OMOP CDM Setup

Start the containers

The dev.compose.yml in the root of the Bunny repository can start a Postgres database container, and an init service omop-lite.

omop-lite will load a small synthetic OMOP CDM of 100 people, enough for Bunny to run queries.

Or you can use it to load your own data files by changing the dev.compose.yml file.

docker compose -f dev.compose.yml up db omop-lite

Configuration

You can connect to the now running OMOP CDM with the following configuration:

DATASOURCE_DB_USERNAME=postgres
DATASOURCE_DB_PASSWORD=postgres
DATASOURCE_DB_DATABASE=omop
DATASOURCE_DB_DRIVERNAME=postgresql
DATASOURCE_DB_SCHEMA=omop
DATASOURCE_DB_PORT=5432
DATASOURCE_DB_HOST=localhost

Start the database container

The dev.compose.yml in the root of the Bunny repository can start a database container with

docker compose -f dev.compose.yml up db

This will initialise a Postgres instance in the container.

Copy the data

Navigate to the folder containing hutch_db.tar and copy it into the container with:

docker cp hutch_db.tar hutch-bunny-dev-db-1:/

Start running bash in your container

docker exec -it hutch-bunny-dev-db-1 bash

Use pg_restore to load the data into the database

pg_restore --dbname=postgres --host=localhost --port=5432 --username=postgres --password hutch_db.tar

If prompted, provide “postgres” as a password

You can then exit the container with ctrl+d or exit