OMOP Odyssey - BroadSea (The Sirens)

Welcome to the Sirens. In the OHDSI ecosystem, the allure of deep data discovery is powerful, but the setup can be treacherous. To navigate these waters, we’re deploying BroadSea, a comprehensive, containerized platform that brings together all the essential OHDSI tools—Atlas, WebAPI, and Hades—into a single, deployable unit.

The Vessel: BroadSea

BroadSea simplifies the deployment of the entire OHDSI analytical stack using Docker. It allows us to spin up a fully functional research environment in minutes, rather than days.

Setting Sail with Docker Compose

We use Docker Compose to orchestrate our BroadSea deployment. This ensures that Atlas, WebAPI, and our results database are all correctly configured and networked.

Integrating with InterSystems OMOP

The most critical part of our mission is connecting BroadSea’s WebAPI to our InterSystems OMOP Cloud Service. This requires some “nostalgic” credential management and manual SQL insertion into the WebAPI source tables.

# Registering the InterSystems Source
export IRIS_JDBC="jdbc:IRIS://k8s-elb.us-east-2.amazonaws.com:443/USER/:::true"
cat << EOF > 200_populate_iris_source_daimon.sql
INSERT INTO webapi.source(source_id, source_name, source_key, source_connection, source_dialect, username, password)
VALUES (2, 'InterSystems OMOP Stage', 'IRIS', '$IRIS_JDBC', 'iris', '$IRIS_USER', '$IRIS_PASS');
# ...
EOF
docker-compose exec broadsea-atlasdb psql -U postgres -f "/docker-entrypoint-initdb.d/200_populate_iris_source_daimon.sql"

Navigating Security

To ensure secure communication between our containers and the InterSystems cloud service, we need to import our SSL certificates into the Java keystores of the BroadSea services.

# Importing the IRIS certificate
docker-compose exec broadsea-hades bash -c "/usr/bin/keytool -importcert -file /home/ohdsi/certificateSQLaaS.pem -keystore /home/ohdsi/keystore.jks -alias IRIScert -storepass changeit -noprompt"

The Arrival: Atlas is Live!

With our connection established and security in place, we can refresh the WebAPI and log into Atlas. Our InterSystems OMOP data is now ready for world-class characterization and cohort building.

The journey through the Sirens has been successful. Our InterSystems data is now fully integrated with the global OHDSI community tools.

Stay tuned for the next stage of the OMOP Odyssey.