This repository contains the dockerized version of the ETL process to convert P21 data to OMOP. Please install a OMOP-Database in cdm version 5.3.1 before starting the job.
Please place the input data in the folder /input/data. You can navigate to this folder and check the readme file to verify the needed file names. They must comply with the defined requirements.
You can configure the job via the .env file.
| Variable | Description |
|---|---|
| DATABASE_IP | IP or DNS of the host serving the database |
| DATABASE_PORT | The port the database is listening on |
| DATABASE_NAME | The name of the OMOP database |
| DATABASE_SCHEMA | The schema of the OMOP tables |
| DATABASE_USER | The user of the OMOP database |
| DATABASE_PASSWORD | The password of the OMOP user |
| OMOP_NETWORK | The Docker network name if you want to connect to the db via Docker |
| VAR_PARALLEL | execute the job in paralel (default false) |
| INIT_MEMORY | The starting memory alloc of the JVM |
| MAX_MEMORY | The maximum memory alloc of the JVM |
docker-compose up
docker-compose down -v