OMOP Docker
Aim of this repository
This repository provide DockerFile and docker compose for an OMOP + WebAPI + ATLAS installation. Useful for educational purpose.
How to use
Configuration
The configuration is performed by defining the environment variables in the env file.
The variables are:
| Parameter | Description |
|---|---|
| POSTGRES_USER | Username of the postgres database |
| POSTGRES_PASSWORD | Password of the postgres database |
| POSTGRES_DB | Name of the postgres database |
| CDM_SCHEMA_NAME | Schema for the OMOP CDM database |
| WEB_API_SCHEMA_NAME | Schema for the WebAPI and Atlas database |
| TEMP_SCHEMA_NAME | Schema for the temporary tables database |
| WEBAPI_URL | Expected URL for the WEBAPI with port |
Get OMOP vocabularies
The Vocabularies should be Downloaded from ATHENA website and the CSV file copied in the CDM/data/vocabularies folder.
If you want to use your own local Vocabularies files, the expected files are : CONCEPT.csv CONCEPT_ANCESTOR.csv CONCEPT_CLASS.csv CONCEPT_RELATIONSHIP.csv CONCEPT_SYNONYM.csv DOMAIN.csv DRUG_STRENGTH.csv RELATIONSHIP.csv VOCABULARY.csv.
Any missing file will result in an empty corresponding table.
The files should be tabulation separated, containing and header and encoded in UTF-8.
Run the docker
docker compose up
Acces to Atlas and WebAPI
Atlas is located in http://$WEBAPI_URL/atlas, by default: http://localhost:8080/atlas
WebAPI is located in http://$WEBAPI_URL/WebAPI, by default: http://localhost:8080/WebAPI
To do
- CDM DockerFile
- Configure the Posgresql database
- Integrate the ATHENA vocabularies in the database
- Data generation (Synthea) according to the environment variable parameters (/!\ Synthea is slow /!)
- WebAPI and Atlas DockerFile