Introduction Presentation: https://www.overleaf.com/read/wxpdnptnkpsy

Source Code: https://github.com/bag-cnag/biodm

Documentation: https://bag-cnag.github.io/biodm/

BioDM is a fast, modular, stateless and asynchronous REST API framework with the following core features:

• Provide standard HTTP REST-to-CRUD endpoints from developper provided entity definitions:

  • SQLAlchemy tables
  • marshmallow schemas

• Inter-operate services ecosystem:

  • Permissions leveraging Keycloak
  • Storage leveraging S3 protocol
  • Jobs & Visualization leveraging Kubernetes cluster

-> Act as an API gateway and log relevant data.

• Also sets up essentials:
  • Liveness endpoint
  • Login and token retrieval system
  • OpenAPI schema generation through apispec

pip3 install git+https://github.com/bag-cnag/biodm

To run the API you will also need an ASGI server, i.e. uvicorn+uvloop by default:

pip3 install uvicorn uvloop

OR

pip3 install -r src/requirements/dev.txt

Then you may run our example after populating src/example/.env with your desired configuration:

cd src/example/
python3 src/example/app.py

Alternatively, if your goal is simply to run example locally you may use the following command beforehand in order to deploy the development stack:

docker compose -f compose.yml up --build -d

This stack comes with an interactive swagger-ui visitable at http://localhost:9080/ once the server is running.

Developed at CNAG

No contributing policy yet. However, issues and pull requests are welcome.

GNU/AGPLv3