Connect to FHIR Data in CloverDX (formerly CloverETL)

The CData JDBC Driver for FHIR enables you to use the data transformation components in CloverDX (formerly CloverETL) to work with FHIR as sources. In this article, you will use the JDBC Driver for FHIR to set up a simple transfer into a flat file. The CData JDBC Driver for FHIR enables you to use the data transformation components in CloverDX (formerly CloverETL) to work with FHIR as sources. In this article, you will use the JDBC Driver for FHIR to set up a simple transfer into a flat file.

Connect to FHIR as a JDBC Data Source

1. Create the connection to FHIR data. In a new CloverDX graph, right-click the Connections node in the Outline pane and click Connections -> Create Connection. The Database Connection wizard is displayed.
2. Click the plus icon to load a driver from a JAR. Browse to the lib subfolder of the installation directory and select the cdata.jdbc.fhir.jar file.
3. Enter the JDBC URL.

   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 JDBC URL is below:

   jdbc:fhir:URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None;

Query FHIR Data with the DBInputTable Component

1. Drag a DBInputTable from the Readers selection of the Palette onto the job flow and double-click it to open the configuration editor.
2. In the DB connection property, select the FHIR JDBC data source from the drop-down menu.
3. Enter the SQL query. For example: SELECT Id, [name-use] FROM Patient WHERE [address-city] = 'New York'

Write the Output of the Query to a UniversalDataWriter

1. Drag a UniversalDataWriter from the Writers selection onto the jobflow.
2. Double-click the UniversalDataWriter to open the configuration editor and add a file URL.
3. Right-click the DBInputTable and then click Extract Metadata.
4. Connect the output port of the DBInputTable to the UniversalDataWriter.
5. In the resulting Select Metadata menu for the UniversalDataWriter, choose the Patient table. (You can also open this menu by right-clicking the input port for the UniversalDataWriter.)
6. Click Run to write to the file.