Biomolecule Toolkit Docker Setup

    HTTP API

    The docker image exposes port 8080 for HTTP traffic. The API endpoints are available under either /bioreg-web/rest/ or /api/. For more information about the endpoints refer to the API documentation at /swagger-ui.html.

    Direct database manipulation operations

    For security reasons, these HTTP endpoints are disabled by default. In case they are required (for playing around with the application in a sandbox environment or demonstration purposes), they can be enabled by activating db_api Spring profile (via environment variable: spring_profiles_active=db_api)

    License

    The product license can be specified via the environment variable CHEMAXON_LICENSE_URL which can have

    • either a URL pointing to the license file served over HTTP

    • or a filesystem path to the license file (use Docker volume to attach a folder containing the license file to /data/bioreg-home)

    Database configuration

    The database configuration can be provided via environment variables with the following defaults:

    
DB_DRIVERCLASSNAME: org.mariadb.jdbc.Driver
DB_MINPOOLSIZE: 1
DB_MAXPOOLSIZE: 10
DB_URL: jdbc:mysql://<BIOREG_DB_HOST defaults to
127.0.0.1>:<BIOREG_DB_PORT defaults to
3306>/bioreg?autoReconnect=true&useUnicode=yes&characterEncoding=UTF-8
DB_USERNAME: bioreg
DB_PASSWORD: bioreg
DB_TYPE: MYSQL

    SSL configuration

    SSL configuration is possible via

    • a set of environment variables:

    spring_profiles_active: must contain enforce-https

    SERVER_SSL_KEYSTORE: must point to the keystore file

    SERVER_SSL_KEYSTOREPASSWORD: the password for the keystore

    • and a volume attachment for the directory containing the keystore file

    Further environment variables with their default values

    
CID_PREFIX: CXN
MAXUPLOADSIZE: 5000
MAXFILESIZE: 5000