From a92d80d860e004b992d1e74881ca9cde53728510 Mon Sep 17 00:00:00 2001
From: James Agnew <jamesagnew@gmail.com>
Date: Wed, 17 May 2017 12:40:10 -0400
Subject: [PATCH] Correctly encode extensions on the root of a resource with
 type reference

---
 .../java/ca/uhn/fhir/parser/JsonParser.java   |   39 +-
 .../fhir/jpa/dao/BaseHapiFhirResourceDao.java |    6 +-
 .../dstu3/ResourceProviderDstu3Test.java      |   28 +-
 .../uhn/fhir/parser/JsonParserDstu3Test.java  |  556 +-
 .../uhn/fhir/parser/XmlParserDstu3Test.java   | 6316 +++++++++--------
 src/changes/changes.xml                       |    4 +
 6 files changed, 3506 insertions(+), 3443 deletions(-)

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
index 112e6a49ab1..e41dc29ca87 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
@@ -151,7 +151,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		return false;
 	}
 
-	private boolean addToHeldExtensions(int valueIdx, List<? extends IBaseExtension<?, ?>> ext, ArrayList<ArrayList<HeldExtension>> list, boolean theIsModifier, CompositeChildElement theChildElem) {
+	private boolean addToHeldExtensions(int valueIdx, List<? extends IBaseExtension<?, ?>> ext, ArrayList<ArrayList<HeldExtension>> list, boolean theIsModifier, CompositeChildElement theChildElem, CompositeChildElement theParent) {
 		if (ext.size() > 0) {
 			list.ensureCapacity(valueIdx);
 			while (list.size() <= valueIdx) {
@@ -161,7 +161,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				list.set(valueIdx, new ArrayList<JsonParser.HeldExtension>());
 			}
 			for (IBaseExtension<?, ?> next : ext) {
-				list.get(valueIdx).add(new HeldExtension(next, theIsModifier, theChildElem));
+				list.get(valueIdx).add(new HeldExtension(next, theIsModifier, theChildElem, theParent));
 			}
 			return true;
 		}
@@ -593,7 +593,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 
 			if (nextChildElem.getDef().getElementName().equals("extension") || nextChildElem.getDef().getElementName().equals("modifierExtension") || nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
 				if (!haveWrittenExtensions) {
-					extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem);
+					extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent);
 					haveWrittenExtensions = true;
 				}
 				continue;
@@ -673,20 +673,20 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				if (primitive) {
 					if (nextValue instanceof ISupportsUndeclaredExtensions) {
 						List<ExtensionDt> ext = ((ISupportsUndeclaredExtensions) nextValue).getUndeclaredExtensions();
-						force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem);
+						force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent);
 
 						ext = ((ISupportsUndeclaredExtensions) nextValue).getUndeclaredModifierExtensions();
-						force |= addToHeldExtensions(valueIdx, ext, modifierExtensions, true, nextChildElem);
+						force |= addToHeldExtensions(valueIdx, ext, modifierExtensions, true, nextChildElem, theParent);
 					} else {
 						if (nextValue instanceof IBaseHasExtensions) {
 							IBaseHasExtensions element = (IBaseHasExtensions) nextValue;
 							List<? extends IBaseExtension<?, ?>> ext = element.getExtension();
-							force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem);
+							force |= addToHeldExtensions(valueIdx, ext, extensions, false, nextChildElem, theParent);
 						}
 						if (nextValue instanceof IBaseHasModifierExtensions) {
 							IBaseHasModifierExtensions element = (IBaseHasModifierExtensions) nextValue;
 							List<? extends IBaseExtension<?, ?>> ext = element.getModifierExtension();
-							force |= addToHeldExtensions(valueIdx, ext, extensions, true, nextChildElem);
+							force |= addToHeldExtensions(valueIdx, ext, extensions, true, nextChildElem, theParent);
 						}
 					}
 					if (nextValue.hasFormatComment()) {
@@ -996,13 +996,14 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 	 * This is useful only for the two cases where extensions are encoded as direct children (e.g. not in some object
 	 * called _name): resource extensions, and extension extensions
 	 * @param theChildElem 
+	 * @param theParent 
 	 */
-	private void extractAndWriteExtensionsAsDirectChild(IBase theElement, JsonLikeWriter theEventWriter, BaseRuntimeElementDefinition<?> theElementDef, RuntimeResourceDefinition theResDef, IBaseResource theResource, CompositeChildElement theChildElem) throws IOException {
+	private void extractAndWriteExtensionsAsDirectChild(IBase theElement, JsonLikeWriter theEventWriter, BaseRuntimeElementDefinition<?> theElementDef, RuntimeResourceDefinition theResDef, IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent) throws IOException {
 		List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
 		List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
 
 		// Undeclared extensions
-		extractUndeclaredExtensions(theElement, extensions, modifierExtensions, theChildElem);
+		extractUndeclaredExtensions(theElement, extensions, modifierExtensions, theChildElem, theParent);
 
 		// Declared extensions
 		if (theElementDef != null) {
@@ -1036,7 +1037,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		}
 	}
 
-	private void extractUndeclaredExtensions(IBase theElement, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions, CompositeChildElement theChildElem) {
+	private void extractUndeclaredExtensions(IBase theElement, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions, CompositeChildElement theChildElem, CompositeChildElement theParent) {
 		if (theElement instanceof ISupportsUndeclaredExtensions) {
 			ISupportsUndeclaredExtensions element = (ISupportsUndeclaredExtensions) theElement;
 			List<ExtensionDt> ext = element.getUndeclaredExtensions();
@@ -1044,7 +1045,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				if (next == null || next.isEmpty()) {
 					continue;
 				}
-				extensions.add(new HeldExtension(next, false, theChildElem));
+				extensions.add(new HeldExtension(next, false, theChildElem, theParent));
 			}
 
 			ext = element.getUndeclaredModifierExtensions();
@@ -1052,7 +1053,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				if (next == null || next.isEmpty()) {
 					continue;
 				}
-				modifierExtensions.add(new HeldExtension(next, true, theChildElem));
+				modifierExtensions.add(new HeldExtension(next, true, theChildElem, theParent));
 			}
 		} else {
 			if (theElement instanceof IBaseHasExtensions) {
@@ -1062,7 +1063,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					if (next == null || (ElementUtil.isEmpty(next.getValue()) && next.getExtension().isEmpty())) {
 						continue;
 					}
-					extensions.add(new HeldExtension(next, false, theChildElem));
+					extensions.add(new HeldExtension(next, false, theChildElem, theParent));
 				}
 			}
 			if (theElement instanceof IBaseHasModifierExtensions) {
@@ -1072,7 +1073,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 					if (next == null || next.isEmpty()) {
 						continue;
 					}
-					modifierExtensions.add(new HeldExtension(next, true, theChildElem));
+					modifierExtensions.add(new HeldExtension(next, true, theChildElem, theParent));
 				}
 			}
 		}
@@ -1775,12 +1776,14 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 		private boolean myModifier;
 		private IBaseExtension<?, ?> myUndeclaredExtension;
 		private IBase myValue;
+		private CompositeChildElement myParent;
 
-		public HeldExtension(IBaseExtension<?, ?> theUndeclaredExtension, boolean theModifier, CompositeChildElement theChildElem) {
+		public HeldExtension(IBaseExtension<?, ?> theUndeclaredExtension, boolean theModifier, CompositeChildElement theChildElem, CompositeChildElement theParent) {
 			assert theUndeclaredExtension != null;
 			myUndeclaredExtension = theUndeclaredExtension;
 			myModifier = theModifier;
 			myChildElem = theChildElem;
+			myParent = theParent;
 		}
 
 		public HeldExtension(RuntimeChildDeclaredExtensionDefinition theDef, IBase theValue, CompositeChildElement theChildElem) {
@@ -1835,10 +1838,10 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				
 				BaseRuntimeElementDefinition<?> def = myDef.getChildElementDefinitionByDatatype(myValue.getClass());
 				if (def.getChildType() == ChildTypeEnum.RESOURCE_BLOCK) {
-					extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem);
+					extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem, null);
 				} else {
 					String childName = myDef.getChildNameByDatatype(myValue.getClass());
-					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false, null, false);
+					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false, myParent, false);
 				}
 
 				theEventWriter.endObject();
@@ -1893,7 +1896,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				if (childDef == null) {
 					throw new ConfigurationException("Unable to encode extension, unregognized child element type: " + value.getClass().getCanonicalName());
 				}
-				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, null, false);
+				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, myParent, false);
 			}
 
 			// theEventWriter.name(myUndeclaredExtension.get);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
index 9af90fc0d2c..5f6acb32b2d 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
@@ -384,7 +384,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		 * to be reflected in the resource shared with interceptors
 		 */
 		if (!thePerformIndexing) {
-			incremenetId(theResource, entity, theResource.getIdElement());
+			incrementId(theResource, entity, theResource.getIdElement());
 		}
 		
 		// Notify JPA interceptors
@@ -415,7 +415,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return outcome;
 	}
 
-	private void incremenetId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
+	private void incrementId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
 		IIdType idType = theResourceId;
 		String newVersion;
 		long newVersionLong;
@@ -1131,7 +1131,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			if (resourceId.hasVersionIdPart() == false) {
 				resourceId = resourceId.withVersion(Long.toString(savedEntity.getVersion()));
 			}
-			incremenetId(theResource, savedEntity, resourceId);
+			incrementId(theResource, savedEntity, resourceId);
 		}
 
 		// Notify interceptors
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
index 9fac2f5ab5f..3b3a1e94661 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
@@ -175,6 +175,25 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		myDaoConfig.setAllowMultipleDelete(true);
 	}
 
+	@Test
+	public void testSaveAndRetrieveResourceWithExtension() {
+		Patient nextPatient = new Patient();
+		nextPatient.setId("Patient/B");
+		nextPatient
+				.addExtension()
+				.setUrl("http://foo")
+				.setValue(new Reference("Practitioner/A"));
+
+		ourClient.update().resource(nextPatient).execute();
+
+		Patient p = ourClient.read().resource(Patient.class).withId("B").execute();
+		
+		String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("http://foo"));
+	}
+
 	private void checkParamMissing(String paramName) throws IOException, ClientProtocolException {
 		HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
 		CloseableHttpResponse resp = ourHttpClient.execute(get);
@@ -1549,12 +1568,11 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 
 		assertEquals(null, responseBundle.getLink("next"));
-		
+
 		assertThat(ids, hasItem("List/A161444"));
 		assertThat(ids, hasItem("List/A161468"));
 		assertThat(ids, hasItem("List/A161500"));
 
-
 		ourLog.info("Expected {} - {}", allIds.size(), allIds);
 		ourLog.info("Actual   {} - {}", ids.size(), ids);
 		assertEquals(allIds, ids);
@@ -1726,7 +1744,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			preDates.add(new Date());
 			Thread.sleep(100);
 			patient.setId(id);
-			patient.getName().get(0).getFamilyElement().setValue(methodName + "_i"+i);
+			patient.getName().get(0).getFamilyElement().setValue(methodName + "_i" + i);
 			ids.add(myPatientDao.update(patient, mySrd).getId().toUnqualified().getValue());
 		}
 
@@ -3149,7 +3167,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
 
 		// should be subject._id
-		HttpGet httpPost = new HttpGet(ourServerBase + "/Observation?subject.id=FOO"); 
+		HttpGet httpPost = new HttpGet(ourServerBase + "/Observation?subject.id=FOO");
 
 		CloseableHttpResponse resp = ourHttpClient.execute(httpPost);
 		try {
@@ -3162,7 +3180,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 		ourLog.info("Outgoing post: {}", httpPost);
 	}
-	
+
 	/**
 	 * See #411
 	 * 
diff --git a/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java b/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
index edf32a2eb9f..ac163282b6e 100644
--- a/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
+++ b/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
@@ -98,6 +98,7 @@ public class JsonParserDstu3Test {
 			assertEquals("Found incorrect type for element subject - Expected OBJECT and found SCALAR (STRING)", e.getMessage());
 		}
 	}
+
 	
