Fix #369 - FhirTerser cloneInto method fails if target contains extension

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeChildExtension.java

@@ -46,6 +46,14 @@ public class RuntimeChildExtension extends RuntimeChildAny {
 	public Set<String> getValidChildNames() {
 		return Collections.singleton(getElementName());
 	}
+
+	@Override
+	public BaseRuntimeElementDefinition<?> getChildByName(String theName) {
+		if ("extension".equals(theName) || "modifierExtension".equals(theName)) {
+			return super.getChildByName("extensionExtension");
+		}
+		return super.getChildByName(theName);
+	}
 	
 //	@Override
 //	public BaseRuntimeElementDefinition<?> getChildElementDefinitionByDatatype(Class<? extends IBase> theDatatype) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeExtensionDtDefinition.java

@@ -43,6 +43,10 @@ public class RuntimeExtensionDtDefinition extends RuntimeCompositeDatatypeDefini
 		return myChildren;
 	}
 
+	public List<BaseRuntimeChildDefinition> getChildrenIncludingUrl() {
+		return super.getChildren();
+	}
+
 	@Override
 	public void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
 		super.sealAndInitialize(theContext, theClassToElementDefinitions);

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

@@ -48,6 +48,7 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
 import ca.uhn.fhir.context.RuntimeChildDirectResource;
+import ca.uhn.fhir.context.RuntimeExtensionDtDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.model.api.ExtensionDt;
@@ -88,16 +89,17 @@ public class FhirTerser {
 				addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
 			}
 		}
-		
+
-		if (theElement instanceof IBaseHasExtensions) {
+		// Commented out because FhirTerserDstu3Test#testGetResourceReferenceInExtension
-			for (IBaseExtension<?, ?> nextExt : ((IBaseHasExtensions)theElement).getExtension()) {
+//		if (theElement instanceof IBaseHasExtensions) {
-				if (nextExt == null) {
+//			for (IBaseExtension<?, ?> nextExt : ((IBaseHasExtensions)theElement).getExtension()) {
-					continue;
+//				if (nextExt == null) {
-				}
+//					continue;
-				theCallback.acceptElement(nextExt.getValue(), null, theChildDefinition, theDefinition);
+//				}
-				addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
+//				theCallback.acceptElement(nextExt.getValue(), null, theChildDefinition, theDefinition);
-			}
+//				addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
-		}
+//			}
+//		}
 		
 		if (theElement instanceof IBaseHasModifierExtensions) {
 			for (IBaseExtension<?, ?> nextExt : ((IBaseHasModifierExtensions)theElement).getModifierExtension()) {
@@ -137,18 +139,25 @@ public class FhirTerser {
 		BaseRuntimeElementCompositeDefinition<?> sourceDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theSource.getClass()); 
 		BaseRuntimeElementCompositeDefinition<?> targetDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theTarget.getClass());
 		
-		for (BaseRuntimeChildDefinition nextChild : sourceDef.getChildren()) {
+		List<BaseRuntimeChildDefinition> children = sourceDef.getChildren();
+		if (sourceDef instanceof RuntimeExtensionDtDefinition) {
+			children = ((RuntimeExtensionDtDefinition)sourceDef).getChildrenIncludingUrl();
+		}
+		
+		for (BaseRuntimeChildDefinition nextChild : children) {
 			for (IBase nextValue : nextChild.getAccessor().getValues(theSource)) {
-				BaseRuntimeChildDefinition targetChild = targetDef.getChildByName(nextChild.getElementName());
+				String elementName = nextChild.getChildNameByDatatype(nextValue.getClass());
+				BaseRuntimeChildDefinition targetChild = targetDef.getChildByName(elementName);
 				if (targetChild == null) {
 					if (theIgnoreMissingFields) {
 						continue;
 					} else {
-						throw new DataFormatException("Type " + theTarget.getClass().getName() + " does not have a child with name " + nextChild.getElementName());
+						throw new DataFormatException("Type " + theTarget.getClass().getName() + " does not have a child with name " + elementName);
 					}
 				}
 				
