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Deploy to ELIXIR-LU

Deploy the GDI User Portal to ELIXIR Luxembourg infrastructure. This deployment uses Docker Compose and includes the User Portal, CKAN, REMS, Keycloak, and API Gateway.

Current deployment endpoints​

The following endpoints are available in the development environment:

  • User Portal: portal.dev.gdi.lu
  • IAM (Identity and Access Management): id.portal.dev.gdi.lu
  • API Gateway: api.portal.dev.gdi.lu
  • Catalogue: catalogue.portal.dev.gdi.lu

Prerequisites​

  • Access to the ELIXIR-LU server
  • Docker and Docker Compose installed
  • Admin access to CKAN, REMS, and Keycloak
  • GitHub repository access to gdi-userportal-deployment

Clone the deployment repository​

Clone the deployment repository to your server:

git clone https://github.com/GenomicDataInfrastructure/gdi-userportal-deployment.git
cd gdi-userportal-deployment

Configure environment variables​

Copy the environment example file and update all secrets:

cp .env.example .env

Edit the .env file and update all the secrets and configuration values as required for your environment.

Deploy REMS​

Build and deploy the REMS service first:

docker compose build
docker compose run --rm -e CMD="migrate" rems
docker compose up -d rems

Configure REMS​

After REMS is running, configure the required API keys and users.

  1. Configure the admin user. Enter the REMS Docker container and configure the admin user.

  2. Configure access-management-service API key. Create an API key for any user and any REST method, limited to the following endpoints:

    • /api/users/create
    • /api/catalogue-items
    • /api/my-applications
    • /api/applications/.*

  3. Configure rems-synchronizer API key. Create an API key and robot for any REST method, limited to the following endpoints:

    • /api/organizations.*
    • /api/forms.*
    • /api/workflows.*
    • /api/resources.*
    • /api/catalogue-items.*

  4. Configure ls-aai API key. Create an API key and robot, limited to: GET /api/permissions/.*

  5. Update environment variables. Include the newly created API keys and users in the environment variables file.

Deploy all services​

Deploy all remaining services:

docker compose up -d

Configure CKAN harvesting​

After all services are running, set up data harvesting in CKAN.

  1. Log in to CKAN: Log in to CKAN as a sysadmin user.

  2. Add harvest sources: Configure and add the required harvest sources for your data catalogues.

  3. Run REMS synchroniser: Wait for the REMS synchroniser to run automatically, or run it manually.

Configure Keycloak and LS-AAI​

Configure authentication and authorisation with Keycloak and LS-AAI integration.

  1. Access Keycloak: Go to your Keycloak instance at id.portal.dev.gdi.lu.

  2. Configure LS-AAI identity provider: Set up LS-AAI as an identity provider in Keycloak.

  3. Add claim to user attribute mapper: Add a mapper that maps the claim sub into elixir_id.

  4. Create OIDC realm for GDI: Create a new OIDC realm for GDI that accepts redirections to User Portal, CKAN, and REMS.

  5. Create client scope: Create a new client scope for the GDI realm.

  6. Add user attribute mapper: Add a new User Attribute Mapper that maps the attribute elixir_id into a claim called elixir_id and a scope called elixir_id.

  7. Create clients: Create a new client for User Portal, REMS, and CKAN.

  8. Add scope to clients: Add the scope elixir_id to the newly created clients.

Next steps

After deploying to ELIXIR-LU: