Connect to FHIR Data in the Denodo Platform

Denodo Platform is a data virtualization product providing a single point of contact for enterprise database data. When paired with the CData JDBC Driver for FHIR, Denodo users can work with live FHIR data alongside other enterprise data sources. This article walks through creating a virtual data source for FHIR in the Denodo Virtual DataPort Administrator.

With built-in optimized data processing, the CData JDBC Driver offers unmatched performance for interacting with live FHIR data. When you issue complex SQL queries to FHIR, the driver pushes supported SQL operations, like filters and aggregations, directly to FHIR and utilizes the embedded SQL engine to process unsupported operations client-side (often SQL functions and JOIN operations). Its built-in dynamic metadata querying allows you to work with and analyze FHIR data using native data types.

Create the FHIR Virtual Port

To connect to live FHIR data from Denodo, you need to copy the JDBC Driver JAR file to the external library directory for Denodo and create a new JDBC Data Source from the Virtual DataPort Administrator tool.

1. Download the CData JDBC Driver for FHIR installer, unzip the package, and run the JAR file to install the driver.
2. Copy the JAR File (and license file if it exists) from the installation location (typically C:\Program Files\CData\CData JDBC Driver for FHIR\lib\) to the Denodo external library directory (C:\Denodo\Denodo Platform\lib-external\jdbc-drivers\cdata-fhir-19).
3. Open the Denodo Virtual DataPort Administrator tool and navigate to the Server Explorer tab.
4. Right-click "admin" and select New -> Data source -> JDBC.
5. Configure the JDBC Connection:
   • Name: your choice, e.g.: fhir
   • Database adapter: Generic
   • Driver class path: C:\Denodo\Denodo Platform\lib-external\jdbc-drivers\cdata-fhir-19
   • Driver class: cdata.jdbc.fhir.FHIRDriver

   • Database URI: Set this to a JDBC URL using the necessary connection properties. For example,

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

     Information on creating the Database URI follows:

     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.

     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.

6. Click the "Test connection" button to confirm the configuration and click Save.

View FHIR Data in the VirtualPort Administrator Tool

After creating the data source, you can create a base view of FHIR data for use in the Denodo Platform.

1. Click the "Create base view" button in the newly created VirtualPort (admin.FHIR).
2. Expand the object tree and select the objects (tables) you wish to import.
3. Click the "Create selected" button to create views of the FHIR data.
   Optional: Click "Create associations from foreign keys" to define relationships between the objects.
4. With the view(s) created, navigate to a table (cdata_fhir_patient) in the Server Explorer and double-click the selected table.
5. In the new tab, click "Execution panel" to open a query panel.
6. Customize the query in the "Execute" tab or use the default:

   SELECT * FROM cdata_fhir_patient CONTEXT ('i18n'='us_est', 'cache_wait_for_load'='true')
   

7. Click Execute to view the data.

With the base view created, you can now work with live FHIR data like you would any other data source in Denodo Platform, for example, querying FHIR in the Denodo Data Catalog.

Download a free, 30-day trial of the CData JDBC Driver for FHIR and start working with your live FHIR data in Denodo Platform. Reach out to our Support Team if you have any questions.