bedhost

bedhost is a Python FastAPI module for the API that powers BEDbase. It needs a path to the bedbase configuration file, which can be provided either via -c/--config argument or read from $BEDBASE_CONFIG environment variable.

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dfgeaf Deployed public instance: https://bedbase.org/

Documentation: https://docs.bedbase.org/bedhost

API: https://api.bedbase.org/

Source Code: https://github.com/databio/bedhost/

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Running for development

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 ../bedbase.org/environment/production.env
BEDBASE_CONFIG=../bedbase.org/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 new database: BEDBASE_CONFIG=../bedbase.org/config/bedbase2.yaml uvicorn bedhost.main:app --reload

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

• 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/img/open_chromatin
• 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/img_path/open_chromatin
• 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/file/bedfile
• 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/file_path/bedfile
• 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata
• 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata?attr_ids=md5sum&attr_ids=genome

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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.

Running container for development

Configuration settings and deployment instructions are in the bedbase.org repository.

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Deploying updates automatically

The bedhost/databio image is built by a github action. It will build and push the latest image whenever a release is made. It will also tag that release with a tag for the release name.

For the dev tag, you must deploy this through manual dispatch