 	/**
 	 * See #563
@@ -116,47 +117,6 @@ public class JsonParserDstu3Test {
 		}
 	}
 	
-	@Test
-	public void testOverrideResourceIdWithBundleEntryFullUrlDisabled_ConfiguredOnFhirContext() {
-		try {
-			String tmp = "{\"resourceType\":\"Bundle\",\"entry\":[{\"fullUrl\":\"http://lalaland.org/patient/pat1\",\"resource\":{\"resourceType\":\"Patient\",\"id\":\"patxuzos\"}}]}";
-			ourCtx.getParserOptions().setOverrideResourceIdWithBundleEntryFullUrl(false);
-			Bundle bundle = (Bundle) ourCtx.newJsonParser().parseResource(tmp);
-			assertEquals(1, bundle.getEntry().size());
-			{
-				Patient o1 = (Patient) bundle.getEntry().get(0).getResource();
-				IIdType o1Id = o1.getIdElement();
-				assertFalse(o1Id.hasBaseUrl());
-				assertEquals("Patient", o1Id.getResourceType());
-				assertEquals("patxuzos", o1Id.getIdPart());
-				assertFalse(o1Id.hasVersionIdPart());
-			}
-		} finally {
-			// ensure we cleanup ourCtx so other tests continue to work
-			ourCtx = FhirContext.forDstu3();
-		}
-	}
-	
-	@Test
-	public void testOverrideResourceIdWithBundleEntryFullUrlDisabled_ConfiguredOnParser() {
-		try {
-			String tmp = "{\"resourceType\":\"Bundle\",\"entry\":[{\"fullUrl\":\"http://lalaland.org/patient/pat1\",\"resource\":{\"resourceType\":\"Patient\",\"id\":\"patxuzos\"}}]}";
-			Bundle bundle = (Bundle) ourCtx.newJsonParser().setOverrideResourceIdWithBundleEntryFullUrl(false).parseResource(tmp);
-			assertEquals(1, bundle.getEntry().size());
-			{
-				Patient o1 = (Patient) bundle.getEntry().get(0).getResource();
-				IIdType o1Id = o1.getIdElement();
-				assertFalse(o1Id.hasBaseUrl());
-				assertEquals("Patient", o1Id.getResourceType());
-				assertEquals("patxuzos", o1Id.getIdPart());
-				assertFalse(o1Id.hasVersionIdPart());
-			}
-		} finally {
-			// ensure we cleanup ourCtx so other tests continue to work
-			ourCtx = FhirContext.forDstu3();
-		}
-	}
-
 	/**
 	 * See #544
 	 */
@@ -184,81 +144,73 @@ public class JsonParserDstu3Test {
 		assertNotNull(subject);
 		assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
 	}
-
 	
+	/**
+	 * Test for the url generated based on the server config
+	 */
 	@Test
-	public void testIncorrectJsonTypesIdAndArray() {
-		
-		// ID should be a String and communication should be an Array
-		String input = "{\"resourceType\": \"Patient\",\n" +
-				"  \"id\": 123,\n" +
-				"  \"communication\": {\n" +
-				"    \"language\": {\n" +
-				"      \"text\": \"Hindi\"\n" +
-				"    },\n" +
-				"    \"preferred\": true\n" +
-				"  }\n" +
-				"}";
+	public void testCustomUrlExtension() {
+		final String expected = "{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}";
 
-		IParser p = ourCtx.newJsonParser();
-		
-		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
-		p.setParserErrorHandler(errorHandler);
-		Patient patient = (Patient) p.parseResource(input);
-		
-		ArgumentCaptor<String> elementName = ArgumentCaptor.forClass(String.class);
-		ArgumentCaptor<ValueType> found = ArgumentCaptor.forClass(ValueType.class);
-		ArgumentCaptor<ValueType> expected = ArgumentCaptor.forClass(ValueType.class);
-		ArgumentCaptor<ScalarType> expectedScalarType = ArgumentCaptor.forClass(ScalarType.class);
-		ArgumentCaptor<ScalarType> foundScalarType = ArgumentCaptor.forClass(ScalarType.class);
-		verify(errorHandler, times(2)).incorrectJsonType(any(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalarType.capture(), found.capture(), foundScalarType.capture());
-		
-		assertEquals(ValueType.SCALAR, found.getAllValues().get(0));
-		assertEquals(ValueType.SCALAR, expected.getAllValues().get(0));
-		assertEquals(ScalarType.NUMBER, foundScalarType.getAllValues().get(0));
-		assertEquals(ScalarType.STRING, expectedScalarType.getAllValues().get(0));
-	
-		assertEquals(ValueType.OBJECT, found.getAllValues().get(1));
-		assertEquals(ValueType.ARRAY, expected.getAllValues().get(1));
-		assertEquals(null, foundScalarType.getAllValues().get(1));
-		assertEquals(null, expectedScalarType.getAllValues().get(1));
-		
-		assertEquals("123", patient.getIdElement().getIdPart());
-		assertEquals("Hindi", patient.getCommunicationFirstRep().getLanguage().getText());
+		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+		patient.setPetName(new StringType("myName"));
+
+		final IParser jsonParser = ourCtx.newJsonParser();
+		jsonParser.setServerBaseUrl("http://www.example.com");
+
+		final String parsedPatient = jsonParser.encodeResourceToString(patient);
+		System.out.println(parsedPatient);
+		assertEquals(expected, parsedPatient);
+
+		// Parse with string
+		MyPatientWithCustomUrlExtension newPatient = jsonParser.parseResource(MyPatientWithCustomUrlExtension.class, parsedPatient);
+		assertEquals("myName", newPatient.getPetName().getValue());
+
+		// Parse with stream
+		newPatient = jsonParser.parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
+		assertEquals("myName", newPatient.getPetName().getValue());
+
+		//Check no NPE if base server not configure
+		newPatient = ourCtx.newJsonParser().parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
+		assertNull("myName", newPatient.getPetName().getValue());
+		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
 	}
 	
 	@Test
-	public void testIncorrectJsonTypesNone() {
-		
-		// ID should be a String and communication should be an Array
-		String input = "{\"resourceType\": \"Patient\",\n" +
-				"  \"id\": \"123\",\n" +
-				"  \"communication\": [{\n" +
-				"    \"language\": {\n" +
-				"      \"text\": \"Hindi\"\n" +
-				"    },\n" +
-				"    \"preferred\": true\n" +
-				"  }]\n" +
-				"}";
+	public void testCustomUrlExtensioninBundle() {
+		final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}";
+
+		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+		patient.setPetName(new StringType("myName"));
+
+		final Bundle bundle = new Bundle();
+		final BundleEntryComponent entry = new BundleEntryComponent();
+		entry.setResource(patient);
+		bundle.addEntry(entry);
+
+		final IParser jsonParser = ourCtx.newJsonParser();
+		jsonParser.setServerBaseUrl("http://www.example.com");
+
+		final String parsedBundle = jsonParser.encodeResourceToString(bundle);
+		System.out.println(parsedBundle);
+		assertEquals(expected, parsedBundle);
+
+		// Parse with string
+		Bundle newBundle = jsonParser.parseResource(Bundle.class, parsedBundle);
+		assertNotNull(newBundle);
+		assertEquals(1, newBundle.getEntry().size());
+		Patient newPatient = (Patient) newBundle.getEntry().get(0).getResource();
+		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
+
+		// Parse with stream
+		newBundle = jsonParser.parseResource(Bundle.class, new StringReader(parsedBundle));
+		assertNotNull(newBundle);
+		assertEquals(1, newBundle.getEntry().size());
+		newPatient = (Patient) newBundle.getEntry().get(0).getResource();
+		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
 
-		IParser p = ourCtx.newJsonParser();
-		
-		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
-		p.setParserErrorHandler(errorHandler);
-		Patient patient = (Patient) p.parseResource(input);
-		
-		ArgumentCaptor<String> elementName = ArgumentCaptor.forClass(String.class);
-		ArgumentCaptor<ValueType> found = ArgumentCaptor.forClass(ValueType.class);
-		ArgumentCaptor<ValueType> expected = ArgumentCaptor.forClass(ValueType.class);
-		ArgumentCaptor<ScalarType> expectedScalarType = ArgumentCaptor.forClass(ScalarType.class);
-		ArgumentCaptor<ScalarType> foundScalarType = ArgumentCaptor.forClass(ScalarType.class);
-		verify(errorHandler, times(0)).incorrectJsonType(any(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalarType.capture(), found.capture(), foundScalarType.capture());
-		
-		assertEquals("123", patient.getIdElement().getIdPart());
-		assertEquals("Hindi", patient.getCommunicationFirstRep().getLanguage().getText());
 	}
 
-	
 	/**
 	 * See #276
 	 */
@@ -285,81 +237,7 @@ public class JsonParserDstu3Test {
 		assertEquals(3, countMatches(encoded, "resourceType"));
 	}
 
-	/**
-	 * #480
-	 */
-	@Test
-	public void testEncodeEmptyValue() {
-		QuestionnaireResponse qr = new QuestionnaireResponse();
-		qr.setId("123");
-		qr.getAuthoredElement().setValueAsString("");
-		qr.getItemFirstRep().setLinkIdElement(new StringType());
-		qr.getItemFirstRep().addItem().setLinkIdElement(new StringType(""));
-		qr.getItemFirstRep().addItem().setLinkIdElement(new StringType("LINKID"));
-
-		String encoded = ourCtx.newJsonParser().encodeResourceToString(qr);
-		ourLog.info(encoded);
-
-		assertThat(encoded, stringContainsInOrder("123"));
-		assertThat(encoded, not(stringContainsInOrder("\"\"")));
-		assertThat(encoded, not(stringContainsInOrder("null")));
-	}
-
-	/**
-	 * #480
-	 */
-	@Test
-	public void testParseEmptyValue() {
-		String input = "{\"resourceType\":\"QuestionnaireResponse\",\"id\":\"123\",\"authored\":\"\",\"group\":{\"linkId\":\"\"}}";
-		IParser parser = ourCtx.newJsonParser();
-		
-		parser.setParserErrorHandler(new LenientErrorHandler().setErrorOnInvalidValue(false));
-		QuestionnaireResponse qr = parser.parseResource(QuestionnaireResponse.class, input);
 	
-		assertEquals("QuestionnaireResponse/123", qr.getIdElement().getValue());
-		assertEquals(null, qr.getAuthored());
-		assertEquals(null, qr.getAuthoredElement().getValue());
-		assertEquals(null, qr.getAuthoredElement().getValueAsString());
-		assertEquals(null, qr.getItemFirstRep().getLinkId());
-		assertEquals(null, qr.getItemFirstRep().getLinkIdElement().getValue());
-	}
-
-	/**
-	 * See #477
-	 */
-	@Test
-	public void testUnexpectedElementsWithUnderscoreAtStartOfName() throws Exception {
-		String input = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/bug477.json"), StandardCharsets.UTF_8);
-
-		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
-
-		// Do it once without the custom error handler just for the logging
-		IParser p = ourCtx.newJsonParser();
-		p.parseResource(Patient.class, input);
-
-		p = ourCtx.newJsonParser();
-		p.setParserErrorHandler(errorHandler);
-
-		Patient parsed = p.parseResource(Patient.class, input);
-		assertEquals("1", parsed.getIdElement().getIdPart());
-
-		ArgumentCaptor<String> elementName = ArgumentCaptor.forClass(String.class);
-		ArgumentCaptor<ValueType> expected = ArgumentCaptor.forClass(ValueType.class);
-		ArgumentCaptor<ValueType> actual = ArgumentCaptor.forClass(ValueType.class);
-		ArgumentCaptor<ScalarType> expectedScalar = ArgumentCaptor.forClass(ScalarType.class);
-		ArgumentCaptor<ScalarType> actualScalar = ArgumentCaptor.forClass(ScalarType.class);
-		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalar.capture(), actual.capture(), actualScalar.capture());
-		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR), actualScalar.capture());
-		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR), actualScalar.capture());
-		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR), actualScalar.capture());
-
-		assertEquals("_id", elementName.getAllValues().get(0));
-		assertEquals(ValueType.OBJECT, expected.getAllValues().get(0));
-		assertEquals(ValueType.SCALAR, actual.getAllValues().get(0));
-		assertEquals(null, expectedScalar.getAllValues().get(0));
-		assertEquals(null, actualScalar.getAllValues().get(0));
-	}
-
 	@Test
 	public void testEncodeAndParseExtensions() throws Exception {
 
