Connect to FHIR Data in RapidMiner

This article shows how you can easily integrate the CData JDBC driver for FHIR into your processes in RapidMiner. This article uses the CData JDBC Driver for FHIR to transfer FHIR data to a process in RapidMiner.

Connect to FHIR in RapidMiner as a JDBC Data Source

You can follow the procedure below to establish a JDBC connection to FHIR:

1. Add a new database driver for FHIR: Click Connections -> Manage Database Drivers.
2. In the resulting wizard, click the Add button and enter a name for the connection.
3. Enter the prefix for the JDBC URL: jdbc:fhir:
4. Enter the path to the cdata.jdbc.fhir.jar file, located in the lib subfolder of the installation directory.
5. Enter the driver class: cdata.jdbc.fhir.FHIRDriver
6. Create a new FHIR connection: Click Connections -> Manage Database Connections.
7. Enter a name for your connection.
8. For Database System, select the FHIR driver you configured previously.
9. Enter your connection string in the Host box.

   Set URL to the Service Base URL of the FHIR server. This is the address where the resources are defined in the FHIR server you would like to connect to. Set ConnectionType to a supported connection type. Set ContentType to the format of your documents. Set AuthScheme based on the authentication requirements for your FHIR server.

   Generic, Azure-based, AWS-based, and Google-based FHIR server implementations are supported.

   Sample Service Base URLs

   • Generic: http://my_fhir_server/r4b/
   • Azure: https://MY_AZURE_FHIR.azurehealthcareapis.com/
   • AWS: https://healthlake.REGION.amazonaws.com/datastore/DATASTORE_ID/r4/
   • Google: https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID/fhir/

   Generic FHIR Instances

   The product supports connections to custom instances of FHIR. Authentication to custom FHIR servers is handled via OAuth (read more about OAuth in the Help documentation. Before you can connect to custom FHIR instances, you must set ConnectionType to Generic.

   Built-in Connection String Designer

   For assistance in constructing the JDBC URL, use the connection string designer built into the FHIR JDBC Driver. Either double-click the JAR file or execute the jar file from the command-line.

   java -jar cdata.jdbc.fhir.jar

   Fill in the connection properties and copy the connection string to the clipboard.

   A typical connection string is below:

   URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None;
10. Enter your username and password if necessary.

You can now use your FHIR connection with the various RapidMiner operators in your process. To retrieve FHIR data, drag the Retrieve operator from the Operators view. With the Retrieve operator selected, you can then define which table to retrieve in the Parameters view by clicking the folder icon next to the "repository entry." In the resulting Repository Browser, you can expand your connection node to select the desired example set.

Finally, wire the output to the Retrieve process to a result, and run the process to see the FHIR data.