🧫 FAIR metrics for Rare Disease research

An API to deploy FAIR metrics tests for the research on Rare Disease community.

FAIR metrics tests are API operations which test if a subject URL is complying with certain requirements defined by a community, they usually check if the resource available at the subject URL complies with the FAIR principles (Findable, Accessible, Interoperable, Reusable).

This API is deployed publicly at https://rare-disease.api.fair-enough.semanticscience.org

🗃️ It can be used with the following FAIR evaluation services::

• https://fair-enough.semanticscience.org
• https://fairsharing.github.io/FAIR-Evaluator-FrontEnd

This FAIR Metrics tests API has been built with the FAIR test python library.

🧑‍💻 Deploy the API

Clone the repository:

git clone https://github.com/LUMC-BioSemantics/RD-FAIRmetric-F4
cd RD-FAIRmetric-F4

🐳 Development with docker (recommended)

From the root of this repository, run the command below, and access the OpenAPI Swagger UI on http://localhost:8000

docker-compose up

The API will automatically reload on changes to the code.

🐍 Development without docker

Note: it has been tested only with Python 3.8

Install dependencies from the source code:

pip install -e .

Start the API locally on http://localhost:8000

uvicorn main:app --reload

🚀 In production with docker

We use the docker-compose.prod.yml file to define the production deployment configuration.

To start the stack with production config:

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

We use a reverse nginx-proxy for docker to route the services.

✅ Test the Metrics API

The tests are run automatically by a GitHub Action workflow at every push to the main branch.

Add tests using the test_test parameter in each metric test in the metrics folder.

Run the tests locally with docker-compose:

docker-compose -f docker-compose.test.yml up --force-recreate

You can enable more detailed logs by changing the command: in the docker-compose.test.yml file to use pytest -s