)

```bash
git clone … && cd longevity-biomarker-tracker
cp .env.example .env
make install          # python deps + pre-commit
make db               # starts MySQL + Adminer on :3307
make run              # FastAPI on :8000
make ui               # Do this in a new terminal. Then open http://localhost:80
# ETL is optional until the transform notebook is finished

Database Schema Updates

The initial database schema is loaded automatically when the database container is first created. For subsequent schema changes:

1. Update the sql/schema.sql file
2. Run the following command to apply changes:

   docker compose exec db mysql -u biomarker_user -pbiomarker_pass longevity < sql/schema.sql

3. Or use this shortcut make db-reset

Notes

• The ETL process (make etl) will generate a tests/sample_dump.sql file with sample data for testing purposes.
• This sample data is used by the CI workflow to test the API functionality.
• NOT for medical diagnostic purposes.

Development Workflow

Pre-commit Hooks

This project uses pre-commit hooks to ensure code quality and consistency. To set up:

# Install pre-commit
make install  # or manually: pip install pre-commit

# Install the git hooks
pre-commit install