Build the container locally

Running with uvicorn provides auto-reload. To configure, this assumes you have previously set up databio/secrets.

1. Source .env file to populate the environment variables referenced in the configuration file.
2. Start bedhost using uvicorn and pass the configuration file via the BEDBASE_CONFIG env var.

source environment/production.env
BEDBASE_CONFIG=deployment/config/api.bedbase.org.yaml uvicorn bedhost.main:app --reload

You can change the database you're connecting to by using a different config file:

• Using a local config: BEDBASE_CONFIG=../bbconf/tests/data/config.yaml uvicorn bedhost.main:app --reload
• With the dev database: BEDBASE_CONFIG=deployment/config/api-dev.bedbase.org.yaml uvicorn bedhost.main:app --reload

Now, you can access the service at http://127.0.0.1:8000. Example endpoints:

• http://127.0.0.1:8000/v1/bed/bbad85f21962bb8d972444f7f9a3a932/metadata?full=true
• http://127.0.0.1:8000/v1/bed/bbad85f21962bb8d972444f7f9a3a932/metadata/plots?full=true
• http://127.0.0.1:8000/v1/objects/bed.bbad85f21962bb8d972444f7f9a3a932.chrombins
• http://127.0.0.1:8000/v1/bed/list?limit=10&offset=0

Running the server in Docker

Building image

• Primary image: docker build -t databio/bedhost -f Dockerfile .
• Dev image docker build -t databio/bedhost:dev -f dev.Dockerfile .
• Test image: docker build -t databio/bedhost:dev -f test.Dockerfile .

Existing images can be found at dockerhub.

Deploying updates automatically

• Deploying bedbase.