-				IBase target = targetChild.getChildByName(nextChild.getElementName()).newInstance();
+				BaseRuntimeElementDefinition<?> childDef = targetChild.getChildByName(elementName);
+				IBase target = childDef.newInstance();
 				targetChild.getMutator().addValue(theTarget, target);
 				cloneInto(nextValue, target, theIgnoreMissingFields);
 			}

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

@@ -28,6 +28,7 @@ import ca.uhn.fhir.model.dstu2.composite.MoneyDt;
 import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
 import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.primitive.MarkdownDt;
@@ -39,28 +40,114 @@ public class FhirTerserDstu2Test {
 	private static FhirContext ourCtx = FhirContext.forDstu2();
 
 	@Test
-	public void testGetResourceReferenceInExtension() {
+	public void testCloneIntoComposite() {
+		QuantityDt source = new QuantityDt();
+		source.setCode("CODE");
+		MoneyDt target = new MoneyDt();
+
+		ourCtx.newTerser().cloneInto(source, target, true);
+
+		assertEquals("CODE", target.getCode());
+	}
+   
+	@Test
+	public void testCloneIntoCompositeMismatchedFields() {
+		QuantityDt source = new QuantityDt();
+		source.setSystem("SYSTEM");
+		source.setUnit("UNIT");
+		IdentifierDt target = new IdentifierDt();
+
+		ourCtx.newTerser().cloneInto(source, target, true);
+
+		assertEquals("SYSTEM", target.getSystem());
+
+		try {
+			ourCtx.newTerser().cloneInto(source, target, false);
+			fail();
+		} catch (DataFormatException e) {
+			// good
+		}
+}
+
+   /**
+	 * See #369
+	 */
+   @Test
+   public void testCloneIntoExtension() {
+       Patient patient = new Patient();
+
+       patient.addUndeclaredExtension(new ExtensionDt(false, "http://example.com", new StringDt("FOO")));
+
+       Patient target = new Patient();
+		ourCtx.newTerser().cloneInto(patient, target, false);
+		
+		List<ExtensionDt> exts = target.getUndeclaredExtensionsByUrl("http://example.com");
+		assertEquals(1, exts.size());
+		assertEquals("FOO", ((StringDt)exts.get(0).getValue()).getValue());
+   }
+
+
+	@Test
+	public void testCloneIntoPrimitive() {
+		StringDt source = new StringDt("STR");
+		MarkdownDt target = new MarkdownDt();
+
+		ourCtx.newTerser().cloneInto(source, target, true);
+
+		assertEquals("STR", target.getValueAsString());
+	}
+
+
+	@Test
+	public void testCloneIntoPrimitiveFails() {
+		StringDt source = new StringDt("STR");
+		MoneyDt target = new MoneyDt();
+
+		ourCtx.newTerser().cloneInto(source, target, true);
+		assertTrue(target.isEmpty());
+
+		try {
+			ourCtx.newTerser().cloneInto(source, target, false);
+			fail();
+		} catch (DataFormatException e) {
+			// good
+		}
+
+	}
+
+	/**
+	 * See #369
+	 */
+   @Test
+   public void testCloneIntoValues() {
+       Observation obs = new Observation();
+       obs.setValue(new StringDt("AAA"));
+       obs.setComments("COMMENTS");
+
+       Observation target = new Observation();
+		ourCtx.newTerser().cloneInto(obs, target, false);
+		
+		assertEquals("AAA", ((StringDt)obs.getValue()).getValue());
+		assertEquals("COMMENTS", obs.getComments());
+   }
+
+	@Test
+	public void testGetAllPopulatedChildElementsOfTypeDescendsIntoContained() {
 		Patient p = new Patient();
 		p.addName().addFamily("PATIENT");
 
 		Organization o = new Organization();
-		o.setName("ORG");
+		o.getNameElement().setValue("ORGANIZATION");
-		ResourceReferenceDt ref = new ResourceReferenceDt(o);
+		p.getContained().getContainedResources().add(o);
-		ExtensionDt ext = new ExtensionDt(false, "urn:foo", ref);
+
-		p.addUndeclaredExtension(ext);
+		FhirTerser t = ourCtx.newTerser();
+		List<StringDt> strings = t.getAllPopulatedChildElementsOfType(p, StringDt.class);
+
+		assertEquals(2, strings.size());
+		assertThat(strings, containsInAnyOrder(new StringDt("PATIENT"), new StringDt("ORGANIZATION")));
 
