Ignore contained resources in IPA generation reference check so they are not removed (hapifhir#6754)

* Ignore contained resources in IPA generation reference check so they are not removed

* Fix coding display to exactly match LOINC, otherwise validator complains

* Add test case to verify contained resource reference being retained

* Credit for hapifhir#6754

---------

Co-authored-by: James Agnew <[email protected]>

Author: xmhorsehead

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_2_0/6754-preserve-contained-resources-in-ips.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 6754
+title: "The IPS generator will no longer strip references to contained resources when
+  assembling data to create an IPS document. Thanks to Xun Ma for the contribution!"

hapi-fhir-jpaserver-ips/src/main/java/ca/uhn/fhir/jpa/ips/generator/IpsGeneratorSvcImpl.java

@@ -234,7 +234,7 @@ private void updateReferencesInInclusionsForSection(
 						.getResourceReference()
 						.getReferenceElement()
 						.getValue();
-				if (isNotBlank(existingReference)) {
+				if (isNotBlank(existingReference) && !existingReference.startsWith("#")) {
 					existingReference = new IdType(existingReference)
 							.toUnqualifiedVersionless()
 							.getValue();
@@ -480,7 +480,7 @@ private CompositionBuilder createComposition(
 
 		compositionBuilder.setStatus(Composition.CompositionStatus.FINAL.toCode());
 		compositionBuilder.setSubject(thePatient.getIdElement().toUnqualifiedVersionless());
-		compositionBuilder.addTypeCoding("http://loinc.org", "60591-5", "Patient Summary Document");
+		compositionBuilder.addTypeCoding("http://loinc.org", "60591-5", "Patient summary Document");
 		compositionBuilder.setDate(InstantType.now());
 		compositionBuilder.setTitle(theStrategy.createTitle(context));
 		compositionBuilder.setConfidentiality(theStrategy.createConfidentiality(context));

hapi-fhir-jpaserver-ips/src/test/java/ca/uhn/fhir/jpa/ips/generator/IpsGeneratorSvcImplTest.java

@@ -617,6 +617,46 @@ public void testReferencesUpdatedInSecondaryInclusions() {
 		assertEquals(1, illnessHistorySection.getEntry().size());
 	}
 
+	/**
+	 * While resources not in the Bundle have their references removed, contained resources should retain their references. They are still included information despite not technically being in the Bundle.
+	 */
+	@Test
+	public void testContainedResourceReferenceNotRemoved() {
+		// Setup Patient
+		initializeGenerationStrategy(
+			List.of(t->Section.newBuilder(t).withNoInfoGenerator(null).build())
+		);
+		registerPatientDaoWithRead();
+
+		// Setup MedicationStatement with contained Medication
+		Medication medication = createSecondaryMedication(MEDICATION_ID);
+		MedicationStatement medicationStatement = createPrimaryMedicationStatement(MEDICATION_ID, MEDICATION_STATEMENT_ID);
+		medicationStatement.addContained(medication);
+		medicationStatement.getMedicationReference().setReference("#" + MEDICATION_ID);
+		IFhirResourceDao<MedicationStatement> medicationStatementDao = registerResourceDaoWithNoData(MedicationStatement.class);
+		when(medicationStatementDao.search(any(), any())).thenReturn(new SimpleBundleProvider(Lists.newArrayList(medicationStatement)));
+
+		Patient patient = new Patient();
+		patient.setId(PATIENT_ID);
+		ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(patient, BundleEntrySearchModeEnum.INCLUDE);
+
+		registerRemainingResourceDaos();
+
+		// Test
+		Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID), null);
+
+		MedicationStatement result = (MedicationStatement) outcome
+			.getEntry()
+			.stream()
+			.filter(t -> medicationStatement.fhirType().equals(t.getResource().getResourceType().name()))
+			.map(Bundle.BundleEntryComponent::getResource)
+			.findFirst().orElseThrow();
+		
+		assert(result.hasMedicationReference());
+		assert(result.getMedicationReference().hasReference());
+		assertEquals(result.getMedicationReference().getReference(), "#" + MEDICATION_ID);
+	}
+
 	@Test
 	public void testPatientIsReturnedAsAnIncludeResource() {
 		// Setup Patient

pom.xml

@@ -979,6 +979,11 @@
 			<name>Dylan Krause</name>
 			<organization>Corbalt</organization>
 		</developer>
+		<developer>
+			<id>xmhorsehead</id>
+			<name>Xun Ma</name>
+			<organization>CSIRO</organization>
+		</developer>
 	</developers>
 
 	<licenses>