Object-Relational Mapping (ORM) with FHIR Data Entities in Java

You can use Hibernate to map object-oriented domain models to a traditional relational database. The tutorial below shows how to use the CData JDBC Driver for FHIR to generate an ORM of your FHIR repository with Hibernate.

Though Eclipse is the IDE of choice for this article, the CData JDBC Driver for FHIR works in any product that supports the Java Runtime Environment. In the Knowledge Base you will find tutorials to connect to FHIR data from IntelliJ IDEA and NetBeans.

Install Hibernate

Follow the steps below to install the Hibernate plug-in in Eclipse.

1. In Eclipse, navigate to Help -> Install New Software.
2. Enter "http://download.jboss.org/jbosstools/neon/stable/updates/" in the Work With box.
3. Enter "Hibernate" into the filter box.
4. Select Hibernate Tools.

Start A New Project

Follow the steps below to add the driver JARs in a new project.

1. Create a new project. Select Java Project as your project type and click Next. Enter a project name and click Finish.
2. Right-click the project and click Properties. Click Java Build Path and then open the Libraries tab.
3. Click Add External JARs to add the cdata.jdbc.fhir.jar library, located in the lib subfolder of the installation directory.

Add a Hibernate Configuration File

Follow the steps below to configure connection properties to FHIR data.

1. Right-click on the new project and select New -> Hibernate -> Hibernate Configuration File (cfg.xml).
2. Select src as the parent folder and click Next.

3. Input the following values:

   • Hibernate version:: 5.2
   • Database dialect: Derby
   • Driver class: cdata.jdbc.fhir.FHIRDriver

   • Connection URL: A JDBC URL, starting with jdbc:fhir: and followed by a semicolon-separated list of connection properties.

     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.)
     

     A typical JDBC URL is below:

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

Connect Hibernate to FHIR Data

Follow the steps below to select the configuration you created in the previous step.

1. Switch to the Hibernate Configurations perspective: Window -> Open Perspective -> Hibernate.
2. Right-click on the Hibernate Configurations panel and click Add Configuration.
3. Set the Hibernate version to 5.2.
4. Click the Browse button and select the project.
5. For the Configuration file field, click Setup -> Use Existing and select the location of the hibernate.cfg.xml file (inside src folder in this demo).
6. In the Classpath tab, if there is nothing under User Entries, click Add External JARS and add the driver jar once more. Click OK once the configuration is done.
7. Expand the Database node of the newly created Hibernate configurations file.

Reverse Engineer FHIR Data

Follow the steps below to generate the reveng.xml configuration file. You will specify the tables you want to access as objects.

1. Switch back to the Package Explorer.
2. Right-click your project, select New -> Hibernate -> Hibernate Reverse Engineering File (reveng.xml). Click Next.
3. Select src as the parent folder and click Next.
4. In the Console configuration drop-down menu, select the Hibernate configuration file you created above and click Refresh.
5. Expand the node and choose the tables you want to reverse engineer. Click Finish when you are done.

Configure Hibernate to Run

Follow the steps below to generate plain old Java objects (POJO) for the FHIR tables.

1. From the menu bar, click Run -> Hibernate Code Generation -> Hibernate Code Generation Configurations.
2. In the Console configuration drop-down menu, select the Hibernate configuration file you created in the previous section. Click Browse by Output directory and select src.
3. Enable the Reverse Engineer from JDBC Connection checkbox. Click the Setup button, click Use Existing, and select the location of the hibernate.reveng.xml file (inside src folder in this demo).
4. In the Exporters tab, check Domain code (.java) and Hibernate XML Mappings (hbm.xml).
5. Click Run.

One or more POJOs are created based on the reverse-engineering setting in the previous step.

Insert Mapping Tags

For each mapping you have generated, you will need to create a mapping tag in hibernate.cfg.xml to point Hibernate to your mapping resource. Open hibernate.cfg.xml and insert the mapping tags as so:

 
 
 cdata.fhir.FHIRDriver
 
 
 jdbc:fhir:URL=http://test.fhir.org/r4b/;ConnectionType=Generic;ContentType=JSON;AuthScheme=None;
 
 
 org.hibernate.dialect.SQLServerDialect
 
 
 
 

Execute SQL

Using the entity you created from the last step, you can now search FHIR data:

import java.util.*;
import org.hibernate.Session;
import org.hibernate.cfg.Configuration;
import org.hibernate.query.Query;

public class App {
 public static void main(final String[] args) {
 Session session = new
 Configuration().configure().buildSessionFactory().openSession();
 String SELECT = "FROM Patient P WHERE [address-city] = :[address-city]";
 Query q = session.createQuery(SELECT, Patient.class);
 q.setParameter("[address-city]","New York");
 List<Patient> resultList = (List<Patient>) q.list();

 for(Patient s: resultList){
 System.out.println(s.getId());
 System.out.println(s.get[name-use]());
 }
 }
}