Terser cloneInto doesn't work for contained resources (#4467)

* Add fix

* Add docs

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

@@ -197,7 +197,8 @@ public class FhirTerser {
 
 		for (BaseRuntimeChildDefinition nextChild : children)
 			for (IBase nextValue : nextChild.getAccessor().getValues(theSource)) {
-				String elementName = nextChild.getChildNameByDatatype(nextValue.getClass());
+				Class<? extends IBase> valueType = nextValue.getClass();
+				String elementName = nextChild.getChildNameByDatatype(valueType);
 				BaseRuntimeChildDefinition targetChild = targetDef.getChildByName(elementName);
 				if (targetChild == null) {
 					if (theIgnoreMissingFields) {
@@ -206,10 +207,24 @@ public class FhirTerser {
 					throw new DataFormatException(Msg.code(1789) + "Type " + theTarget.getClass().getName() + " does not have a child with name " + elementName);
 				}
 
-				BaseRuntimeElementDefinition<?> element = myContext.getElementDefinition(nextValue.getClass());
+				BaseRuntimeElementDefinition<?> element = myContext.getElementDefinition(valueType);
 				Object instanceConstructorArg = targetChild.getInstanceConstructorArguments();
 				IBase target;
-				if (instanceConstructorArg != null) {
+				if (element == null && BaseContainedDt.class.isAssignableFrom(valueType)) {
+					/*
+					 * This is a hack for DSTU2 - The way we did contained resources in
+					 * the DSTU2 model was weird, since the element isn't actually a FHIR type.
+					 * This is fixed in DSTU3+ so this hack only applies there.
+					 */
+					BaseContainedDt containedTarget = (BaseContainedDt) ReflectionUtil.newInstance(valueType);
+					BaseContainedDt containedSource = (BaseContainedDt) nextValue;
+					for (IResource next : containedSource.getContainedResources()) {
+						List containedResources = containedTarget.getContainedResources();
+						containedResources.add(next);
+					}
+					targetChild.getMutator().addValue(theTarget, containedTarget);
+					continue;
+				} else if (instanceConstructorArg != null) {
 					target = element.newInstance(instanceConstructorArg);
 				} else {
 					target = element.newInstance();

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4467-fix-clone-into-for-contained.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4467
+title: "The FhirTerser#clone method failed to clone resources when contained resources were
+   present in the source resource. This has been fixed."

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/util/FhirTerserDstu2Test.java

@@ -19,10 +19,13 @@ import ca.uhn.fhir.parser.DataFormatException;
 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.IPrimitiveType;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Test;
 import org.mockito.ArgumentCaptor;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.lang.reflect.ParameterizedType;
 import java.lang.reflect.Type;
@@ -30,6 +33,7 @@ import java.util.List;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.containsString;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNull;
@@ -41,7 +45,8 @@ import static org.mockito.Mockito.when;
 
 public class FhirTerserDstu2Test {
 
-	private static FhirContext ourCtx = FhirContext.forDstu2();
+	private static FhirContext ourCtx = FhirContext.forDstu2Cached();
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirTerserDstu2Test.class);
 
 	@Test
 	public void testCloneIntoComposite() {
@@ -54,6 +59,27 @@ public class FhirTerserDstu2Test {
 		assertEquals("CODE", target.getCode());
 	}
 
+	@Test
+	public void testCloneResource() {
+		Organization org = new Organization();
+		org.setName("Contained Org Name");
+		Patient patient = new Patient();
+		patient.setActive(true);
+		patient.getManagingOrganization().setResource(org);
+
+		// Re-encode
+		String string = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info("Encoded: {}", string);
+		patient = ourCtx.newJsonParser().parseResource(Patient.class, string);
+
+		Patient clonedPatient = ourCtx.newTerser().clone(patient);
+		assertEquals(true, clonedPatient.getActive().booleanValue());
+		string = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(clonedPatient);
+		ourLog.info("Encoded: {}", string);
+		assertThat(string, containsString("\"contained\""));
+	}
+
+
 	@Test
 	public void testCloneIntoCompositeMismatchedFields() {
 		QuantityDt source = new QuantityDt();