@@ -445,7 +323,7 @@ public class JsonParserDstu3Test {
 		assertEquals("CHILD", ((StringType) given2ext2.getValue()).getValue());
 
 	}
-
+	
 	@Test
 	public void testEncodeAndParseMetaProfileAndTags() {
 		Patient p = new Patient();
@@ -524,6 +402,7 @@ public class JsonParserDstu3Test {
 		assertEquals("sec_label2", tagList.get(1).getDisplay());
 	}
 
+	
 	/**
 	 * See #336
 	 */
@@ -740,6 +619,26 @@ public class JsonParserDstu3Test {
 		assertThat(encoded, not(containsString("Label")));
 	}
 
+	/**
+	 * #480
+	 */
+	@Test
+	public void testEncodeEmptyValue() {
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.setId("123");
+		qr.getAuthoredElement().setValueAsString("");
+		qr.getItemFirstRep().setLinkIdElement(new StringType());
+		qr.getItemFirstRep().addItem().setLinkIdElement(new StringType(""));
+		qr.getItemFirstRep().addItem().setLinkIdElement(new StringType("LINKID"));
+
+		String encoded = ourCtx.newJsonParser().encodeResourceToString(qr);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder("123"));
+		assertThat(encoded, not(stringContainsInOrder("\"\"")));
+		assertThat(encoded, not(stringContainsInOrder("null")));
+	}
+
 	@Test
 	public void testEncodeExtendedInfrastructureComponent() {
 		IParser parser = ourCtx.newJsonParser();
@@ -794,6 +693,25 @@ public class JsonParserDstu3Test {
 
 	}
 
+	@Test
+	public void testEncodeExtensionOnRoot() {
+		Patient p = new Patient();
+		p.setId("Patient/B");
+		p
+				.addExtension()
+				.setUrl("http://foo")
+				.setValue(new Reference("Practitioner/A"));
+		
+		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
+		parser.setDontEncodeElements(new HashSet<String>(Arrays.asList("*.id", "*.meta")));
+
+		String encoded = parser.encodeResourceToString(p);
+		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("http://foo"));
+		assertThat(encoded, containsString("Practitioner/A"));
+	}
+
 	@Test
 	public void testEncodeExtensionUndeclaredNonModifier() {
 		Observation obs = new Observation();
@@ -1387,6 +1305,98 @@ public class JsonParserDstu3Test {
 		assertEquals("{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.0000000000000001}}", str);
 	}
 
+	@Test
+	public void testIncorrectJsonTypesIdAndArray() {
+		
+		// ID should be a String and communication should be an Array
+		String input = "{\"resourceType\": \"Patient\",\n" +
+				"  \"id\": 123,\n" +
+				"  \"communication\": {\n" +
+				"    \"language\": {\n" +
+				"      \"text\": \"Hindi\"\n" +
+				"    },\n" +
+				"    \"preferred\": true\n" +
+				"  }\n" +
+				"}";
+
+		IParser p = ourCtx.newJsonParser();
+		
+		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
+		p.setParserErrorHandler(errorHandler);
+		Patient patient = (Patient) p.parseResource(input);
+		
+		ArgumentCaptor<String> elementName = ArgumentCaptor.forClass(String.class);
+		ArgumentCaptor<ValueType> found = ArgumentCaptor.forClass(ValueType.class);
+		ArgumentCaptor<ValueType> expected = ArgumentCaptor.forClass(ValueType.class);
+		ArgumentCaptor<ScalarType> expectedScalarType = ArgumentCaptor.forClass(ScalarType.class);
+		ArgumentCaptor<ScalarType> foundScalarType = ArgumentCaptor.forClass(ScalarType.class);
+		verify(errorHandler, times(2)).incorrectJsonType(any(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalarType.capture(), found.capture(), foundScalarType.capture());
+		
+		assertEquals(ValueType.SCALAR, found.getAllValues().get(0));
+		assertEquals(ValueType.SCALAR, expected.getAllValues().get(0));
+		assertEquals(ScalarType.NUMBER, foundScalarType.getAllValues().get(0));
+		assertEquals(ScalarType.STRING, expectedScalarType.getAllValues().get(0));
+	
+		assertEquals(ValueType.OBJECT, found.getAllValues().get(1));
+		assertEquals(ValueType.ARRAY, expected.getAllValues().get(1));
+		assertEquals(null, foundScalarType.getAllValues().get(1));
+		assertEquals(null, expectedScalarType.getAllValues().get(1));
+		
+		assertEquals("123", patient.getIdElement().getIdPart());
+		assertEquals("Hindi", patient.getCommunicationFirstRep().getLanguage().getText());
+	}
+
+	@Test
+	public void testIncorrectJsonTypesNone() {
+		
+		// ID should be a String and communication should be an Array
+		String input = "{\"resourceType\": \"Patient\",\n" +
+				"  \"id\": \"123\",\n" +
+				"  \"communication\": [{\n" +
+				"    \"language\": {\n" +
+				"      \"text\": \"Hindi\"\n" +
+				"    },\n" +
+				"    \"preferred\": true\n" +
+				"  }]\n" +
+				"}";
+
+		IParser p = ourCtx.newJsonParser();
+		
+		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
+		p.setParserErrorHandler(errorHandler);
+		Patient patient = (Patient) p.parseResource(input);
+		
+		ArgumentCaptor<String> elementName = ArgumentCaptor.forClass(String.class);
+		ArgumentCaptor<ValueType> found = ArgumentCaptor.forClass(ValueType.class);
+		ArgumentCaptor<ValueType> expected = ArgumentCaptor.forClass(ValueType.class);
+		ArgumentCaptor<ScalarType> expectedScalarType = ArgumentCaptor.forClass(ScalarType.class);
+		ArgumentCaptor<ScalarType> foundScalarType = ArgumentCaptor.forClass(ScalarType.class);
+		verify(errorHandler, times(0)).incorrectJsonType(any(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalarType.capture(), found.capture(), foundScalarType.capture());
+		
+		assertEquals("123", patient.getIdElement().getIdPart());
+		assertEquals("Hindi", patient.getCommunicationFirstRep().getLanguage().getText());
+	}
+
+	@Test
+	public void testInvalidDateTimeValueInvalid() throws Exception {
+		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
+		
+		String res = "{ \"resourceType\": \"Observation\", \"valueDateTime\": \"foo\" }";
+		IParser parser = ourCtx.newJsonParser();
+		parser.setParserErrorHandler(errorHandler);
+		Observation parsed = parser.parseResource(Observation.class, res);
+		
+		assertEquals(null, parsed.getValueDateTimeType().getValue());
+		assertEquals("foo", parsed.getValueDateTimeType().getValueAsString());
+		
+		ArgumentCaptor<String> msgCaptor = ArgumentCaptor.forClass(String.class);
+		verify(errorHandler, times(1)).invalidValue(isNull(IParseLocation.class), eq("foo"), msgCaptor.capture());
+		assertEquals("Invalid date/time format: \"foo\"", msgCaptor.getValue());
+		
+		String encoded = ourCtx.newJsonParser().encodeResourceToString(parsed);
+		assertEquals("{\"resourceType\":\"Observation\",\"valueDateTime\":\"foo\"}", encoded);		
+	}
+
 	/**
 	 * #516
 	 */
@@ -1439,26 +1449,6 @@ public class JsonParserDstu3Test {
 		assertEquals("{\"resourceType\":\"Patient\",\"gender\":\"foo\"}", encoded);		
 	}
 
-	@Test
-	public void testInvalidDateTimeValueInvalid() throws Exception {
-		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
-		
-		String res = "{ \"resourceType\": \"Observation\", \"valueDateTime\": \"foo\" }";
-		IParser parser = ourCtx.newJsonParser();
-		parser.setParserErrorHandler(errorHandler);
-		Observation parsed = parser.parseResource(Observation.class, res);
-		
-		assertEquals(null, parsed.getValueDateTimeType().getValue());
-		assertEquals("foo", parsed.getValueDateTimeType().getValueAsString());
-		
-		ArgumentCaptor<String> msgCaptor = ArgumentCaptor.forClass(String.class);
-		verify(errorHandler, times(1)).invalidValue(isNull(IParseLocation.class), eq("foo"), msgCaptor.capture());
-		assertEquals("Invalid date/time format: \"foo\"", msgCaptor.getValue());
-		
-		String encoded = ourCtx.newJsonParser().encodeResourceToString(parsed);
-		assertEquals("{\"resourceType\":\"Observation\",\"valueDateTime\":\"foo\"}", encoded);		
-	}
-
 	/**
 	 * #65
 	 */
@@ -1533,6 +1523,47 @@ public class JsonParserDstu3Test {
 		assertThat(ourCtx.newJsonParser().setOmitResourceId(true).encodeResourceToString(p), not(containsString("123")));
 	}
 
+	@Test
+	public void testOverrideResourceIdWithBundleEntryFullUrlDisabled_ConfiguredOnFhirContext() {
+		try {
+			String tmp = "{\"resourceType\":\"Bundle\",\"entry\":[{\"fullUrl\":\"http://lalaland.org/patient/pat1\",\"resource\":{\"resourceType\":\"Patient\",\"id\":\"patxuzos\"}}]}";
+			ourCtx.getParserOptions().setOverrideResourceIdWithBundleEntryFullUrl(false);
+			Bundle bundle = (Bundle) ourCtx.newJsonParser().parseResource(tmp);
+			assertEquals(1, bundle.getEntry().size());
+			{
+				Patient o1 = (Patient) bundle.getEntry().get(0).getResource();
+				IIdType o1Id = o1.getIdElement();
+				assertFalse(o1Id.hasBaseUrl());
+				assertEquals("Patient", o1Id.getResourceType());
+				assertEquals("patxuzos", o1Id.getIdPart());
+				assertFalse(o1Id.hasVersionIdPart());
+			}
+		} finally {
+			// ensure we cleanup ourCtx so other tests continue to work
+			ourCtx = FhirContext.forDstu3();
+		}
+	}
+
+	@Test
+	public void testOverrideResourceIdWithBundleEntryFullUrlDisabled_ConfiguredOnParser() {
+		try {
+			String tmp = "{\"resourceType\":\"Bundle\",\"entry\":[{\"fullUrl\":\"http://lalaland.org/patient/pat1\",\"resource\":{\"resourceType\":\"Patient\",\"id\":\"patxuzos\"}}]}";
+			Bundle bundle = (Bundle) ourCtx.newJsonParser().setOverrideResourceIdWithBundleEntryFullUrl(false).parseResource(tmp);
+			assertEquals(1, bundle.getEntry().size());
+			{
+				Patient o1 = (Patient) bundle.getEntry().get(0).getResource();
+				IIdType o1Id = o1.getIdElement();
+				assertFalse(o1Id.hasBaseUrl());
+				assertEquals("Patient", o1Id.getResourceType());
+				assertEquals("patxuzos", o1Id.getIdPart());
+				assertFalse(o1Id.hasVersionIdPart());
+			}
+		} finally {
+			// ensure we cleanup ourCtx so other tests continue to work
+			ourCtx = FhirContext.forDstu3();
+		}
+	}
+
 	@Test
 	@Ignore
 	public void testParseAndEncodeBundle() throws Exception {
@@ -1872,6 +1903,25 @@ public class JsonParserDstu3Test {
 		assertEquals("patient family", p.getName().get(0).getFamilyElement().getValue());
 	}
 
