slobentanzer / igvf-catalog

Catalog API for the IGVF project

igvf-catalog

Catalog API repository for the IGVF project

Run with Docker Compose

1. Clone repository and make sure Docker is running.
2. Start services and load data inserts:

# From repository.
$ docker compose up
# Note if any dependencies have changed (e.g. switching between branches that
# rely on different versions of snovault) use the build flag as well
# to rebuild the underlying Docker image:
$ docker compose up --build

3. Browse at localhost:2023.
4. ArangoDB Client is available at localhost:8529. Default username and password are igvf.

Running locally

1. Clone repository.
2. Install Python 3.11.
3. Install Node 18.13.0.
4. Install ArangoDB 3.10.0. (https://www.arangodb.com/docs/stable/installation.html)
5. Install JS dependencies: npm install
6. Install Python dependencies: pip install -r data/requirements.txt. It's recommended to have a tool to create an isolated Python environment, such as virtualenv.
7. Update config/development.json with your ArangoDB root credentials.
8. Load sample data with cd data && python3 dev_setup.py.
9. Run tests: npm test and cd data && pytest.
10. Run the server npm run dev:server.
11. Server should be available at: localhost:2023 for Swagger interface, and localhost:2023/trpc for tRPC interface.

Automatic linting

This repo includes configuration for pre-commit hooks. To use pre-commit, install pre-commit, and activate the hooks:

pip install pre-commit==3.2.1
pre-commit install