UNICAS Beacon v2 Network deployment with Docker

This repository serves for deploying both Frontend and Backend with Docker.

It is based in the following components:

OMOP beacon extension: https://gitlab.bsc.es/impact-data/impd-beacon_omopcdm
Beacon Network backend: https://github.com/elixir-europe/beacon-network-backend
Beacon Network UI: https://github.com/elixir-europe/beacon-network-ui

You may also need access to an OMOP database. Check this tutorial to create an OMOP database using synthetic data.

Deploy

Download the code from this repository,

git clone https://github.com/bsc-health-data/beacon-network-unicas.git
cd beacon-network-unicas

Segurity with keycloak (optional)

Please first create a .env file inside the frontend folder so that you can modify some variables. Take into account that the file below will not be copied to GitHub as it contains keys and for security reasons it should ignored:

REACT_APP_CLIENT_ID="ID of your LS Login"
REACT_APP_CLIENT_SECRET="password of your LS Login"
REACT_APP_KEYCLOAK_CLIENT_SECRET="password of your Keycloak login"
REACT_APP_KEYCLOAK_CLIENT_ID='ID of your Keycloak login'
REACT_APP_KEYCLOAK_CLIENT_REALM='REALM of your Keycloak login'

If you want to use Life Science Identifier you will need to have created your Life Science environment; please first create a user . After that you will need to register a service registry in order to be able to administrate your logins. Please go here and ask for a New Service - type OIDC -.

You can also deploy your own keycloak instance (may need some changes to the code, work in progress)

Then, edit the file config.json, which can be found inside folder frontend/. You need to decide where you want the UI to point to when making requests. Find below an example:

{
   "API_URL": "https://unicas.test/beacon-network/v2.0.0",
   "REDIRECT_URL": "https://unicas.test",
   "KEYCLOAK_URL": "https://unicas.test"
 }

Add/Remove Beacons from the network

You must add the Beacon's URL to the wildfly/BEACON-INF/beacon-network.json file.

The structure of this JSON file should be an array containing the URL of the validated Beacon, like this:

[
    "your.beacon.url/api"
]

After adding the URL to the beacon-network.json file, the Beacon Network will automatically fetch the new Beacon, ensuring its integration into the network. This process facilitates the incorporation of Beacons into the ELIXIR Beacon Network.

To remove the Beacon, you just need to remove the URL from the beacon-network.json file.

OMOP DB configuration

Create a .env file with POSTGRES_URL pointing to your database installation

POSTGRES_URL='postgresql://DB_HOST/DB_NAME'

Adjust configuration for localhost test environment

Comment the https related line in nginx/default.json

#    proxy_set_header X-Forwarded-Proto https;

Uncomment lines at docker-compose.yaml

  - KC_HOSTNAME_STRICT=false
  - KC_HOSTNAME_STRICT_HTTPS=false

Run

Run docker compose to build and start the containers:

 docker compose up -d

Congrats! You have created Beacon Network FrontEnd in http://localhost:8080/ and the backend in http://localhost:8080/beacon-network/v2.0.0/. Adjust the URLs based on your setup.

Update the docker images

To update the ELIXIR Beacon Network (EBN) with a new image, follow these steps: Pull the latest image:

docker-compose pull

Recreate and rebuild the containers with the new image:

docker-compose up --force-recreate --build -d

These commands will download the latest image for the EBN and recreate the containers using the new image. The --force-recreate flag ensures that the containers are recreated even if they are already running, and the --build flag rebuilds the containers if necessary. The `-d flag runs the containers in detached mode.

bsc-health-data / beacon-network-unicas

readme