+	/**
+	 * #480
+	 */
+	@Test
+	public void testParseEmptyValue() {
+		String input = "{\"resourceType\":\"QuestionnaireResponse\",\"id\":\"123\",\"authored\":\"\",\"group\":{\"linkId\":\"\"}}";
+		IParser parser = ourCtx.newJsonParser();
+		
+		parser.setParserErrorHandler(new LenientErrorHandler().setErrorOnInvalidValue(false));
+		QuestionnaireResponse qr = parser.parseResource(QuestionnaireResponse.class, input);
+	
+		assertEquals("QuestionnaireResponse/123", qr.getIdElement().getValue());
+		assertEquals(null, qr.getAuthored());
+		assertEquals(null, qr.getAuthoredElement().getValue());
+		assertEquals(null, qr.getAuthoredElement().getValueAsString());
+		assertEquals(null, qr.getItemFirstRep().getLinkId());
+		assertEquals(null, qr.getItemFirstRep().getLinkIdElement().getValue());
+	}
+
 	/**
 	 * See #335
 	 */
@@ -2224,6 +2274,42 @@ public class JsonParserDstu3Test {
 		Assert.assertThat(message, containsString("contained"));
 	}
 
+	/**
+	 * See #477
+	 */
+	@Test
+	public void testUnexpectedElementsWithUnderscoreAtStartOfName() throws Exception {
+		String input = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/bug477.json"), StandardCharsets.UTF_8);
+
+		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
+
+		// Do it once without the custom error handler just for the logging
+		IParser p = ourCtx.newJsonParser();
+		p.parseResource(Patient.class, input);
+
+		p = ourCtx.newJsonParser();
+		p.setParserErrorHandler(errorHandler);
+
+		Patient parsed = p.parseResource(Patient.class, input);
+		assertEquals("1", parsed.getIdElement().getIdPart());
+
+		ArgumentCaptor<String> elementName = ArgumentCaptor.forClass(String.class);
+		ArgumentCaptor<ValueType> expected = ArgumentCaptor.forClass(ValueType.class);
+		ArgumentCaptor<ValueType> actual = ArgumentCaptor.forClass(ValueType.class);
+		ArgumentCaptor<ScalarType> expectedScalar = ArgumentCaptor.forClass(ScalarType.class);
+		ArgumentCaptor<ScalarType> actualScalar = ArgumentCaptor.forClass(ScalarType.class);
+		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalar.capture(), actual.capture(), actualScalar.capture());
+		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR), actualScalar.capture());
+		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR), actualScalar.capture());
+		verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR), actualScalar.capture());
+
+		assertEquals("_id", elementName.getAllValues().get(0));
+		assertEquals(ValueType.OBJECT, expected.getAllValues().get(0));
+		assertEquals(ValueType.SCALAR, actual.getAllValues().get(0));
+		assertEquals(null, expectedScalar.getAllValues().get(0));
+		assertEquals(null, actualScalar.getAllValues().get(0));
+	}
+
 	@Test
 	public void testValidateCustomStructure() throws Exception {
 
@@ -2247,72 +2333,6 @@ public class JsonParserDstu3Test {
 		assertTrue(result.isSuccessful());
 	}
 
-	/**
-	 * Test for the url generated based on the server config
-	 */
-	@Test
-	public void testCustomUrlExtension() {
-		final String expected = "{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}";
-
-		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
-		patient.setPetName(new StringType("myName"));
-
-		final IParser jsonParser = ourCtx.newJsonParser();
-		jsonParser.setServerBaseUrl("http://www.example.com");
-
-		final String parsedPatient = jsonParser.encodeResourceToString(patient);
-		System.out.println(parsedPatient);
-		assertEquals(expected, parsedPatient);
-
-		// Parse with string
-		MyPatientWithCustomUrlExtension newPatient = jsonParser.parseResource(MyPatientWithCustomUrlExtension.class, parsedPatient);
-		assertEquals("myName", newPatient.getPetName().getValue());
-
-		// Parse with stream
-		newPatient = jsonParser.parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
-		assertEquals("myName", newPatient.getPetName().getValue());
-
-		//Check no NPE if base server not configure
-		newPatient = ourCtx.newJsonParser().parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
-		assertNull("myName", newPatient.getPetName().getValue());
-		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
-	}
-
-	@Test
-	public void testCustomUrlExtensioninBundle() {
-		final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}";
-
-		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
-		patient.setPetName(new StringType("myName"));
-
-		final Bundle bundle = new Bundle();
-		final BundleEntryComponent entry = new BundleEntryComponent();
-		entry.setResource(patient);
-		bundle.addEntry(entry);
-
-		final IParser jsonParser = ourCtx.newJsonParser();
-		jsonParser.setServerBaseUrl("http://www.example.com");
-
-		final String parsedBundle = jsonParser.encodeResourceToString(bundle);
-		System.out.println(parsedBundle);
-		assertEquals(expected, parsedBundle);
-
-		// Parse with string
-		Bundle newBundle = jsonParser.parseResource(Bundle.class, parsedBundle);
-		assertNotNull(newBundle);
-		assertEquals(1, newBundle.getEntry().size());
-		Patient newPatient = (Patient) newBundle.getEntry().get(0).getResource();
-		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
-
-		// Parse with stream
-		newBundle = jsonParser.parseResource(Bundle.class, new StringReader(parsedBundle));
-		assertNotNull(newBundle);
-		assertEquals(1, newBundle.getEntry().size());
-		newPatient = (Patient) newBundle.getEntry().get(0).getResource();
-		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
-
-	}
-
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
diff --git a/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java b/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
index 081b306aacf..e782d8913c1 100644
--- a/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
+++ b/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
@@ -69,17 +69,1917 @@ import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.util.TestUtil;
 
