fix NPE on replace-references with logical reference (#7164)

* fix replace-references NPE on logical reference

* addressed code review comments

Author: mrdnctrk

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_4_0/7163-fix-replace-references-NPE.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 7163
+title: "Previously, the `$hapi.fhir.replace-references` operation was failing with a NPE when a referencing resource 
+had a logical reference. This has now been fixed."

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ReplaceReferencesR4Test.java

@@ -17,6 +17,7 @@
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Patient;
@@ -450,6 +451,38 @@ void testReplaceReferences_SourceResourceNotReferencedByAnyResource_SucceedAndSh
 		assertThat(provenances).isEmpty();
 	}
 
+	@ParameterizedTest
+	@CsvSource (value = {
+		"false",
+		"true"
+	})
+	void testReplaceReferences_ReferencingResourceHasAnAdditionalLogicalReference_Succeeds(boolean theIsAsync) {
+
+		IIdType sourcePatientId = myPatientDao.create(new Patient(), mySrd).getId().toUnqualifiedVersionless();
+		IIdType targetPatientId = myPatientDao.create(new Patient(), mySrd).getId().toUnqualifiedVersionless();
+
+		// Create an Observation resource that references the source patient
+		// and has an additional logical reference.
+		Observation observation = new Observation();
+		observation.setSubject(new Reference(sourcePatientId));
+		Reference logicalReference = new Reference();
+		logicalReference.setIdentifier(new Identifier().setSystem("performerSys").setValue("drWho"));
+		observation.addPerformer(logicalReference);
+
+		IIdType obsId = myObservationDao.create(observation, mySrd).getId().toUnqualifiedVersionless();
+
+		executeReplaceReferences(sourcePatientId, targetPatientId, theIsAsync);
+
+		Observation obsAfter = myObservationDao.read(obsId, mySrd);
+		assertThat(obsAfter.getSubject().getReference()).isEqualTo(targetPatientId.toString());
+		// The logical reference should not have been replaced
+		assertThat(obsAfter.getPerformer()).hasSize(1);
+		assertThat(obsAfter.getPerformerFirstRep().getIdentifier().getSystem()).isEqualTo("performerSys");
+		assertThat(obsAfter.getPerformerFirstRep().getIdentifier().getValue()).isEqualTo("drWho");
+
+		myTestHelper.assertReplaceReferencesProvenance(sourcePatientId.withVersion("1"), targetPatientId.withVersion("1"), 1, Set.of(obsId.withVersion("2").toString()), null);
+	}
+
 	@Override
 	protected boolean verboseClientLogging() {
 		return true;

hapi-fhir-storage/src/main/java/ca/uhn/fhir/replacereferences/ReplaceReferencesPatchBundleSvc.java

@@ -28,6 +28,7 @@
 import ca.uhn.fhir.util.BundleBuilder;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 import jakarta.annotation.Nonnull;
+import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
@@ -111,11 +112,14 @@ private Bundle buildPatchBundle(
 	}
 
 	private static boolean matches(ResourceReferenceInfo refInfo, IIdType theSourceId) {
-		return refInfo.getResourceReference()
-				.getReferenceElement()
-				.toUnqualified()
-				.getValueAsString()
-				.equals(theSourceId.getValueAsString());
+
+		IBaseReference iBaseRef = refInfo.getResourceReference();
+		if (iBaseRef == null || (iBaseRef instanceof Reference ref && !ref.hasReferenceElement())) {
+			// the reference doesn't have a reference element, it is probably just a logical reference (using an
+			// identifier). so this is not a match.
+			return false;
+		}
+		return iBaseRef.getReferenceElement().toUnqualified().getValueAsString().equals(theSourceId.getValueAsString());
 	}
 
 	private String getFhirPathForPatch(IBaseResource theReferencingResource, ResourceReferenceInfo theRefInfo) {