This repository will incorperate both backend and frontend components to the website

Using fastapi framework with a postgres database to store genotype-phenotype map data.

• List traits
• List regions
• LD between variants

• Docker and Docker Compose
• Visual Studio Code with Remote - Containers extension for development

1. Clone the repository:

   git clone https://github.com/mrcieu/genotype-phenotype-api.git
   cd genotype-phenotype-api
   

2. Create a .env file

   ANALYTICS_KEY=7a2b8f79-c837-45fa-ac48-0967ba8acf1b
   DB_PROCESSED_PATH="data/processed.db"
   DB_ASSOCS_PATH="data/assocs.db"
   LOCAL_DB_DIR="/local-scratch/projects/genotype-phenotype-map/results/2025_01_28-13_04"
   

3. Open the project in VSCode:

   code .
   

4. When prompted, click "Reopen in Container". This will start the development environment.

5. Once the container is built and running, you can start the FastAPI server by running:

   uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload
   

6. The API will be available at http://localhost:8000, and the code will hot-reload on changes.

Or if not using VSCode

1. Clone the repository:

   git clone https://github.com/mrcieu/genotype-phenotype-api.git
   cd genotype-phenotype-api
   

2. Create a .env file

   ANALYTICS_KEY=<key from https://my-api-analytics.vercel.app>
   

3. Build and run the Docker containers:

   docker-compose up --build
   

4. The API will be available at http://localhost:8000

No production yet but a dev version is available -

Setup a tunnel (need to be on vpn):

ssh -L 8001:localhost:8000 <username>@ieu-p1.epi.bris.ac.uk

Then check e.g.

curl http://localhost:8001/health

Or connect to http://localhost:8001/docs on your browser.

• Backend README can be found here
• Frontend README can be found here

The project includes a GitHub Actions workflow for Continuous Integration and Deployment. On each push to the main branch, it will:

1. Run the unit tests
2. Build a Docker image
3. Push the image to Docker Hub (using secrets DOCKER_USERNAME and DOCKER_PASSWORD configured in github repo)

1. Fork the repository
2. Create your feature branch (git checkout -b feature/AmazingFeature)
3. Commit your changes (git commit -m 'Add some AmazingFeature')
4. Push to the branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

This project is licensed under the GPL3 License.

TODO