omop-lite

A small container to get an OMOP CDM Vocabulary Postgres database running quickly.

Drop your Vocabularies into vocabs/, and run the container.

Environment Variables

You can configure the Docker container using the following environment variables:

• DB_HOST: The hostname of the PostgreSQL database. Default is db.
• DB_PORT: The port number of the PostgreSQL database. Default is 5432.
• DB_USER: The username for the PostgreSQL database. Default is postgres.
• DB_PASSWORD: The password for the PostgreSQL database. Default is password.
• DB_NAME: The name of the PostgreSQL database. Default is omop.
• SCHEMA_NAME: The name of the schema to be created/used in the database. Default is omop.
• VOCAB_DATA_DIR: The directory containing the vocabulary CSV files. Default is vocabs.

Usage

docker run -v ./vocabs:/vocabs ghcr.io/AndyRae/omop-lite

# docker-compose.yml
services:
  omop-lite:
    image: ghcr.io/andyrae/omop-lite
    volumes:
      - ./vocabs:/vocabs
    depends_on:
      - db

  db:
    image: postgres:latest
    environment:
      - POSTGRES_DB=omop
      - POSTGRES_PASSWORD=password
    ports:
      - "5432:5432"

Bring Your Own Vocabularies

You can provide your own data for loading into the tables by placing your CSV files in the vocabs/ directory. This should contain .csv files matching the vocab tables (DRUG_STRENGTH.csv, CONCEPT.csv, etc.).

Setup Script

The setup.sh script included in the Docker image will:

1. Create the schema if it does not already exist.
2. Execute the SQL files to set up the database schema, constraints, and indexes.
3. Load data from the .csv files located in the VOCAB_DATA_DIR.