BioDM: A fast and RESTful Data Management framework

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 <https://github.com/sqlalchemy/sqlalchemy/>`_ tables
- `marshmallow <https://github.com/marshmallow-code/marshmallow>`_ schemas
Inter-operate services ecosystem:
- Permissions leveraging Keycloak
- Storage leveraging S3 protocol
- Jobs & Visualization leveraging Kubernetes cluster
Also sets up essentials:
- Liveness endpoint
- Login and token retrieval system
- OpenAPI schema generation through apispec

It sits on the F**indability and **A**ccessibility part of the **F.A.I.R principles, while remaining flexible for the remainder to be implemented.

Quickstart

Install

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

To run an API instance you will also need an ASGI server, e.g. uvicorn+uvloop:

pip3 install uvicorn uvloop

Run Example project

Provided within this repository.

Note: Prior to this step, it is recommended to create and activate a new python3 (>=3.11) virtual environment.

pip3 install -r src/requirements/dev.txt
pip3 install .

you may use the following in order to deploy the development stack:

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

It is recommended to give them hostnames. In particular keycloak does hard checks and login shall fail without this step.

sudo cat >> /etc/hosts <<EOF
# biodm-dev
10.10.0.2       postgres.local
10.10.0.3       keycloak.local host.minikube.internal
10.10.0.4       s3bucket.local
EOF

Then you may run example:

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

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

To use kubernetes functionalities or tweak default configuration you should visit getting started section of the documentation.

BioDM: A fast and RESTful Data Management framework