-		List<IBaseReference> refs = ourCtx.newTerser().getAllPopulatedChildElementsOfType(p, IBaseReference.class);
-		assertEquals(1, refs.size());
-		assertSame(ref, refs.get(0));
 	}
 
-
-	@AfterClass
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-
 	@Test
 	public void testGetAllPopulatedChildElementsOfTypeDoesntDescendIntoEmbedded() {
 		Patient p = new Patient();
@@ -79,79 +166,21 @@ public class FhirTerserDstu2Test {
 	}
 
 	@Test
-	public void testCloneIntoPrimitive() {
+	public void testGetResourceReferenceInExtension() {
-		StringDt source = new StringDt("STR");
-		MarkdownDt target = new MarkdownDt();
-
-		ourCtx.newTerser().cloneInto(source, target, true);
-
-		assertEquals("STR", target.getValueAsString());
-	}
-
-	@Test
-	public void testCloneIntoPrimitiveFails() {
-		StringDt source = new StringDt("STR");
-		MoneyDt target = new MoneyDt();
-
-		ourCtx.newTerser().cloneInto(source, target, true);
-		assertTrue(target.isEmpty());
-
-		try {
-			ourCtx.newTerser().cloneInto(source, target, false);
-			fail();
-		} catch (DataFormatException e) {
-			// good
-		}
-
-	}
-
-	@Test
-	public void testCloneIntoComposite() {
-		QuantityDt source = new QuantityDt();
-		source.setCode("CODE");
-		MoneyDt target = new MoneyDt();
-
-		ourCtx.newTerser().cloneInto(source, target, true);
-
-		assertEquals("CODE", target.getCode());
-	}
-
-	@Test
-	public void testCloneIntoCompositeMismatchedFields() {
-		QuantityDt source = new QuantityDt();
-		source.setSystem("SYSTEM");
-		source.setUnit("UNIT");
-		IdentifierDt target = new IdentifierDt();
-
-		ourCtx.newTerser().cloneInto(source, target, true);
-
-		assertEquals("SYSTEM", target.getSystem());
-
-		try {
-			ourCtx.newTerser().cloneInto(source, target, false);
-			fail();
-		} catch (DataFormatException e) {
-			// good
-		}
-}
-	
-	@Test
-	public void testGetAllPopulatedChildElementsOfTypeDescendsIntoContained() {
 		Patient p = new Patient();
 		p.addName().addFamily("PATIENT");
 
 		Organization o = new Organization();
-		o.getNameElement().setValue("ORGANIZATION");
+		o.setName("ORG");
-		p.getContained().getContainedResources().add(o);
+		ResourceReferenceDt ref = new ResourceReferenceDt(o);
-
+		ExtensionDt ext = new ExtensionDt(false, "urn:foo", ref);
-		FhirTerser t = ourCtx.newTerser();
+		p.addUndeclaredExtension(ext);
-		List<StringDt> strings = t.getAllPopulatedChildElementsOfType(p, StringDt.class);
-
-		assertEquals(2, strings.size());
-		assertThat(strings, containsInAnyOrder(new StringDt("PATIENT"), new StringDt("ORGANIZATION")));
 
+		List<IBaseReference> refs = ourCtx.newTerser().getAllPopulatedChildElementsOfType(p, IBaseReference.class);
+		assertEquals(1, refs.size());
+		assertSame(ref, refs.get(0));
 	}
-
+	
 	@Test
 	public void testVisitWithModelVisitor2() {
 		IModelVisitor2 visitor = mock(IModelVisitor2.class);
@@ -178,6 +207,11 @@ public class FhirTerserDstu2Test {
 
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
 	/**
 	 * See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
 	 */

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/util/FhirTerserDstu3Test.java

