add exclusions to terser reference method (#5343)

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java

@@ -287,9 +287,33 @@ public class FhirTerser {
 		return retVal;
 	}
 
+	/**
+	 * Extracts all outbound references from a resource
+	 *
+	 * @param theResource the resource to be analyzed
+	 * @return a list of references to other resources
+	 */
 	public List<ResourceReferenceInfo> getAllResourceReferences(final IBaseResource theResource) {
+		return getAllResourceReferencesExcluding(theResource, Lists.newArrayList());
+	}
+
+	/**
+	 * Extracts all outbound references from a resource, excluding any that are located on black-listed parts of the
+	 * resource
+	 *
+	 * @param theResource       the resource to be analyzed
+	 * @param thePathsToExclude a list of dot-delimited paths not to include in the result
+	 * @return a list of references to other resources
+	 */
+	public List<ResourceReferenceInfo> getAllResourceReferencesExcluding(
+			final IBaseResource theResource, List<String> thePathsToExclude) {
 		final ArrayList<ResourceReferenceInfo> retVal = new ArrayList<>();
 		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
+		List<List<String>> tokenizedPathsToExclude = thePathsToExclude.stream()
+				.map(path -> StringUtils.split(path, "."))
+				.map(Lists::newArrayList)
+				.collect(Collectors.toList());
+
 		visit(newMap(), theResource, theResource, null, null, def, new IModelVisitor() {
 			@Override
 			public void acceptElement(
@@ -301,6 +325,10 @@ public class FhirTerser {
 				if (theElement == null || theElement.isEmpty()) {
 					return;
 				}
+
+				if (thePathToElement != null && pathShouldBeExcluded(tokenizedPathsToExclude, thePathToElement)) {
+					return;
+				}
 				if (IBaseReference.class.isAssignableFrom(theElement.getClass())) {
 					retVal.add(new ResourceReferenceInfo(
 							myContext, theOuterResource, thePathToElement, (IBaseReference) theElement));
@@ -310,6 +338,19 @@ public class FhirTerser {
 		return retVal;
 	}
 
+	private boolean pathShouldBeExcluded(List<List<String>> theTokenizedPathsToExclude, List<String> thePathToElement) {
+		return theTokenizedPathsToExclude.stream().anyMatch(p -> {
+			// Check whether the path to the element starts with the path to be excluded
+			if (p.size() > thePathToElement.size()) {
+				return false;
+			}
+
+			List<String> prefix = thePathToElement.subList(0, p.size());
+
+			return Objects.equals(p, prefix);
+		});
+	}
+
 	private BaseRuntimeChildDefinition getDefinition(
 			BaseRuntimeElementCompositeDefinition<?> theCurrentDef, List<String> theSubList) {
 		BaseRuntimeChildDefinition nextDef = theCurrentDef.getChildByNameOrThrowDataFormatException(theSubList.get(0));

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/FhirTerserR4Test.java

@@ -12,6 +12,7 @@ import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseExtension;
 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.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Bundle;
@@ -32,6 +33,7 @@ import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Patient.LinkType;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.PrimitiveType;
+import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.ResourceType;
@@ -511,6 +513,54 @@ public class FhirTerserR4Test {
 
 	}
 
+	@Test
+	public void testGetAllResourceReferences() {
+		// setup
+		Provenance p = new Provenance();
+		p.addTarget(new Reference("Observation/1"));
+		p.addTarget(new Reference("Observation/2"));
+		p.setLocation(new Reference("Location/3"));
+		p.getAgentFirstRep().setWho(new Reference("Practitioner/4"));
+		p.getAgentFirstRep().setOnBehalfOf(new Reference("Organization/5"));
+		p.getEntityFirstRep().setWhat(new Reference("DocumentReference/6"));
+
+		// execute
+		FhirTerser t = myCtx.newTerser();
+		List<ResourceReferenceInfo> references = t.getAllResourceReferences(p);
+
+		// validate
+		assertEquals(6, references.size());
+		assertThat(toResourceIds(references), containsInAnyOrder("Observation/1", "Observation/2", "Location/3", "Practitioner/4", "Organization/5", "DocumentReference/6"));
+	}
+
+	@Test
+	public void testGetAllResourceReferencesExcluding() {
+		// setup
+		Provenance p = new Provenance();
+		p.addTarget(new Reference("Observation/1"));
+		p.addTarget(new Reference("Observation/2"));
+		p.setLocation(new Reference("Location/3"));
+		p.getAgentFirstRep().setWho(new Reference("Practitioner/4"));
+		p.getAgentFirstRep().setOnBehalfOf(new Reference("Organization/5"));
+		p.getEntityFirstRep().setWhat(new Reference("DocumentReference/6"));
+
+		// execute
+		FhirTerser t = myCtx.newTerser();
+		List<ResourceReferenceInfo> references = t.getAllResourceReferencesExcluding(p, List.of("target"));
+
+		// validate
+		assertEquals(4, references.size());
+		assertThat(toResourceIds(references), containsInAnyOrder("Location/3", "Practitioner/4", "Organization/5", "DocumentReference/6"));
+	}
+
+	private List<String> toResourceIds(List<ResourceReferenceInfo> references) {
+		return references.stream()
+			 .map(ResourceReferenceInfo::getResourceReference)
+			 .map(IBaseReference::getReferenceElement)
+			 .map(IIdType::getValue)
+			 .collect(Collectors.toList());
+	}
+
 	@Test
 	public void testGetResourceReferenceInExtension() {
 		Patient p = new Patient();