 public class XmlParserDstu3Test {
-  private static FhirContext ourCtx = FhirContext.forDstu3();
-  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu3Test.class);
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu3Test.class);
+
+	@After
+	public void after() {
+		if (ourCtx == null) {
+			ourCtx = FhirContext.forDstu3();
+		}
+		ourCtx.setNarrativeGenerator(null);
+	}
+
+	/**
+	 * See #544
+	 */
+	@Test
+	public void testBundleStitchReferencesByUuid() throws Exception {
+		Bundle bundle = new Bundle();
+
+		DocumentManifest dm = new DocumentManifest();
+		dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
+		bundle.addEntry().setResource(dm);
+
+		Patient patient = new Patient();
+		patient.addName().setFamily("FAMILY");
+		bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
+		ourLog.info(encoded);
+
+		bundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
+		dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
+
+		assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
+
+		Patient subject = (Patient) dm.getSubject().getResource();
+		assertNotNull(subject);
+		assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
+	}
+
+	@Test
+	public void testBundleWithBinary() {
+
+		String bundle = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <base value=\"http://localhost:52788\"/>\n" +
+				"   <total value=\"1\"/>\n" +
+				"   <link>\n" +
+				"      <relation value=\"self\"/>\n" +
+				"      <url value=\"http://localhost:52788/Binary?_pretty=true\"/>\n" +
+				"   </link>\n" +
+				"   <entry>\n" +
+				"      <resource>\n" +
+				"         <Binary xmlns=\"http://hl7.org/fhir\">\n" +
+				"            <id value=\"1\"/>\n" +
+				"            <meta/>\n" +
+				"            <contentType value=\"text/plain\"/>\n" +
+				"            <content value=\"AQIDBA==\"/>\n" +
+				"         </Binary>\n" +
+				"      </resource>\n" +
+				"   </entry>\n" +
+				"</Bundle>";
+
+		Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, bundle);
+		assertEquals(1, b.getEntry().size());
+
+		Binary bin = (Binary) b.getEntry().get(0).getResource();
+		assertArrayEquals(new byte[] { 1, 2, 3, 4 }, bin.getContent());
+
+	}
+
+	@Test
+	public void testContainedResourceInExtensionUndeclared() {
+		Patient p = new Patient();
+		p.addName().setFamily("PATIENT");
+
+		Organization o = new Organization();
+		o.setName("ORG");
+		p.addExtension(new Extension("urn:foo", new Reference(o)));
+
+		String str = ourCtx.newXmlParser().encodeResourceToString(p);
+		ourLog.info(str);
+
+		p = ourCtx.newXmlParser().parseResource(Patient.class, str);
+		assertEquals("PATIENT", p.getName().get(0).getFamily());
+
+		List<Extension> exts = p.getExtensionsByUrl("urn:foo");
+		assertEquals(1, exts.size());
+		Reference rr = (Reference) exts.get(0).getValue();
+		o = (Organization) rr.getResource();
+		assertEquals("ORG", o.getName());
+	}
+
+	@Test(expected = DataFormatException.class)
+	public void testContainedResourceWithNoId() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+		parser.parseResource(Bundle.class, string);
+	}
+
+	@Test()
+	public void testContainedResourceWithNoIdLenient() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new LenientErrorHandler());
+		parser.parseResource(Bundle.class, string);
+	}
+
+	/**
+	 * Test for the url generated based on the server config
+	 */
+	@Test
+	public void testCustomUrlExtension() {
+		final String expected = "<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://www.example.com/petname\"><valueString value=\"myName\"/></extension></Patient>";
+
+		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+		patient.setPetName(new StringType("myName"));
+
+		final IParser xmlParser = ourCtx.newXmlParser();
+		xmlParser.setServerBaseUrl("http://www.example.com");
+
+		final String parsedPatient = xmlParser.encodeResourceToString(patient);
+		System.out.println(parsedPatient);
+		assertEquals(expected, parsedPatient);
+
+		// Parse with string
+		MyPatientWithCustomUrlExtension newPatient = xmlParser.parseResource(MyPatientWithCustomUrlExtension.class, parsedPatient);
+		assertEquals("myName", newPatient.getPetName().getValue());
+
+		// Parse with stream
+		newPatient = xmlParser.parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
+		assertEquals("myName", newPatient.getPetName().getValue());
+
+		// Check no NPE if base server not configure
+		newPatient = ourCtx.newXmlParser().parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
+		assertNull("myName", newPatient.getPetName().getValue());
+		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
+	}
+
+	@Test
+	public void testCustomUrlExtensioninBundle() {
+		final String expected = "<Bundle xmlns=\"http://hl7.org/fhir\"><entry><resource><Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://www.example.com/petname\"><valueString value=\"myName\"/></extension></Patient></resource></entry></Bundle>";
+
+		final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
+		patient.setPetName(new StringType("myName"));
+
+		final Bundle bundle = new Bundle();
+		final BundleEntryComponent entry = new BundleEntryComponent();
+		entry.setResource(patient);
+		bundle.addEntry(entry);
+
+		final IParser xmlParser = ourCtx.newXmlParser();
+		xmlParser.setServerBaseUrl("http://www.example.com");
+
+		final String parsedBundle = xmlParser.encodeResourceToString(bundle);
+		System.out.println(parsedBundle);
+		assertEquals(expected, parsedBundle);
+
+		// Parse with string
+		Bundle newBundle = xmlParser.parseResource(Bundle.class, parsedBundle);
+		assertNotNull(newBundle);
+		assertEquals(1, newBundle.getEntry().size());
+		Patient newPatient = (Patient) newBundle.getEntry().get(0).getResource();
+		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
+
+		// Parse with stream
+		newBundle = xmlParser.parseResource(Bundle.class, new StringReader(parsedBundle));
+		assertNotNull(newBundle);
+		assertEquals(1, newBundle.getEntry().size());
+		newPatient = (Patient) newBundle.getEntry().get(0).getResource();
+		assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
+
+	}
+
+	@Test
+	public void testDuration() {
+		Encounter enc = new Encounter();
+		Duration duration = new Duration();
+		duration.setUnit("day").setValue(123L);
+		enc.setLength(duration);
+
+		String str = ourCtx.newXmlParser().encodeResourceToString(enc);
+		ourLog.info(str);
+
+		assertThat(str, not(containsString("meta")));
+		assertThat(str, containsString("<length><value value=\"123\"/><unit value=\"day\"/></length>"));
+	}
+
+	@Test
+	public void testEncodeAndParseBundleWithResourceRefs() {
+
+		Patient pt = new Patient();
+		pt.setId("patid");
+		pt.addName().setFamily("PATIENT");
+
+		Organization org = new Organization();
+		org.setId("orgid");
+		org.setName("ORG");
+		pt.getManagingOrganization().setResource(org);
+
+		Bundle bundle = new Bundle();
+		bundle.addEntry().setResource(pt);
+		bundle.addEntry().setResource(org);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder(
+				"<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<managingOrganization>",
+				"<reference value=\"Organization/orgid\"/>",
+				"</managingOrganization>"));
+
+		bundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
+		pt = (Patient) bundle.getEntry().get(0).getResource();
+		org = (Organization) bundle.getEntry().get(1).getResource();
+
+		assertEquals("Organization/orgid", org.getIdElement().getValue());
+		assertEquals("Organization/orgid", pt.getManagingOrganization().getReferenceElement().getValue());
+		assertSame(org, pt.getManagingOrganization().getResource());
+	}
+
+	@Test
+	public void testEncodeAndParseCompositeExtension() {
+		PatientWithCustomCompositeExtension pat = new PatientWithCustomCompositeExtension();
+		pat.setId("123");
+		pat.setFooParentExtension(new FooParentExtension());
+		pat.getFooParentExtension().setChildA(new StringType("ValueA"));
+		pat.getFooParentExtension().setChildB(new StringType("ValueB"));
+
+		String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(pat);
+		ourLog.info(enc);
+
+		pat = ourCtx.newXmlParser().parseResource(PatientWithCustomCompositeExtension.class, enc);
+
+		assertEquals("ValueA", pat.getFooParentExtension().getChildA().getValue());
+		assertEquals("ValueB", pat.getFooParentExtension().getChildB().getValue());
+	}
+
+	@Test
+	public void testEncodeAndParseContained() {
+		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
+
+		// Create an organization, note that the organization does not have an ID
+		Organization org = new Organization();
+		org.getNameElement().setValue("Contained Test Organization");
+
+		// Create a patient
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
+
+		// Put the organization as a reference in the patient resource
+		patient.getManagingOrganization().setResource(org);
+
+		String encoded = xmlParser.encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, containsString("<contained>"));
+		assertThat(encoded, containsString("<reference value=\"#1\"/>"));
+
+		// Create a bundle with just the patient resource
+		Bundle b = new Bundle();
+		b.addEntry().setResource(patient);
+
+		// Encode the bundle
+		encoded = xmlParser.encodeResourceToString(b);
+		ourLog.info(encoded);
+		assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<id value=\"1\"/>", "</contained>")));
+		assertThat(encoded, containsString("<reference value=\"#1\"/>"));
+		assertThat(encoded, stringContainsInOrder(Arrays.asList("<entry>", "</entry>")));
+		assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<entry>", "</entry>", "<entry>"))));
+
+		// Re-parse the bundle
+		patient = (Patient) xmlParser.parseResource(xmlParser.encodeResourceToString(patient));
+		assertEquals("#1", patient.getManagingOrganization().getReference());
+
+		assertNotNull(patient.getManagingOrganization().getResource());
+		org = (Organization) patient.getManagingOrganization().getResource();
+		assertEquals("#1", org.getIdElement().getValue());
+		assertEquals("Contained Test Organization", org.getName());
+
+		// And re-encode a second time
+		encoded = xmlParser.encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<Organization ", "<id value=\"1\"/>", "</Organization", "</contained>", "<reference value=\"#1\"/>")));
+		assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<contained>", "<Org", "<contained>"))));
+		assertThat(encoded, containsString("<reference value=\"#1\"/>"));
+
+		// And re-encode once more, with the references cleared
+		patient.getContained().clear();
+		patient.getManagingOrganization().setReference((String) null);
+		encoded = xmlParser.encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<Organization ", "<id value=\"1\"/>", "</Organization", "</contained>", "<reference value=\"#1\"/>")));
+		assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<contained>", "<Org", "<contained>"))));
+		assertThat(encoded, containsString("<reference value=\"#1\"/>"));
+
+		// And re-encode once more, with the references cleared and a manually set local ID
+		patient.getContained().clear();
+		patient.getManagingOrganization().setReference((String) null);
+		patient.getManagingOrganization().getResource().setId(("#333"));
+		encoded = xmlParser.encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<Organization ", "<id value=\"333\"/>", "</Organization", "</contained>", "<reference value=\"#333\"/>")));
+		assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<contained>", "<Org", "<contained>"))));
+
+	}
+
+	@Test
+	public void testEncodeAndParseContainedCustomTypes() {
+		ourCtx = FhirContext.forDstu3();
+		ourCtx.setDefaultTypeForProfile(CustomObservation.PROFILE, CustomObservation.class);
+		ourCtx.setDefaultTypeForProfile(CustomDiagnosticReport.PROFILE, CustomDiagnosticReport.class);
+
+		CustomObservation obs = new CustomObservation();
+		obs.setStatus(ObservationStatus.FINAL);
+
+		CustomDiagnosticReport dr = new CustomDiagnosticReport();
+		dr.setStatus(DiagnosticReportStatus.FINAL);
+		dr.addResult().setResource(obs);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setPrettyPrint(true);
+
+		String output = parser.encodeResourceToString(dr);
+		ourLog.info(output);
+
+		assertThat(output, stringContainsInOrder(
+				"<DiagnosticReport xmlns=\"http://hl7.org/fhir\">",
+				"<meta>",
+				"<profile value=\"http://custom_DiagnosticReport\"/>",
+				"</meta>",
+				"<contained>",
+				"<Observation xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"1\"/>",
+				"<meta>",
+				"<profile value=\"http://custom_Observation\"/>",
+				"</meta>",
+				"<status value=\"final\"/>",
+				"</Observation>",
+				"</contained>",
+				"<status value=\"final\"/>",
+				"<result>",
+				"<reference value=\"#1\"/>",
+				"</result>",
+				"</DiagnosticReport>"));
+
+		/*
+		 * Now PARSE!
+		 */
+
+		dr = (CustomDiagnosticReport) parser.parseResource(output);
+		assertEquals(DiagnosticReportStatus.FINAL, dr.getStatus());
+
+		assertEquals("#1", dr.getResult().get(0).getReference());
+		obs = (CustomObservation) dr.getResult().get(0).getResource();
+		assertEquals(ObservationStatus.FINAL, obs.getStatus());
+
+		ourCtx = null;
+	}
+
+	@Test
+	public void testEncodeAndParseContainedNonCustomTypes() {
+		ourCtx = FhirContext.forDstu3();
+
+		Observation obs = new Observation();
+		obs.setStatus(ObservationStatus.FINAL);
+
+		DiagnosticReport dr = new DiagnosticReport();
+		dr.setStatus(DiagnosticReportStatus.FINAL);
+		dr.addResult().setResource(obs);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setPrettyPrint(true);
