TechStack-Germany

Standard Infrastructure and Technology Stack used for OMOP CDM implementations in Germany

Versions of included software

Application	Version
Atlas	2.14.0
WebAPI	2.14.0
Postgres	16
OMOP CDM	5.3.1
GermanVocab	2023-02-16

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Step 1 - Configuration

The included docker-compose.yml starts a Postgres instance with a default database called ohdsi as well as the OHDSI WebAPI and Atlas. The DB is initialized with a dedicated ohdsi_admin_user with full read and write access to the ohdsi DB.

You will have to manually specify a password for both the postgres as well as the ohdsi_admin_user. You can specify the environment variables POSTGRES_PASSWORD and OHDSI_ADMIN_PASSWORD to set them.

First, copy the sample.env file to .env.

cp sample.env .env

Now you can adjust the credentials of the users in the .env file.

The default settings of the deployment will work for testing purposes on a local host. If you want to connect Atlas and the WebAPI via DNS entries, you will have to adjust the following lines:

config-local.js

url: 'http://localhost:9876/WebAPI/'

docker-compose.yml

SECURITY_ORIGIN: "http://localhost:8080"

Step 2 - Start the Database and OHDSI container

docker-compose up -d

Note that this uses .env to populate POSTGRES_PASSWORD and OHDSI_ADMIN_PASSWORD automaticaly.

Step 3 - Initialize the CDM Schema

# Load the OHDSI_ADMIN_PASSWORD from sample.env in the current shell environment
source .env
# Run the init container
docker run --rm -it --network=$DOCKER_NETWORK \
  -e PGPASSWORD=$OHDSI_ADMIN_PASSWORD \
  -e PGUSER=ohdsi_admin_user \
  -e PGHOST=omopdb \
  -e PGDATABASE=ohdsi \
  -e WEBAPI_URL=http://webapi.$DOCKER_NETWORK:8080/WebAPI \
  -e SETUP_CDS=true \
  -e SETUP_SYNPUF=false \
  <<IMAGE>>

You should only run this init container once. In case you have to init the database once again, you have to remove the volumes of the corresponding containers as well: docker-compose down -v

The init container has the following configuration options:

Environment variable	Description	Default
SETUP_CDS	Set to false if a CDM schema containing the CDS vocabs data should not be setup.	false
SETUP_SYNPUF	Set to true if a CDM schema containing the SynPUF 1K data should be setup.	false
WEBAPI_URL	Required. The base URL of the WebAPI. Used to check if the WebAPI's internal DB migrations have completed.	""
PGHOST	Required. Hostname of the Postgres DB. Note that all PG* variables can be used, see: https://www.postgresql.org/docs/13/libpq-envars.html.	""
PGUSER	Username used to connect to the DB specified with PGHOST DB	postgres
PGPASSWORD	Required. Password of the PGUSER user DB	""
PGDATABASE	Name of the database where the CDS CDM should be created. Currently, the init job requires both the WebAPI (the ohdsi schema) and the CDM to be placed within the same database.	ohdsi

Step 4 Check the installation

You can access Atlas and the WebAPI like this:

Application	URL
Atlas	http://localhost:8080/atlas
WebAPI	http://localhost:9876/WebAPI/info