The NACHC fhir-to-omop Standalone Application

The NACHC fhir-to-omop Standalone Application is a Java application that can be run as an application thereby avoiding most of the dependencies listed in the Installing and First Steps page.

Everything you need to:

- Build Your OMOP CDM Database
- Get the IDs of the Patients on Your FHIR Server
- Download Patients from Your FHIR Server
- Upload Your FHIR Patients into Your OMOP CDM Database

How to Get NACHC fhir-to-omop Standalone Application

The NACHC fhir-to-omop is packaged as a zip file with each release. The latest version can be downloaded by going to the releases page and clicking on the link for the fhir-to-omop zip file link for the latest release. (you will probably need to expand the drop-down for the Assets)

Contents of the zip file

After you've downloaded the zip, unzip the file. The zip file contains the following:

lib: A folder containing all of the dependencies for the application
app.properties: The app.properties file that has all of the configuration information for the application. The version of the file provided here includes everything required to create a default instnace except for the connection information for the FHIR server will use to get patients.
fhir-to-omop.bat: A bat file that calls the Java code. This is the bat file you will call to access the application.
fhir-to-omop.jar The jar file that contains the fhir-to-omop Java classes.

Using the Application

The application is called by calling the bat file using the parameter for the desired action. The download ids call allows for a second parameter that will limit the number of patient IDs downloaded by the application. Each call has a long version of the parameter and a short version. All of the function of the application can be seen by simply calling the bat file without any parameters.