+
+		String output = parser.encodeResourceToString(dr);
+		ourLog.info(output);
+
+		assertThat(output, stringContainsInOrder(
+				"<DiagnosticReport xmlns=\"http://hl7.org/fhir\">",
+				"<contained>",
+				"<Observation xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"1\"/>",
+				"<status value=\"final\"/>",
+				"</Observation>",
+				"</contained>",
+				"<status value=\"final\"/>",
+				"<result>",
+				"<reference value=\"#1\"/>",
+				"</result>",
+				"</DiagnosticReport>"));
+
+		/*
+		 * Now PARSE!
+		 */
+
+		dr = (DiagnosticReport) parser.parseResource(output);
+		assertEquals(DiagnosticReportStatus.FINAL, dr.getStatus());
+
+		assertEquals("#1", dr.getResult().get(0).getReference());
+		obs = (Observation) dr.getResult().get(0).getResource();
+		assertEquals(ObservationStatus.FINAL, obs.getStatus());
+
+		ourCtx = null;
+	}
+
+	@Test
+	public void testEncodeAndParseExtensionOnCode() {
+		Organization o = new Organization();
+		o.setName("ORG");
+		o.addExtension(new Extension("urn:foo", new CodeType("acode")));
+
+		String str = ourCtx.newXmlParser().encodeResourceToString(o);
+		ourLog.info(str);
+		assertThat(str, containsString("<valueCode value=\"acode\"/>"));
+
+		o = ourCtx.newXmlParser().parseResource(Organization.class, str);
+
+		List<Extension> exts = o.getExtensionsByUrl("urn:foo");
+		assertEquals(1, exts.size());
+		CodeType code = (CodeType) exts.get(0).getValue();
+		assertEquals("acode", code.getValue());
+
+	}
+
+	@Test
+	public void testEncodeAndParseExtensionOnReference() {
+		DataElement de = new DataElement();
+		ElementDefinitionBindingComponent b = de.addElement().getBinding();
+		b.setDescription("BINDING");
+
+		Organization o = new Organization();
+		o.setName("ORG");
+		b.addExtension(new Extension("urn:foo", new Reference(o)));
+
+		String str = ourCtx.newXmlParser().encodeResourceToString(de);
+		ourLog.info(str);
+
+		de = ourCtx.newXmlParser().parseResource(DataElement.class, str);
+		b = de.getElement().get(0).getBinding();
+		assertEquals("BINDING", b.getDescription());
+
+		List<Extension> exts = b.getExtensionsByUrl("urn:foo");
+		assertEquals(1, exts.size());
+		Reference rr = (Reference) exts.get(0).getValue();
+		o = (Organization) rr.getResource();
+		assertEquals("ORG", o.getName());
+
+	}
+
+	@Test
+	public void testEncodeAndParseExtensions() throws Exception {
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setUse(IdentifierUse.OFFICIAL).setSystem("urn:example").setValue("7000135");
+
+		Extension ext = new Extension();
+		ext.setUrl("http://example.com/extensions#someext");
+		ext.setValue(new DateTimeType("2011-01-02T11:13:15"));
+		patient.addExtension(ext);
+
+		Extension parent = new Extension().setUrl("http://example.com#parent");
+		patient.addExtension(parent);
+		Extension child1 = new Extension().setUrl("http://example.com#child").setValue(new StringType("value1"));
+		parent.addExtension(child1);
+		Extension child2 = new Extension().setUrl("http://example.com#child").setValue(new StringType("value2"));
+		parent.addExtension(child2);
+
+		Extension modExt = new Extension();
+		modExt.setUrl("http://example.com/extensions#modext");
+		modExt.setValue(new DateType("1995-01-02"));
+		patient.addModifierExtension(modExt);
+
+		HumanName name = patient.addName();
+		name.setFamily("Blah");
+		StringType given = name.addGivenElement();
+		given.setValue("Joe");
+		Extension ext2 = new Extension().setUrl("http://examples.com#givenext").setValue(new StringType("given"));
+		given.addExtension(ext2);
+
+		StringType given2 = name.addGivenElement();
+		given2.setValue("Shmoe");
+		Extension given2ext = new Extension().setUrl("http://examples.com#givenext_parent");
+		given2.addExtension(given2ext);
+		given2ext.addExtension(new Extension().setUrl("http://examples.com#givenext_child").setValue(new StringType("CHILD")));
+
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(output);
+
+		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
+		assertThat(enc, containsString("<modifierExtension url=\"http://example.com/extensions#modext\"><valueDate value=\"1995-01-02\"/></modifierExtension>"));
+		assertThat(enc, containsString(
+				"<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
+		assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
+		assertThat(enc, containsString(
+				"<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
+
+		/*
+		 * Now parse this back
+		 */
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, enc);
+		ext = parsed.getExtension().get(0);
+		assertEquals("http://example.com/extensions#someext", ext.getUrl());
+		assertEquals("2011-01-02T11:13:15", ((DateTimeType) ext.getValue()).getValueAsString());
+
+		parent = patient.getExtension().get(1);
+		assertEquals("http://example.com#parent", parent.getUrl());
+		assertNull(parent.getValue());
+		child1 = parent.getExtension().get(0);
+		assertEquals("http://example.com#child", child1.getUrl());
+		assertEquals("value1", ((StringType) child1.getValue()).getValueAsString());
+		child2 = parent.getExtension().get(1);
+		assertEquals("http://example.com#child", child2.getUrl());
+		assertEquals("value2", ((StringType) child2.getValue()).getValueAsString());
+
+		modExt = parsed.getModifierExtension().get(0);
+		assertEquals("http://example.com/extensions#modext", modExt.getUrl());
+		assertEquals("1995-01-02", ((DateType) modExt.getValue()).getValueAsString());
+
+		name = parsed.getName().get(0);
+
+		ext2 = name.getGiven().get(0).getExtension().get(0);
+		assertEquals("http://examples.com#givenext", ext2.getUrl());
+		assertEquals("given", ((StringType) ext2.getValue()).getValueAsString());
+
+		given2ext = name.getGiven().get(1).getExtension().get(0);
+		assertEquals("http://examples.com#givenext_parent", given2ext.getUrl());
+		assertNull(given2ext.getValue());
+		Extension given2ext2 = given2ext.getExtension().get(0);
+		assertEquals("http://examples.com#givenext_child", given2ext2.getUrl());
+		assertEquals("CHILD", ((StringType) given2ext2.getValue()).getValue());
+
+	}
+
+	/**
+	 * See #216
+	 */
+	@Test
+	public void testEncodeAndParseIdentifierDstu2() {
+		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(new CodeableConcept().addCoding(new Coding().setSystem("http://hl7.org/fhir/v2/0203").setCode("MR")));
+
+		String out = xmlParser.encodeResourceToString(patient);
+		ourLog.info(out);
+
+		assertThat(out, stringContainsInOrder("<identifier>",
+				"<type>",
+				"<coding>",
+				"<system value=\"http://hl7.org/fhir/v2/0203\"/>",
+				"<code value=\"MR\"/>",
+				"</coding>",
+				"</type>",
+				"<system value=\"SYS\"/>",
+				"<value value=\"VAL\"/>",
+				"</identifier>"));
+
+		patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
+		assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
+		assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
+	}
+
+	/**
+	 * See #347
+	 */
+	@Test
+	public void testEncodeAndParseMedicationRequest() {
+		MedicationRequest mo = new MedicationRequest();
+		mo.getAuthoredOnElement().setValueAsString("2015-10-05");
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(mo);
+		ourLog.info(encoded);
+
+		mo = ourCtx.newXmlParser().parseResource(MedicationRequest.class, encoded);
+		assertEquals("2015-10-05", mo.getAuthoredOnElement().getValueAsString());
+	}
+
+	@Test
+	public void testEncodeAndParseMetaProfileAndTags() {
+		Patient p = new Patient();
+		p.addName().setFamily("FAMILY");
+
+		p.getMeta().addProfile("http://foo/Profile1");
+		p.getMeta().addProfile("http://foo/Profile2");
+
+		p.getMeta().addTag().setSystem("scheme1").setCode("term1").setDisplay("label1");
+		p.getMeta().addTag().setSystem("scheme2").setCode("term2").setDisplay("label2");
+
+		p.getMeta().addSecurity().setSystem("sec_scheme1").setCode("sec_term1").setDisplay("sec_label1");
+		p.getMeta().addSecurity().setSystem("sec_scheme2").setCode("sec_term2").setDisplay("sec_label2");
+
+		String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(enc);
+
+		assertThat(enc, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<meta>",
+				"<meta>",
+				"<profile value=\"http://foo/Profile1\"/>",
+				"<profile value=\"http://foo/Profile2\"/>",
+				"<tag>",
+				"<system value=\"scheme1\"/>",
+				"<code value=\"term1\"/>",
+				"<display value=\"label1\"/>",
+				"</tag>",
+				"<tag>",
+				"<system value=\"scheme2\"/>",
+				"<code value=\"term2\"/>",
+				"<display value=\"label2\"/>",
+				"</tag>",
+				"</meta>",
+				"</meta>",
+				"<name>",
+				"<family value=\"FAMILY\"/>",
+				"</name>",
+				"</Patient>"));
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, enc);
+		List<UriType> gotLabels = parsed.getMeta().getProfile();
+		assertEquals(2, gotLabels.size());
+		UriType label = gotLabels.get(0);
+		assertEquals("http://foo/Profile1", label.getValue());
+		label = gotLabels.get(1);
+		assertEquals("http://foo/Profile2", label.getValue());
+
+		List<Coding> tagList = parsed.getMeta().getTag();
+		assertEquals(2, tagList.size());
+		assertEquals("scheme1", tagList.get(0).getSystem());
+		assertEquals("term1", tagList.get(0).getCode());
+		assertEquals("label1", tagList.get(0).getDisplay());
+		assertEquals("scheme2", tagList.get(1).getSystem());
+		assertEquals("term2", tagList.get(1).getCode());
+		assertEquals("label2", tagList.get(1).getDisplay());
+
+		tagList = parsed.getMeta().getSecurity();
+		assertEquals(2, tagList.size());
+		assertEquals("sec_scheme1", tagList.get(0).getSystem());
+		assertEquals("sec_term1", tagList.get(0).getCode());
+		assertEquals("sec_label1", tagList.get(0).getDisplay());
+		assertEquals("sec_scheme2", tagList.get(1).getSystem());
+		assertEquals("sec_term2", tagList.get(1).getCode());
+		assertEquals("sec_label2", tagList.get(1).getDisplay());
+	}
+
+	@Test
+	public void testEncodeAndParseMetaProfiles() {
+		Patient p = new Patient();
+		p.addName().setFamily("FAMILY");
+
+		p.getMeta().addTag().setSystem("scheme1").setCode("term1").setDisplay("label1");
+		p.getMeta().addTag().setSystem("scheme2").setCode("term2").setDisplay("label2");
+
+		String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(enc);
+
+		assertThat(enc, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<meta>",
+				"<meta>",
+				"<tag>",
+				"<system value=\"scheme1\"/>",
+				"<code value=\"term1\"/>",
+				"<display value=\"label1\"/>",
+				"</tag>",
+				"<tag>",
+				"<system value=\"scheme2\"/>",
+				"<code value=\"term2\"/>",
+				"<display value=\"label2\"/>",
+				"</tag>",
+				"</meta>",
+				"</meta>",
+				"<name>",
+				"<family value=\"FAMILY\"/>",
+				"</name>",
+				"</Patient>"));
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, enc);
+		assertThat(parsed.getMeta().getProfile(), empty());
+
+		List<Coding> tagList = parsed.getMeta().getTag();
+		assertEquals(2, tagList.size());
+		assertEquals("scheme1", tagList.get(0).getSystem());
+		assertEquals("term1", tagList.get(0).getCode());
+		assertEquals("label1", tagList.get(0).getDisplay());
+		assertEquals("scheme2", tagList.get(1).getSystem());
+		assertEquals("term2", tagList.get(1).getCode());
+		assertEquals("label2", tagList.get(1).getDisplay());
+	}
+
+	/**
+	 * See #336
+	 */
+	@Test
+	public void testEncodeAndParseNullPrimitiveWithExtensions() {
+
+		Patient p = new Patient();
+		p.setId("patid");
+		HumanName name = p.addName();
+		name.addGivenElement().setValue(null).setId("f0").addExtension(new Extension("http://foo", new StringType("FOOEXT0")));
+		name.addGivenElement().setValue("V1").setId("f1").addExtension((Extension) new Extension("http://foo", new StringType("FOOEXT1")).setId("ext1id"));
+		name.addGivenElement(); // this one shouldn't get encoded
+		name.addGivenElement().setValue(null).addExtension(new Extension("http://foo", new StringType("FOOEXT3")));
+		name.setId("nameid");
+
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(output);
+
+		output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
+		String expected = "<Patient xmlns=\"http://hl7.org/fhir\"><id value=\"patid\"/><name id=\"nameid\"><given id=\"f0\"><extension url=\"http://foo\"><valueString value=\"FOOEXT0\"/></extension></given><given id=\"f1\" value=\"V1\"><extension id=\"ext1id\" url=\"http://foo\"><valueString value=\"FOOEXT1\"/></extension></given><given><extension url=\"http://foo\"><valueString value=\"FOOEXT3\"/></extension></given></name></Patient>";
+
+		ourLog.info("Expected: {}", expected);
+		ourLog.info("Actual  : {}", output);
+
+		assertEquals(expected, output);
+
+		p = ourCtx.newXmlParser().parseResource(Patient.class, output);
+		assertEquals("patid", p.getIdElement().getIdPart());
+
+		name = p.getName().get(0);
+		assertEquals("nameid", name.getId());
+		assertEquals(3, name.getGiven().size());
+
+		assertEquals(null, name.getGiven().get(0).getValue());
+		assertEquals("V1", name.getGiven().get(1).getValue());
+		assertEquals(null, name.getGiven().get(2).getValue());
+
+		assertEquals("f0", name.getGiven().get(0).getId());
+		assertEquals("f1", name.getGiven().get(1).getId());
+		assertEquals(null, name.getGiven().get(2).getId());
+
+		assertEquals(1, name.getGiven().get(0).getExtension().size());
+		assertEquals("http://foo", name.getGiven().get(0).getExtension().get(0).getUrl());
+		assertEquals("FOOEXT0", ((StringType) name.getGiven().get(0).getExtension().get(0).getValue()).getValue());
+		assertEquals(null, name.getGiven().get(0).getExtension().get(0).getId());
+
+		assertEquals(1, name.getGiven().get(1).getExtension().size());
