This repository is an implementation of the Beacon v2.0 Model and contains:
- The (Python 3.9+) source code for beacon,
- A MongoDB database with sample data to demo the capabilities of the Beacon API.
- AAI and LS-AAI integrated.
To give the right permissions for AAI you will need to set the permissions of the users inside permissions folder, within the public_datasets.yml, registered_datasets.yml, controlled_datasets.yml files, or run the beacon admin page that allows you to manage all the permissions in a friendly way and no need to open .yml files. Just start the UI, that will run in http://localhost:8010, by executing this command from the deploy folder after the containers are up and running:
docker exec beacon-permissions bash permissions/permissions-ui/start.shPlease, bear in mind that the name of the user has to be the same that you used when creating the user in LS or in IDP, whatever the AAI method you are working with. To give a user a certain type of response for their queries, please modify this file response_type.yml adding the maximum type of response you want to allow every user.
Also, you will need to edit the file conf.py and introduce the domain where your keycloak is being hosted inside ldp_user_info and the issuers you trust for your token inside trusted_issuers. In case you want to run your local container, use this configuration:
idp_user_info = 'http://idp:8080/auth/realms/Beacon/protocol/openid-connect/userinfo'
lsaai_user_info = 'https://login.elixir-czech.org/oidc/userinfo'
trusted_issuers = ['http://idp:8080/auth/realms/Beacon', 'https://login.elixir-czech.org/oidc/']When you have your access token, pass it in a header with Authorization: Bearer in your POST request to get your answers. This token works coming from either from LS AAI or from keycloak (idp container).
- Fusions (
mateName) are not supported.
We thank the CSC Finland team for their contribution with a python implementing of version 1. They, in turn, got help from members of NBIS and DDBJ.