EnsEMBL - Production DBSpy Web Application

FastAPI Web application for monitoring MySQL database statistics.

System Requirements

• Python 3.8+
• MySQL Client

Configuration

In order to connect to available MySQL servers, a text file in CSV format must be provided to DBSpy (please refer to hosts.csv for an example of the format). Such file must be readable by the web app and the path can be configured via the environment variable HOSTS_FILE (Default: HOSTS_FILE=./hosts.csv)

Logging level can be set via LOG_LEVEL environment variable (e.g. LOG_LEVEL=debug). Note that such variable will be read by default by Gunicorn.

Several Gunicorn config settings can be modified via the environment. Please refer to gunicorn_config.py for documented usage.

Usage

For development/testing purposes, the web server can be run using Uvicorn directly, for example:

uvicorn ensembl.production.dbspy.main:app --reload

Please refer to Uvicorn Documentation for more information on running Uvicorn in development and production environments.

DBSpy can also run as a Docker container (see Dockerfile)

Testing

Integration tests are implemented using Docker Compose and Pytest. Please refer to .travis.yml for more insight on tests configuration.

In order to run tests manually, run the following commands:

pip install -r requirements-test.txt
pip install .
docker-compose -f tests/docker-compose.yml up -d
pytest tests

Please wait for Docker Compose to finish building the images on the first run before running the tests with Pytest.