@@ -0,0 +1,256 @@
+package ca.uhn.fhir.util;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+import java.lang.reflect.ParameterizedType;
+import java.lang.reflect.Type;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.Extension;
+import org.hl7.fhir.dstu3.model.Identifier;
+import org.hl7.fhir.dstu3.model.MarkdownType;
+import org.hl7.fhir.dstu3.model.Money;
+import org.hl7.fhir.dstu3.model.Observation;
+import org.hl7.fhir.dstu3.model.Organization;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.Patient.LinkType;
+import org.hl7.fhir.dstu3.model.Quantity;
+import org.hl7.fhir.dstu3.model.Reference;
+import org.hl7.fhir.dstu3.model.StringType;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+import org.junit.AfterClass;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.DataFormatException;
+
+public class FhirTerserDstu3Test {
+
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+
+	@Test
+	public void testCloneIntoComposite() {
+		Quantity source = new Quantity();
+		source.setCode("CODE");
+		Money target = new Money();
+
+		ourCtx.newTerser().cloneInto(source, target, true);
+
+		assertEquals("CODE", target.getCode());
+	}
+   
+	@Test
+	public void testCloneIntoCompositeMismatchedFields() {
+		Quantity source = new Quantity();
+		source.setSystem("SYSTEM");
+		source.setUnit("UNIT");
+		Identifier target = new Identifier();
+
+		ourCtx.newTerser().cloneInto(source, target, true);
+
+		assertEquals("SYSTEM", target.getSystem());
+
+		try {
+			ourCtx.newTerser().cloneInto(source, target, false);
+			fail();
+		} catch (DataFormatException e) {
+			// good
+		}
+}
+
+   /**
+	 * See #369
+	 */
+   @Test
+   public void testCloneIntoExtension() {
+       Patient patient = new Patient();
+
+       patient.addExtension(new Extension("http://example.com", new StringType("FOO")));
+
+       Patient target = new Patient();
+		ourCtx.newTerser().cloneInto(patient, target, false);
+		
+		List<Extension> exts = target.getExtensionsByUrl("http://example.com");
+		assertEquals(1, exts.size());
+		assertEquals("FOO", ((StringType)exts.get(0).getValue()).getValue());
+   }
+
+
+	@Test
+	public void testCloneIntoPrimitive() {
+		StringType source = new StringType("STR");
+		MarkdownType target = new MarkdownType();
+
+		ourCtx.newTerser().cloneInto(source, target, true);
+
+		assertEquals("STR", target.getValueAsString());
+	}
+
+
+	@Test
+	public void testCloneIntoPrimitiveFails() {
+		StringType source = new StringType("STR");
+		Money target = new Money();
+
+		ourCtx.newTerser().cloneInto(source, target, true);
+		assertTrue(target.isEmpty());
+
+		try {
+			ourCtx.newTerser().cloneInto(source, target, false);
+			fail();
+		} catch (DataFormatException e) {
+			// good
+		}
+
+	}
+
+	/**
+	 * See #369
+	 */
+   @Test
+   public void testCloneIntoValues() {
+       Observation obs = new Observation();
+       obs.setValue(new StringType("AAA"));
+       obs.setComment("COMMENTS");
+
+       Observation target = new Observation();
+		ourCtx.newTerser().cloneInto(obs, target, false);
+		
+		assertEquals("AAA", ((StringType)obs.getValue()).getValue());
+		assertEquals("COMMENTS", obs.getComment());
+   }
+
+	@Test
+	public void testGetAllPopulatedChildElementsOfTypeDescendsIntoContained() {
+		Patient p = new Patient();
+		p.addName().addFamily("PATIENT");
+
+		Organization o = new Organization();
+		o.getNameElement().setValue("ORGANIZATION");
+		p.getContained().add(o);
+
+		FhirTerser t = ourCtx.newTerser();
+		List<StringType> strings = t.getAllPopulatedChildElementsOfType(p, StringType.class);
+
+		assertThat(toStrings(strings), containsInAnyOrder("PATIENT","ORGANIZATION"));
+
+	}
+
+	@Test
+	public void testGetAllPopulatedChildElementsOfTypeDoesntDescendIntoEmbedded() {
+		Patient p = new Patient();
+		p.addName().addFamily("PATIENT");
+
+		Bundle b = new Bundle();
