Configuring Database Connection

All Starter Kit web services (i.e. core applications based on GA4GH API specifications) are configurable with a YAML config file. Part of the YAML config file includes a databaseProps object, which modifies the behavior of database connection properties.

databaseProps can be modified to connect to any database that has been set up with the appropriate table schema for the starter kit service being run. For more information on setting up a database with the correct table schema, see Using Starter Kit Utils.

The Starter Kit supports connections to either SQLite or PostgreSQL based databases.

Configurable databaseProps properties

A full explanation of configurable database connectivity properties is outlined below.

Attribute	Description	Data Type	Default
url	A valid JDBC database connection URL, indicating the database type (SQLite or PostgreSQL) and location. The default URL connects to the test SQLite database bundled within the docker container. For more information, see Constructing a valid JDBC URL	string (JDBC URL)	jdbc:sqlite:./ga4gh-starter-kit.dev.db
username	Database user with sufficient privileges to access required tables	string
password	Password for the above username	string
poolSize	Total connections to the database	integer	1
showSQL	Outputs SQL to console for each database operation	boolean	true

Constructing a Valid JDBC URL

SQLite

SQLite JDBC URLs are formatted as follows:

jdbc:sqlite:${SQLITE_DATABASE_FILE_PATH}

where ${SQLITE_DATABASE_FILE_PATH} is the (absolute or relative) path to the local file acting as the database. For example, if the database file is at /data/database/starter-kit.db, the JDBC URL would be:

jdbc:sqlite:/data/database/starter-kit.db

PostgreSQL

PostgreSQL JDBC URLs can take one of the following forms:

• jdbc:postgresql:${DATABASE}
• jdbc:postgresql://${HOST}/${DATABASE}
• jdbc:postgresql://${HOST}:${PORT}/${DATABASE}

where:

• ${DATABASE} is the database name,
• ${HOST} is the host/domain name where the database is running. Does not need to be specified if database is running at the default localhost
• ${PORT} is the networking port the database host is listening on. Does not need to be specified if it is listening on the default port 5432.

For example, if the target database was named "StarterKitDB", was running at "drs-db-starterkit.example.com" on port 5555, the JDBC URL would be:

jdbc:postgresql://drs-db-starterkit.example.com:5555/StarterKitDB

Example databaseProps

The following snippet displays an example databaseProps YAML configuration to configure the behavior of a starter kit service. A drs service is used in the example, but the serverProps object is equally applicable to any starter kit service.

drs:
  databaseProps:
    url: jdbc:postgresql://starter-kit-demo-db.ga4gh.org:5555/drsdb
    username: ga4gh-admin
    password: makeSureThisIsSecure123
    poolSize: 8
    showSQL: false