+		assertEquals("http://foo", name.getGiven().get(1).getExtension().get(0).getUrl());
+		assertEquals("FOOEXT1", ((StringType) name.getGiven().get(1).getExtension().get(0).getValue()).getValue());
+		assertEquals("ext1id", name.getGiven().get(1).getExtension().get(0).getId());
+
+		assertEquals(1, name.getGiven().get(2).getExtension().size());
+		assertEquals("http://foo", name.getGiven().get(2).getExtension().get(0).getUrl());
+		assertEquals("FOOEXT3", ((StringType) name.getGiven().get(2).getExtension().get(0).getValue()).getValue());
+		assertEquals(null, name.getGiven().get(2).getExtension().get(0).getId());
+
+	}
+
+	@Test
+	public void testEncodeAndParseProfiledDatatype() {
+		MedicationRequest mo = new MedicationRequest();
+		mo.addDosageInstruction().getTiming().getRepeat().setBounds(new Duration().setCode("code"));
+		String out = ourCtx.newXmlParser().encodeResourceToString(mo);
+		ourLog.info(out);
+		assertThat(out, containsString("</boundsDuration>"));
+
+		mo = ourCtx.newXmlParser().parseResource(MedicationRequest.class, out);
+		Duration duration = (Duration) mo.getDosageInstruction().get(0).getTiming().getRepeat().getBounds();
+		assertEquals("code", duration.getCode());
+	}
+
+	/**
+	 * See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
+	 */
+	@Test
+	public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
+		IParser xmlParser = ourCtx.newXmlParser();
+
+		MedicationStatement ms = new MedicationStatement();
+		ms.addDosage().setDose(new SimpleQuantity().setValue(123));
+
+		String output = xmlParser.encodeResourceToString(ms);
+		assertThat(output, containsString("<doseQuantity><value value=\"123\"/></doseQuantity>"));
+	}
+
+	@Test
+	public void testEncodeAndParseSecurityLabels() {
+		Patient p = new Patient();
+		p.addName().setFamily("FAMILY");
+
+		List<Coding> labels = new ArrayList<Coding>();
+		labels.add(new Coding().setSystem("SYSTEM1").setCode("CODE1").setDisplay("DISPLAY1").setVersion("VERSION1"));
+		labels.add(new Coding().setSystem("SYSTEM2").setCode("CODE2").setDisplay("DISPLAY2").setVersion("VERSION2"));
+		p.getMeta().getSecurity().addAll(labels);
+
+		String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(enc);
+
+		assertThat(enc, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<meta>",
+				"<security>",
+				"<system value=\"SYSTEM1\"/>",
+				"<version value=\"VERSION1\"/>",
+				"<code value=\"CODE1\"/>",
+				"<display value=\"DISPLAY1\"/>",
+				"</security>",
+				"<security>",
+				"<system value=\"SYSTEM2\"/>",
+				"<version value=\"VERSION2\"/>",
+				"<code value=\"CODE2\"/>",
+				"<display value=\"DISPLAY2\"/>",
+				"</security>",
+				"</meta>",
+				"<name>",
+				"<family value=\"FAMILY\"/>",
+				"</name>",
+				"</Patient>"));
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, enc);
+		List<Coding> gotLabels = parsed.getMeta().getSecurity();
+
+		assertEquals(2, gotLabels.size());
+
+		Coding label = gotLabels.get(0);
+		assertEquals("SYSTEM1", label.getSystem());
+		assertEquals("CODE1", label.getCode());
+		assertEquals("DISPLAY1", label.getDisplay());
+		assertEquals("VERSION1", label.getVersion());
+
+		label = gotLabels.get(1);
+		assertEquals("SYSTEM2", label.getSystem());
+		assertEquals("CODE2", label.getCode());
+		assertEquals("DISPLAY2", label.getDisplay());
+		assertEquals("VERSION2", label.getVersion());
+	}
+
+	/**
+	 * See #103
+	 */
+	@Test
+	public void testEncodeAndReEncodeContainedJson() {
+		Composition comp = new Composition();
+		comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section0_Allergy0")));
+		comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section1_Allergy0")));
+		comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section2_Allergy0")));
+
+		IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
+
+		String string = parser.encodeResourceToString(comp);
+		ourLog.info(string);
+
+		Composition parsed = parser.parseResource(Composition.class, string);
+		parsed.getSection().remove(0);
+
+		string = parser.encodeResourceToString(parsed);
+		ourLog.info(string);
+
+		parsed = parser.parseResource(Composition.class, string);
+		assertEquals(2, parsed.getContained().size());
+	}
+
+	/**
+	 * See #103
+	 */
+	@Test
+	public void testEncodeAndReEncodeContainedXml() {
+		Composition comp = new Composition();
+		comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section0_Allergy0")));
+		comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section1_Allergy0")));
+		comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section2_Allergy0")));
+
+		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
+
+		String string = parser.encodeResourceToString(comp);
+		ourLog.info(string);
+
+		Composition parsed = parser.parseResource(Composition.class, string);
+		parsed.getSection().remove(0);
+
+		string = parser.encodeResourceToString(parsed);
+		ourLog.info(string);
+
+		parsed = parser.parseResource(Composition.class, string);
+		assertEquals(2, parsed.getContained().size());
+	}
+
+	@Test
+	public void testEncodeBinaryWithNoContentType() {
+		Binary b = new Binary();
+		b.setContent(new byte[] { 1, 2, 3, 4 });
+
+		String output = ourCtx.newXmlParser().encodeResourceToString(b);
+		ourLog.info(output);
+
+		assertEquals("<Binary xmlns=\"http://hl7.org/fhir\"><content value=\"AQIDBA==\"/></Binary>", output);
+	}
+
+	@Test
+	public void testEncodeBundleWithContained() {
+		DiagnosticReport rpt = new DiagnosticReport();
+		rpt.addResult().setResource(new Observation().setCode(new CodeableConcept().setText("Sharp1")).setId("#1"));
+		rpt.addResult().setResource(new Observation().setCode(new CodeableConcept().setText("Uuid1")).setId("urn:uuid:UUID1"));
+
+		Bundle b = new Bundle();
+		b.addEntry().setResource(rpt);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder("<DiagnosticReport", "<contained", "<Observation", "<text value=\"Sharp1\"", "</DiagnosticReport"));
+		assertThat(encoded, not(stringContainsInOrder("<DiagnosticReport", "<contained", "<Observation", "<contained", "<Observation", "</DiagnosticReport")));
+	}
+
+	@Test
+	public void testEncodeChainedContainedResourcer() {
+		Organization gp = new Organization();
+		gp.setName("grandparent");
+
+		Organization parent = new Organization();
+		parent.setName("parent");
+		parent.getPartOf().setResource(gp);
+
+		Organization child = new Organization();
+		child.setName("child");
+		child.getPartOf().setResource(parent);
+
+		Patient patient = new Patient();
+		patient.getManagingOrganization().setResource(child);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		patient = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
+
+		child = (Organization) patient.getManagingOrganization().getResource();
+		assertEquals("child", child.getName());
+
+		parent = (Organization) child.getPartOf().getResource();
+		assertEquals("parent", parent.getName());
+
+		gp = (Organization) parent.getPartOf().getResource();
+		assertEquals("grandparent", gp.getName());
+	}
+
+	/**
+	 * See #326
+	 */
+	@Test
+	public void testEncodeContainedResource() {
+		Patient patient = new Patient();
+		patient.getBirthDateElement().setValueAsString("2016-04-05");
+		patient.addExtension().setUrl("test").setValue(new Reference(new Condition()));
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder(
+				"<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<contained>",
+				"<Condition xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"1\"/>",
+				"</Condition>",
+				"</contained>",
+				"<extension url=\"test\">",
+				"<valueReference>",
+				"<reference value=\"#1\"/>",
+				"</valueReference>",
+				"</extension>",
+				"<birthDate value=\"2016-04-05\"/>",
+				"</Patient>"));
+
+	}
+
+	/**
+	 * See #113
+	 */
+	@Test
+	public void testEncodeContainedResources() {
+
+		MedicationRequest medicationPrescript = new MedicationRequest();
+
+		String medId = "123";
+		CodeableConcept codeDt = new CodeableConcept().addCoding(new Coding().setSystem("urn:sys").setCode("code1"));
+
+		// Adding medication to Contained.
+		Medication medResource = new Medication();
+		medResource.setCode(codeDt);
+		medResource.setId("#" + String.valueOf(medId));
+		medicationPrescript.getContained().add(medResource);
+
+		// Medication reference. This should point to the contained resource.
+		Reference medRefDt = new Reference("#" + medId);
+		medRefDt.setDisplay("MedRef");
+		medicationPrescript.setMedication(medRefDt);
+
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String encoded = p.encodeResourceToString(medicationPrescript);
+		ourLog.info(encoded);
+
+		// @formatter:on
+		assertThat(encoded,
+				stringContainsInOrder("<MedicationRequest xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
+						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
+						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationRequest>"));
+
+	}
+
+	/**
+	 * See #113
+	 */
+	@Test
+	public void testEncodeContainedResourcesAutomatic() {
+
+		MedicationRequest medicationPrescript = new MedicationRequest();
+		String nameDisp = "MedRef";
+		CodeableConcept codeDt = new CodeableConcept().addCoding(new Coding("urn:sys", "code1", null));
+
+		// Adding medication to Contained.
+		Medication medResource = new Medication();
+		// No ID set
+		medResource.setCode(codeDt);
+
+		// Medication reference. This should point to the contained resource.
+		Reference medRefDt = new Reference();
+		medRefDt.setDisplay(nameDisp);
+		// Resource reference set, but no ID
+		medRefDt.setResource(medResource);
+		medicationPrescript.setMedication(medRefDt);
+
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String encoded = p.encodeResourceToString(medicationPrescript);
+		ourLog.info(encoded);
+
+		assertThat(encoded,
+				stringContainsInOrder("<MedicationRequest xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>",
+						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>",
+						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationRequest>"));
+
+	}
+
+	/**
+	 * See #113
+	 */
+	@Test
+	public void testEncodeContainedResourcesManualContainUsingNonLocalId() {
+
+		MedicationRequest medicationPrescript = new MedicationRequest();
+
+		String medId = "123";
+		CodeableConcept codeDt = new CodeableConcept().addCoding(new Coding("urn:sys", "code1", null));
+
+		// Adding medication to Contained.
+		Medication medResource = new Medication();
+		medResource.setCode(codeDt);
+		medResource.setId(String.valueOf(medId)); // ID does not start with '#'
+		medicationPrescript.getContained().add(medResource);
+
+		// Medication reference. This should point to the contained resource.
+		Reference medRefDt = new Reference("#" + medId);
+		medRefDt.setDisplay("MedRef");
+		medicationPrescript.setMedication(medRefDt);
+
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String encoded = p.encodeResourceToString(medicationPrescript);
+		ourLog.info(encoded);
+
+		assertThat(encoded,
+				stringContainsInOrder("<MedicationRequest xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
+						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
+						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationRequest>"));
+
+	}
+
+	@Test
+	public void testEncodeContainedWithNarrativeIsSuppresed() throws Exception {
+		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
+
+		// Create an organization, note that the organization does not have an ID
+		Organization org = new Organization();
+		org.getNameElement().setValue("Contained Test Organization");
+		org.getText().setDivAsString("<div>FOOBAR</div>");
+
+		// Create a patient
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
+		patient.getText().setDivAsString("<div>BARFOO</div>");
+		patient.getManagingOrganization().setResource(org);
+
+		String encoded = parser.encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder("<Patient", "<text>", "<div xmlns=\"http://www.w3.org/1999/xhtml\">BARFOO</div>", "<contained>", "<Organization", "</Organization"));
+		assertThat(encoded, not(stringContainsInOrder("<Patient", "<text>", "<contained>", "<Organization", "<text", "</Organization")));
+
+		assertThat(encoded, not(containsString("FOOBAR")));
+		assertThat(encoded, (containsString("BARFOO")));
+
+	}
+
+	@Test
+	public void testEncodeContainedWithNonLocalId() throws Exception {
+
+		Patient p = new Patient();
+		p.setId("Patient1");
+		p.setBirthDate(new SimpleDateFormat("yyyy-mm-dd HH:mm:ss").parse("2016-04-15 10:15:30"));
+
+		ProcedureRequest pr = new ProcedureRequest();
+		pr.setId("1234567");
+		pr.setSubject(new Reference(p));
+		pr.setCode(new CodeableConcept().addCoding(new Coding("breastfeeding-readiness-assessment", "Breastfeeding Readiness Assessment", "Breastfeeding Readiness Assessment")));
+		// pr.setReason(new StringType("Single Live Birth"));
+		// pr.setScheduled(new DateType(new Date()));
+		pr.setContext(new Reference("Live Birth Encounter"));
+		pr.setPerformer(new Reference("Charge Nurse"));
+		pr.setStatus(ProcedureRequest.ProcedureRequestStatus.DRAFT);
+
+		GuidanceResponse.GuidanceResponseStatus status = GuidanceResponse.GuidanceResponseStatus.SUCCESS;
+
+		GuidanceResponse gr = new GuidanceResponse()
+				.setRequestId("123")
+				.setModule(new Reference("Evaluate Operation"))
+				.setStatus(status);
+
+		gr.setReason(new Reference(pr));
+		gr.getContained().add(p);
+		gr.getContained().add(pr);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setPrettyPrint(true);
+		ourLog.info(parser.encodeResourceToString(gr));
