Add FHIR Data to Informatica Enterprise Data Catalog

Informatica provides a powerful, elegant means of transporting and transforming your data. By utilizing the CData JDBC Driver for FHIR, you are gaining access to a driver based on industry-proven standards that integrates seamlessly with Informatica's Enterprise Data Catalog. This tutorial shows how to classify and organize FHIR data across any environment.

Load the JDBC Driver

To load the JDBC Driver:

1. Install the JDBC Driver on the host running Informatica. For this article, it is assumed that the driver was installed into cdata.jdbc.fhir.FHIRDriver.
$ java -jar setup.jar
2. Navigate to the JDBC install directory and create a zip file called genericJDBC.zip containing the driver and its license file.
$ cd ~/cdata-jdbc-driver-for-fhir/lib $ zip genericJDBC.zip cdata.jdbc.fhir.jar cdata.jdbc.fhir.lic
3. Move the genericJDBC.zip file into the Catalog Service directory within Informatica. For this article, it is assumed that Informatica is installed into /opt/informatica. Working in this folder will probably require root permissions, so make sure to su or sudo to root before continuing.
# mv genericJDBC.zip /opt/informatica/services/CatalogService/ScannerBinaries
4. Edit the custom deployment configuration to unpack the zip file.
# cd /opt/informatica/services/CatalogService/ScannerBinaries/CustomDeployer/ # nano scannerDeployer.xml

After unpacking the existing ExecutionContextProperty nodes, add a new ExecutionContextProperty node with this content.

<ExecutionContextProperty isLocationProperty="true" dependencyToUnpack="genericJDBC.zip"> <PropertyName>JDBCScanner_DriverLocation</PropertyName> <PropertyValue>scanner_miti/genericJDBC/Drivers</PropertyValue> </ExecutionContextProperty>
5. Refresh the Catalog Service from the Admin console.

Configure the JDBC Resource

To configure the JDBC resource:

1. Open the Catalog administrator and add a new JDBC resource with the following properties:
• Driver Class: cdata.jdbc.fhir.FHIRDriver
• URL: jdbc.fhir: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.

When you configure the JDBC URL, you may also want to set the Max Rows connection property. This will limit the number of rows returned, which is especially helpful for improving performance when designing reports and visualizations.

Typical additional connection string properties follow:

JDBC;MSTR_JDBC_JAR_FOLDER=PATH\TO\JAR\;DRIVER=cdata.jdbc.fhir.FHIRDriver;URL={jdbc:fhir:URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None;};
2. Username: user
3. Password: password

Note that the Username and Password properties are required, even if the driver you are using does not require them. In those cases, you can enter a placeholder value instead.

4. Configure the metadata options to perform at least one source metadata scan. This scan uses the driver to determine what tables, views, and stored procedures are available through the service.
• Source Metadata: Enable this option.
• Catalog: Set this to the appropriate catalog for multi-catalog data sources. Otherwise, set this to CData.
• Schema: Set this to the appropriate schema for multi-schema data sources. Otherwise, set this to the name of the service (for example, Couchbase).
• Case-sensitivity: Generally this option should be disabled. Enable it only for data sources which are case-sensitive.
• Import stored procedures: Enable this if you want to import stored procedure definitions in addition to tables and views.

Other metadata scanners may be enabled as desired.

5. Complete the driver configuration, optionally configuring custom attributes and a scanner schedule.
6. Perform the metadata scan by navigating to the Monitoring tab and clicking Run. Depending upon the data source, this may takes a few minutes.

When the scan is complete, a summary of all of the metadata objects is displayed along with the status of the Metadata Load job. If any errors occur, you can open the Log Location link for the job to see the errors reported by Informatica or the driver.

Validate the Discovered Metadata

Open the Catalog Service browser to view the metadata extracted from the data source. Depending upon the options you selected when configuring the metadata scanner, you may see any combination of tables, views, and stored procedures for the resource you defined.