Agari-Folio

Agari-Folio is the heart of the Agari Genomics Data stack and provides robust pathogen, schema, organisation, project and submission management and API endpoints with granular role-based access control.

Features

• Pathogen and schema management
• Organization management
• Project and study management
• Submission and file management
• Search enpoints
• Fine-grained permissions and roles
• RESTful API with JWT authentication
• Integration with Keycloak for identity management

API Documentation

Interactive API documentation (Swagger UI) is available at:

http://<your-host>:<port>/docs

Replace <your-host> and <port> with your deployment details.

Development

Create a virtual environment and activate it.

Install python dependencies:

pip install -U  --upgrade-strategy=eager -r requirements.txt

Configure environment variables for accessing backing services (see settings.py)

Run folio

python app.py

Event logging

The even log endpoint can return logs of the following types

• project_created, project_deleted, project_privacy, project_overwrite
• user_added, user_invited, user_accepted, project_user_deleted
• org_user_added, org_user_invited, org_user_accepted
• submission_created, file_uploaded, submission_validated, submission_published, submission_unpublished
• data_download

Tests

pip install -r requirements_test.txt

To run/dev tests locally, start the backing services (postgres, keycloak) using docker-compose, then configure your environment variables for folio to speak to them.

docker compose up

Wait for the services to be ready

and run tests

pytest

Fixtures will try to clean up what they create, but this can fail if there are errors, leaving the database in a bad state. You can clean this up using a database client, or by dropping the docker-compose volumes with docker compose down --volumes and creating fresh instances.

Tests should try to clean up what isn't managed by fixtures, e.g. with a try ... finally. One day perhaps the transaction management can be plugged into flask so that the test client can abort a transaction wrapping the request.

Pytest

• fixtures go in conftest.py
• fixtures are invoked as argument names to test functions
• test module names start with test_
• fixtures can clean up by yielding their value - pytest will call next to invoke the cleanup code after the fixture's scope ends.
• pytest prints values in an assertion that fails, so you often don't have to explicitly print values. If you're likely to need more detail, that can be passed as a second argument, e.g. response.get_json()
• pytest -v gives a bit more detail of variable values when an assertion fails