Connect to FHIR Data in as an External Source in Dremio

The CData JDBC Driver for FHIR implements JDBC Standards and allows various applications, including Dremio, to work with live FHIR data. Dremio is a data lakehouse platform designed to empower self-service, interactive analytics on the data lake. With the CData JDBC Driver, you can include live FHIR data as a part of your enterprise data lake. This article describes how to connect to FHIR data from Dremio as an External Source.

The CData JDBC Driver enables high-speed access to live FHIR data in Dremio. Once you install the driver, authenticate with FHIR and gain immediate access to FHIR data within your data lake. By surfacing FHIR data using native data types and handling complex filters, aggregations, & other operations automatically, the CData JDBC Driver grants seamless access to FHIR data.

Build the ARP Connector

To use the CData JDBC Driver in Dremio, you need to build an Advanced Relation Pushdown (ARP) Connector. You can view the source code for the Connector on GitHub or download the ZIP file (GitHub.com) directly. Once you copy or extract the files, run the following command from the root directory of the connector (the directory containing the pom.xml file) to build the connector.

mvn clean install

Once the JAR file for the connector is built (in the target directory), you are ready to copy the ARP connector and JDBC Driver to your Dremio instance.

Installing the Connector and JDBC Driver

Install the ARP Connector to %DREMIO_HOME%/jars/ and the JDBC Driver for FHIR to %DREMIO_HOME%/jars/3rdparty. You can use commands similar to the following:

ARP Connector

docker cp PATH\TO\dremio-fhir-plugin-20.0.0.jar dremio_image_name:/opt/dremio/jars/

JDBC Driver for FHIR

docker cp PATH\TO\cdata.jdbc.fhir.jar dremio_image_name:/opt/dremio/jars/3rdparty/

Connecting to FHIR

FHIR will now appear as an External Source option in Dremio. The ARP Connector built uses a JDBC URL to connect to FHIR data. The JDBC Driver has a built-in connection string designer that you can use (see below).

Built-in Connection String Designer

For assistance in constructing the JDBC URL, use the connection string designer built into the FHIR JDBC Driver. 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.

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.

NOTE: To use the JDBC Driver in Dremio, 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.

Add the Runtime Key (RTK) to the JDBC URL. You will end up with a JDBC URL similar to the following:

jdbc:fhir:RTK=5246...;URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None;

Access FHIR as an External Source

To add FHIR as an External Source, click to add a new source and select FHIR. Copy the JDBC URL and paste it into the New FHIR Source wizard.

Save the connection and you are ready to query live FHIR data in Dremio, easily incorporating FHIR data into your data lake.

More Information & Free Trial

Using the CData JDBC Driver for FHIR in Dremio, you can incorporate live FHIR data into your data lake. Check out our CData JDBC Driver for FHIR page for more information about connecting to FHIR. Download a free, 30 day trial of the CData JDBC Driver for FHIR and get started today.