omoponfhir / omoponfhir-main

Main OMOPonFHIR Settings
Apache License 2.0
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NOTE: Our main repo has been changed to omoponfhir-main-r4-sql repository. We will moving our implementation to SqlRender and stop working on JPA. OMOPonFHIR.org site is now pointing to this new repo.

OMOPonFHIR Implementation version 1

Database Dependencies

Please follow the instruction in README. This database contains couple of sample synthetic patients.

How to install and run.

To download, git clone --recurse https://github.com/omoponfhir/omoponfhir-main.git

Before running the application update the values of the JDBC_URL, JDBC_USERNAME, and JDBC_PASSWORD environment variables in the Dockerfile. They must contain the data necessary for your application to connect to an OMOP V5 database. After updating the ENV variables in the Dockerfile, you can do either

  1. use docker compose to build and run

    sudo docker-compose up --build -d
  2. or use docker build and run

    sudo docker build -t omoponfhir .
    sudo docker run --name omoponfhir -p 8080:8080 -d omoponfhir:latest

NOTE: The OMOPonFHIR server is set to READ-ONLY. If you want to write to OMOPonFHIR, web.xml in WEB-INFO must have readOnly set to False.

Environment Variables

Environment variables are required to be set in order for OMOPonFHIR server to run correctly. The follows are environment variables. If Docker is used, these can be specified in the Dockerfile. If rancher is used for the docker image, the rancher can set the environment variable. If running from Java application server, please refer to the application server setting to add the environment variables.

Application URLs

Additional Information

Status: Details available in http://omoponfhir.org/

Contributors:

Please use Issues to report any problems. If you are willing to contribute, please fork this repository and do the pull requests.