Build FHIR-Connected ETL Processes in Google Data Fusion

Google Data Fusion allows users to perform self-service data integration to consolidate disparate data. Uploading the CData JDBC Driver for FHIR enables users to access live FHIR data from within their Google Data Fusion pipelines. While the CData JDBC Driver enables piping FHIR data to any data source natively supported in Google Data Fusion, this article explains how to pipe data from FHIR to Google BigQuery,

Upload the CData JDBC Driver for FHIR to Google Data Fusion

Upload the CData JDBC Driver for FHIR to your Google Data Fusion instance to work with live FHIR data. Due to the naming restrictions for JDBC drivers in Google Data Fusion, create a copy or rename the JAR file to match the following format driver-version.jar. For example: cdatafhir-2020.jar

1. Open your Google Data Fusion instance
2. Click the to add an entity and upload a driver 👁 Image
   
3. On the "Upload driver" tab, drag or browse to the renamed JAR file.
4. On the "Driver configuration" tab:
   • Name: Create a name for the driver (cdata.jdbc.fhir) and make note of the name
   • Class name: Set the JDBC class name: (cdata.jdbc.fhir.FHIRDriver)
   👁 Configuring the driver (Salesforce is shown.)
   
5. Click "Finish"

Connect to FHIR Data in Google Data Fusion

With the JDBC Driver uploaded, you are ready to work with live FHIR data in Google Data Fusion Pipelines.

1. Navigate to the Pipeline Studio to create a new Pipeline
2. From the "Source" options, click "Database" to add a source for the JDBC Driver 👁 Adding a database source
   
3. Click "Properties" on the Database source to edit the properties

   NOTE: To use the JDBC Driver in Google Data Fusion, you will need a license (full or trial) and a Runtime Key (RTK). For more information on obtaining this license (or a trial), contact our sales team.

   • Set the Label
   • Set Reference Name to a value for any future references (i.e.: cdata-fhir)
   • Set Plugin Type to "jdbc"
   • Set Connection String to the JDBC URL for FHIR. For example:
     
     jdbc:fhir:RTK=5246...;URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None;

     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.

     👁 Using the built-in connection string designer to generate a JDBC URL (Salesforce is shown.)
     
   • Set Import Query to a SQL query that will extract the data you want from FHIR, i.e.:
     SELECT * FROM Patient
   👁 Configuring the database source
   
4. From the "Sink" tab, click to add a destination sink (we use Google BigQuery in this example)
5. Click "Properties" on the BigQuery sink to edit the properties
   • Set the Label
   • Set Reference Name to a value like fhir-bigquery
   • Set Project ID to a specific Google BigQuery Project ID (or leave as the default, "auto-detect")
   • Set Dataset to a specific Google BigQuery dataset
   • Set Table to the name of the table you wish to insert FHIR data into
   👁 Configuring the BigQuery sink
   

With the Source and Sink configured, you are ready to pipe FHIR data into Google BigQuery. Save and deploy the pipeline. When you run the pipeline, Google Data Fusion will request live data from FHIR and import it into Google BigQuery. 👁 Image

While this is a simple pipeline, you can create more complex FHIR pipelines with transforms, analytics, conditions, and more. Download a free, 30-day trial of the CData JDBC Driver for FHIR and start working with your live FHIR data in Google Data Fusion today.