+		b.addEntry().setResource(p);
+		b.addLink().setRelation("BUNDLE");
+
+		FhirTerser t = ourCtx.newTerser();
+		List<StringType> strings = t.getAllPopulatedChildElementsOfType(b, StringType.class);
+
+		assertEquals(1, strings.size());
+		assertThat(toStrings(strings), containsInAnyOrder("BUNDLE"));
+
+	}
+
+	@Test
+	public void testGetResourceReferenceInExtension() {
+		Patient p = new Patient();
+		p.addName().addFamily("PATIENT");
+
+		Organization o = new Organization();
+		o.setName("ORG");
+		Reference ref = new Reference(o);
+		Extension ext = new Extension("urn:foo", ref);
+		p.addExtension(ext);
+
+		FhirTerser t = ourCtx.newTerser();
+		List<IBaseReference> refs = t.getAllPopulatedChildElementsOfType(p, IBaseReference.class);
+		assertEquals(1, refs.size());
+		assertSame(ref, refs.get(0));
+	}
+
+	@Test
+	public void testVisitWithModelVisitor2() {
+		IModelVisitor2 visitor = mock(IModelVisitor2.class);
+
+		ArgumentCaptor<IBase> element = ArgumentCaptor.forClass(IBase.class);
+		ArgumentCaptor<List<IBase>> containingElementPath = ArgumentCaptor.forClass(getListClass(IBase.class));
+		ArgumentCaptor<List<BaseRuntimeChildDefinition>> childDefinitionPath = ArgumentCaptor.forClass(getListClass(BaseRuntimeChildDefinition.class));
+		ArgumentCaptor<List<BaseRuntimeElementDefinition<?>>> elementDefinitionPath = ArgumentCaptor.forClass(getListClass2());
+		when(visitor.acceptElement(element.capture(), containingElementPath.capture(), childDefinitionPath.capture(), elementDefinitionPath.capture())).thenReturn(true);
+
+		Patient p = new Patient();
+		p.addLink().getTypeElement().setValue(LinkType.REFER);
+		ourCtx.newTerser().visit(p, visitor);
+
+		assertEquals(3, element.getAllValues().size());
+		assertSame(p, element.getAllValues().get(0));
+		assertSame(p.getLinkFirstRep(), element.getAllValues().get(1));
+		assertSame(p.getLinkFirstRep().getTypeElement(), element.getAllValues().get(2));
+
+		assertEquals(3, containingElementPath.getAllValues().size());
+		// assertEquals(0, containingElementPath.getAllValues().get(0).size());
+		// assertEquals(1, containingElementPath.getAllValues().get(1).size());
+		// assertEquals(2, containingElementPath.getAllValues().get(2).size());
+
+	}
+	
+	private List<String> toStrings(List<StringType> theStrings) {
+		ArrayList<String> retVal = new ArrayList<String>();
+		for (StringType next : theStrings) {
+			retVal.add(next.getValue());
+		}
+		return retVal;
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	/**
+	 * See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
+	 */
+	private static <T> Class<List<T>> getListClass(Class<T> theClass) {
+		return new ClassGetter<List<T>>() {
+		}.get();
+	}
+
+	/**
+	 * See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
+	 */
+	private static Class<List<BaseRuntimeElementDefinition<?>>> getListClass2() {
+		return new ClassGetter<List<BaseRuntimeElementDefinition<?>>>() {
+		}.get();
+	}
+
+	/**
+	 * See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
+	 */
+	private static abstract class ClassGetter<T> {
+		@SuppressWarnings("unchecked")
+		public final Class<T> get() {
+			final ParameterizedType superclass = (ParameterizedType) getClass().getGenericSuperclass();
+			Type type = superclass.getActualTypeArguments()[0];
+			if (type instanceof ParameterizedType) {
+				return (Class<T>) ((ParameterizedType) type).getOwnerType();
+			}
+			return (Class<T>) type;
+		}
+	}
+
+}

src/changes/changes.xml

@@ -229,6 +229,11 @@
 				</ul>
 				]]>
 			</action>
+			<action type="fix" issue="369">
+				FhirTerser.cloneInto method failed to clone correctly if the source 
+				had any extensions. Thanks to GitHub user @Virdulys for submitting and
+				providing a test case!
+			</action>
 		</release>
 		<release version="1.5" date="2016-04-20">
 			<action type="fix" issue="339">