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Stage

Stage is the React-based portal UI that researchers use to query and explore Overture data.

If you have not yet deployed Arranger, return to Arranger.

Setting up Stage​

  1. Create an env file: Create a file named .env.stage with the following content:

    # ==============================
    # Stage Environment Variables
    # ==============================

    # Stage Variables
    NEXTAUTH_URL=http://localhost:3000/api/auth
    NEXT_PUBLIC_LAB_NAME=Overture QuickStart Portal
    NEXT_PUBLIC_ADMIN_EMAIL=contact@overture.bio
    NEXT_PUBLIC_DEBUG=true
    # Keycloak Variables
    NEXT_PUBLIC_AUTH_PROVIDER=keycloak
    ACCESSTOKEN_ENCRYPTION_SECRET=super_secret
    SESSION_ENCRYPTION_SECRET=this_is_a_super_secret_secret
    NEXT_PUBLIC_KEYCLOAK_HOST=http://keycloak:8080
    NEXT_PUBLIC_KEYCLOAK_REALM=myrealm
    NEXT_PUBLIC_KEYCLOAK_CLIENT_ID=webclient
    KEYCLOAK_CLIENT_SECRET=ikksyrYaKX07acf4hpGrpKWcUGaFkEdM
    NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE=dms
    # Arranger Variables
    NEXT_PUBLIC_ARRANGER_DOCUMENT_TYPE=file
    NEXT_PUBLIC_ARRANGER_INDEX=file_centric
    NEXT_PUBLIC_ARRANGER_API_URL=http://arranger-server:5050
    NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS=repositories.code, object_id, analysis.analysis_id, study_id, file_type, file.name, file.size, file.md5sum, file.index_file.object_id, donors.donor_id, donors.specimens.samples.sample_id
    Click here for a detailed breakdown

    Stage Variables​

    • NEXTAUTH_URL specifies the base URL for NextAuth.js, which handles authentication in the portal.

    • NEXT_PUBLIC_LAB_NAME is the name displayed in the top left of the portal interface.

    • NEXT_PUBLIC_ADMIN_EMAIL is the administrator or support contact email.

    • NEXT_PUBLIC_DEBUG enables debug mode.

    Keycloak Variables​

    • NEXT_PUBLIC_AUTH_PROVIDER specifies the authentication provider, in this case Keycloak.

    • ACCESSTOKEN_ENCRYPTION_SECRET defines the secret used to encrypt access tokens.

    • SESSION_ENCRYPTION_SECRET specifies the secret used to encrypt session cookies.

    • NEXT_PUBLIC_KEYCLOAK_HOST specifies the Keycloak server URL.

    • NEXT_PUBLIC_KEYCLOAK_REALM defines the Keycloak realm used for authentication.

    • NEXT_PUBLIC_KEYCLOAK_CLIENT_ID and KEYCLOAK_CLIENT_SECRET are the Keycloak client credentials.

    • NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE specifies the audience for permission claims.

    Arranger Variables​

    • NEXT_PUBLIC_ARRANGER_DOCUMENT_TYPE defines the document type for Arranger (file-centric or analysis-centric).

    • NEXT_PUBLIC_ARRANGER_INDEX defines the Arranger index used by the portal.

    • NEXT_PUBLIC_ARRANGER_API_URL is the URL of the Arranger GraphQL API.

    • NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS lists the columns included in the manifest generated for downloads.

  2. Run Stage: Use the docker run command with your .env.stage file:

    docker run --env-file .env.stage \
        --name stage \
        -p 3000:3000 \
        ghcr.io/overture-stack/stage:3ede4e2

    The front-end portal will now be available in your browser at localhost:3000.

info

Stage depends on Arranger, so confirm Arranger is accessible before attempting to use the portal.