Quickstart

Basic Usage

Make sure you have the following:

• An running OMOP data source

• Docker installed

Make sure you have Docker installed. Create a new directory and copy the following contents into a file called docker-compose.yml:

docker-compose.yml

services:

    # OHDSI API
    ohdsi-api:
        image: harbor2.vantage6.ai/infrastructure/ohdsi-api:latest
        ports:
        - 5000:8000
        container_name: ohdsi-api
        env_file:
        - .connection-details.env
        command: ["gunicorn", "-b", "0.0.0.0", "-w", "1", "api:app"]

    # RabbitMQ
    rabbitmq:
        image: rabbitmq:3-management
        ports:
        - 5672:5672
        - 15672:15672
        container_name: rabbitmq

    # PostgreSQL for celery
    db:
        image: postgres:9.6
        ports:
        - 5454:5432
        container_name: postgres
        env_file:
        - .connection-details.env
        volumes:
        - ./data/postgres:/var/lib/postgresql/data

    celery-worker:
        image: harbor2.vantage6.ai/infrastructure/ohdsi-api:latest
        container_name: celery-worker
        command: celery -A api.celery_app worker -l DEBUG -P solo
        env_file:
        - .connection-details.env
        depends_on:
        - rabbitmq

Then you need to create a .connection-details.env file with the connection details to the OMOP data source:

.connection-details.env

POSTGRES_USER=postgres
POSTGRES_PASSWORD=Celery@Postgr3s!
POSTGRES_DB=celery

CELERY_BROKER_URL=amqp://guest:guest@rabbitmq:5672/
CELERY_RESULT_BACKEND=db+postgresql://postgres:Celery@Postgr3s!@db/[DATABASE]

OMOP_DBMS=postgresql
OMOP_SERVER=omop-data-source
OMOP_PORT=5432
OMOP_USER=ohdsi
OMOP_PASSWORD=ohdsi
OMOP_DATABASE=ohdsi
OMOP_CDM_SCHEMA=cdm
OMOP_RESULT_SCHEMA=results

Finally, start the API by running:

docker compose up -d

This will start the API on port 5000. You can now access the API on http://localhost:5000. To see all available endpoints, visit http://localhost:5000/apidocs.