This repository is an implementation of the Beacon v2.0 Model and extends the Reference Implementation by implementing a FHIR endpoint that allows to query /individuals and /biosamples endpoints from a FHIR Store that contains data represented as FHIR Resources compliant with the BBMRI Sample Locator model.
For the deployment and the documentation of the Beacon reference implementation please refer to the main repository.
Here only the deployment with a FHIR backend is documented
To deploy a Beacon service that queries data from a FHIR store, it is possible to use Docker.
The docker image needs a configuration file mounted at /beacon/config.yml path of the container
To create a config.yml file, use the conf/config.fhir.yml template and edit it
with the information of your beacon.
In particular fill:
- Info section: just some data about the beacon
- Organization: information about the organization that is exposing the beacon
- Project Info:
- FHIR Store Info: connection parameters of the FHIR Store to use as backend
Three environment variables, all related to Nginx, must be set:
- SERVER_NAME: same as Nginx's server name directive
- PORT: the port used for the service
- SSL_ENABLED: true or false to enable SSL (recommended)
In case SSL is enabled, the key-certificate pair must be mounted on /etc/ssl/certs/beacon.key and
/etc/ssl/certs/beacon.cert
The /deploy/docker-compose.fhir.yaml is an example that deploy a Beacon and the FHIR store to query.
An example of a standalone Beacon service that queries an external FHIR store is:
docker run -e SERVER_NAME=beacon -e PORT=5050 -e SSL_ENABLED=false -v <conf-file>:/beacon/beacon/conf.py -p 5050:5050 crs4/beacon:2.0-fhir
This work has been partially supported by the European Joint Programme on Rare Disease (EJPRD) project (grant agreement N. 825575)