+	}
+
+	@Test
+	public void testEncodeDeclaredBlock() throws Exception {
+		FooMessageSourceComponent source = new FooMessageHeaderWithExplicitField.FooMessageSourceComponent();
+		source.getMessageHeaderApplicationId().setValue("APPID");
+		source.setName("NAME");
+
+		FooMessageHeaderWithExplicitField header = new FooMessageHeaderWithExplicitField();
+		header.setSourceNew(source);
+
+		header.addDestination().setName("DEST");
+
+		Bundle bundle = new Bundle();
+		bundle.addEntry().setResource(header);
+
+		IParser p = ourCtx.newXmlParser();
+		p.setPrettyPrint(true);
+
+		String encode = p.encodeResourceToString(bundle);
+		ourLog.info(encode);
+
+		assertThat(encode, containsString("<value value=\"APPID\"/>"));
+		assertThat(encode, stringContainsInOrder("<dest", "<source"));
+	}
+
+	/**
+	 * Make sure whitespace is preserved for pre tags
+	 */
+	@Test
+	public void testEncodeDivWithPreNonPrettyPrint() {
+
+		Patient p = new Patient();
+		p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
+
+		String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
+		ourLog.info(output);
+
+		assertThat(output, stringContainsInOrder(
+				"<text><div",
+				"<p>A P TAG</p><p>",
+				"<pre>line1\nline2\nline3  <b>BOLD</b></pre>"));
+
+	}
+
+	@Test
+	public void testEncodeDivWithPrePrettyPrint() {
+
+		Patient p = new Patient();
+		p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
+
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(output);
+
+		assertThat(output, stringContainsInOrder(
+				"   <text>",
+				"      <div",
+				"         <pre>line1\nline2\nline3  <b>BOLD</b></pre>"));
+
+	}
+
+	@Test
+	public void testEncodeDoesntIncludeUuidId() {
+		Patient p = new Patient();
+		p.setId(new IdType("urn:uuid:42795ed8-041f-4ebf-b6f4-78ef6f64c2f2"));
+		p.addIdentifier().setSystem("ACME");
+
+		String actual = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		assertThat(actual, not(containsString("78ef6f64c2f2")));
+	}
+
+	@Test
+	public void testEncodeEmptyBinary() {
+		String output = ourCtx.newXmlParser().encodeResourceToString(new Binary());
+		assertEquals("<Binary xmlns=\"http://hl7.org/fhir\"/>", output);
+	}
+
+	/**
+	 * #158
+	 */
+	@Test
+	public void testEncodeEmptyTag() {
+		ArrayList<Coding> tagList = new ArrayList<Coding>();
+		tagList.add(new Coding());
+		tagList.add(new Coding().setDisplay("Label"));
+
+		Patient p = new Patient();
+		p.getMeta().getTag().addAll(tagList);
+
+		String encoded = ourCtx.newXmlParser().encodeResourceToString(p);
+		assertThat(encoded, not(containsString("tag")));
+	}
+
+	/**
+	 * #158
+	 */
+	@Test
+	public void testEncodeEmptyTag2() {
+		ArrayList<Coding> tagList = new ArrayList<Coding>();
+		tagList.add(new Coding().setSystem("scheme").setCode("code"));
+		tagList.add(new Coding().setDisplay("Label"));
+
+		Patient p = new Patient();
+		p.getMeta().getTag().addAll(tagList);
+
+		String encoded = ourCtx.newXmlParser().encodeResourceToString(p);
+		assertThat(encoded, containsString("tag"));
+		assertThat(encoded, containsString("scheme"));
+		assertThat(encoded, not(containsString("Label")));
+	}
+
+	@Test
+	public void testEncodeExtensionOnRoot() {
+		Patient p = new Patient();
+		p.setId("Patient/B");
+		p
+				.addExtension()
+				.setUrl("http://foo")
+				.setValue(new Reference("Practitioner/A"));
+		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
+		parser.setDontEncodeElements(new HashSet<String>(Arrays.asList("*.id", "*.meta")));
+
+		String encoded = parser.encodeResourceToString(p);
+		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("http://foo"));
+		assertThat(encoded, containsString("Practitioner/A"));
+	}
+
+	@Test
+	public void testEncodeExtensionUndeclaredNonModifier() {
+		Observation obs = new Observation();
+		obs.setId("1");
+		obs.getMeta().addProfile("http://profile");
+		Extension ext = obs.addExtension();
+		ext.setUrl("http://exturl").setValue(new StringType("ext_url_value"));
+
+		obs.getCode().setText("CODE");
+
+		IParser parser = ourCtx.newXmlParser();
+
+		String output = parser.setPrettyPrint(true).encodeResourceToString(obs);
+		ourLog.info(output);
+
+		assertThat(output, stringContainsInOrder(
+				"<id value=\"1\"/>",
+				"<meta>",
+				"<profile value=\"http://profile\"/>",
+				"<extension url=\"http://exturl\">",
+				"<valueString value=\"ext_url_value\"/>",
+				"<text value=\"CODE\"/>"));
+		assertThat(output, not(stringContainsInOrder(
+				"<url value=\"http://exturl\"/>")));
+
+		obs = parser.parseResource(Observation.class, output);
+		assertEquals(1, obs.getExtension().size());
+		assertEquals("http://exturl", obs.getExtension().get(0).getUrl());
+		assertEquals("ext_url_value", ((StringType) obs.getExtension().get(0).getValue()).getValue());
+	}
+
+	@Test
+	public void testEncodeExtensionUndeclaredNonModifierWithChildExtension() {
+		Observation obs = new Observation();
+		obs.setId("1");
+		obs.getMeta().addProfile("http://profile");
+		Extension ext = obs.addExtension();
+		ext.setUrl("http://exturl");
+
+		Extension subExt = ext.addExtension();
+		subExt.setUrl("http://subext").setValue(new StringType("sub_ext_value"));
+
+		obs.getCode().setText("CODE");
+
+		IParser parser = ourCtx.newXmlParser();
+
+		String output = parser.setPrettyPrint(true).encodeResourceToString(obs);
+		ourLog.info(output);
+
+		assertThat(output, stringContainsInOrder(
+				"<id value=\"1\"/>",
+				"<meta>",
+				"<profile value=\"http://profile\"/>",
+				"<extension url=\"http://exturl\">",
+				"<extension url=\"http://subext\">",
+				"<valueString value=\"sub_ext_value\"/>",
+				"<text value=\"CODE\"/>"));
+		assertThat(output, not(stringContainsInOrder(
+				"<url value=\"http://exturl\"/>")));
+
+		obs = parser.parseResource(Observation.class, output);
+		assertEquals(1, obs.getExtension().size());
+		assertEquals("http://exturl", obs.getExtension().get(0).getUrl());
+		assertEquals(1, obs.getExtension().get(0).getExtension().size());
+		assertEquals("http://subext", obs.getExtension().get(0).getExtension().get(0).getUrl());
+		assertEquals("sub_ext_value", ((StringType) obs.getExtension().get(0).getExtension().get(0).getValue()).getValue());
+	}
+
+	/**
+	 * See #327
+	 */
+	@Test
+	public void testEncodeExtensionWithContainedResource() {
+
+		TestPatientFor327 patient = new TestPatientFor327();
+		patient.setBirthDateElement(new DateType("2016-04-14"));
+
+		List<Reference> conditions = new ArrayList<Reference>();
+		Condition condition = new Condition();
+		condition.addBodySite().setText("BODY SITE");
+		conditions.add(new Reference(condition));
+		patient.setCondition(conditions);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder(
+				"<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<contained>",
+				"<Condition xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"1\"/>",
+				"<bodySite>",
+				"<text value=\"BODY SITE\"/>",
+				"</bodySite>",
+				"</Condition>",
+				"</contained>",
+				"<extension url=\"testCondition\">",
+				"<valueReference>",
+				"<reference value=\"#1\"/>",
+				"</valueReference>",
+				"</extension>",
+				"<birthDate value=\"2016-04-14\"/>",
+				"</Patient>"));
+
+	}
+
+	@Test
+	public void testEncodeExtensionWithResourceContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		Patient patient = new Patient();
+		patient.addAddress().setUse(AddressUse.HOME);
+		patient.addExtension(new Extension("urn:foo", new Reference("Organization/123")));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueReference><reference value=\"Organization/123\"/></valueReference></extension>"));
+
+		Patient actual = parser.parseResource(Patient.class, val);
+		assertEquals(AddressUse.HOME, patient.getAddress().get(0).getUse());
+		List<Extension> ext = actual.getExtension();
+		assertEquals(1, ext.size());
+		Reference ref = (Reference) ext.get(0).getValue();
+		assertEquals("Organization/123", ref.getReference());
+
+	}
+
+	@Test
+	public void testEncodeHistoryEncodeVersionsAtPath3() {
+		ourCtx = FhirContext.forDstu3();
+
+		assertNull(ourCtx.newXmlParser().getStripVersionsFromReferences());
+
+		AuditEvent auditEvent = new AuditEvent();
+		auditEvent.addEntity().setReference(new Reference("http://foo.com/Organization/2/_history/1"));
+
+		IParser parser = ourCtx.newXmlParser();
+
+		parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
+		String enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
+		ourLog.info(enc);
+		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2/_history/1\"/>"));
+
+		parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<String>());
+		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
+		ourLog.info(enc);
+		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
+
+		parser.setDontStripVersionsFromReferencesAtPaths((String[]) null);
+		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
+		ourLog.info(enc);
+		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
+
+		parser.setDontStripVersionsFromReferencesAtPaths((List<String>) null);
+		enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
+		ourLog.info(enc);
+		assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
+
+	}
+
+	@Test
+	public void testEncodeNarrativeSuppressed() {
+		Patient patient = new Patient();
+		patient.setId("Patient/1/_history/1");
+		patient.getText().setDivAsString("<div>THE DIV</div>");
+		patient.addName().setFamily("FAMILY");
+		patient.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode("D")));
+		patient.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode("D")));
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).setSuppressNarratives(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("<Patient"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, not(containsString("text")));
+		assertThat(encoded, not(containsString("THE DIV")));
+		assertThat(encoded, containsString("family"));
+		assertThat(encoded, containsString("maritalStatus"));
+	}
+
+	@Test
+	public void testEncodeNonContained() {
+		// Create an organization
+		Organization org = new Organization();
+		org.setId("Organization/65546");
+		org.getNameElement().setValue("Contained Test Organization");
+
+		// Create a patient
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
+		patient.getManagingOrganization().setResource(org);
+
+		// Create a list containing both resources. In a server method, you might just
+		// return this list, but here we will create a bundle to encode.
+		List<IBaseResource> resources = new ArrayList<IBaseResource>();
+		resources.add(org);
+		resources.add(patient);
+
+		// Create a bundle with both
+		Bundle b = new Bundle();
+		b.addEntry().setResource(org);
+		b.addEntry().setResource(patient);
+
+		// Encode the buntdle
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b);
+		ourLog.info(encoded);
+		assertThat(encoded, not(containsString("<contained>")));
+		assertThat(encoded, stringContainsInOrder("<Organization", "<id value=\"65546\"/>", "</Organization>"));
+		assertThat(encoded, containsString("<reference value=\"Organization/65546\"/>"));
+		assertThat(encoded, stringContainsInOrder("<Patient", "<id value=\"1333\"/>", "</Patient>"));
+
+		encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, not(containsString("<contained>")));
+		assertThat(encoded, containsString("<reference value=\"Organization/65546\"/>"));
+
+	}
+
+	/**
+	 * See #312
+	 */
+	@Test
+	public void testEncodeNullElement() {
+		Patient patient = new Patient();
+		patient.addName().getGiven().add(null);
+
+		IParser parser = ourCtx.newXmlParser();
+		String xml = parser.encodeResourceToString(patient);
+
+		ourLog.info(xml);
+		assertEquals("<Patient xmlns=\"http://hl7.org/fhir\"/>", xml);
+	}
+
+	/**
+	 * See #312
+	 */
+	@Test
+	public void testEncodeNullExtension() {
+		Patient patient = new Patient();
+		patient.getExtension().add(null); // Purposely add null
+		patient.getModifierExtension().add(null); // Purposely add null
+		patient.getExtension().add(new Extension("http://hello.world", new StringType("Hello World")));
+		patient.getName().add(null);
+		patient.addName().getGiven().add(null);
+
+		IParser parser = ourCtx.newXmlParser();
+		String xml = parser.encodeResourceToString(patient);
+
+		ourLog.info(xml);
+		assertEquals("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://hello.world\"><valueString value=\"Hello World\"/></extension></Patient>", xml);
+	}
+
+	@Test
+	public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
+
+		Patient patient = new Patient();
+		patient.setId("phitcc_pat_normal");
+		patient.addName().addGiven("Patty").setUse(NameUse.NICKNAME);
+		patient.addTelecom().setSystem(ContactPointSystem.EMAIL).setValue("patpain@ehealthinnovation.org");
+		patient.setGender(AdministrativeGender.FEMALE);
+		patient.setBirthDateElement(new DateType("2001-10-13"));
+
+		DateTimeType obsEffectiveTime = new DateTimeType("2015-04-11T12:22:01-04:00");
+
+		Observation obsParent = new Observation();
+		obsParent.setId("phitcc_obs_bp_parent");
+		obsParent.getSubject().setResource(patient);
+		obsParent.setStatus(ObservationStatus.FINAL);
+		obsParent.setEffective(obsEffectiveTime);
+
+		Observation obsSystolic = new Observation();
+		obsSystolic.setId("phitcc_obs_bp_dia");
+		obsSystolic.getSubject().setResource(patient);
+		obsSystolic.setEffective(obsEffectiveTime);
+		obsParent.addRelated().setType(ObservationRelationshipType.HASMEMBER).setTarget(new Reference(obsSystolic));
+
+		Observation obsDiastolic = new Observation();
+		obsDiastolic.setId("phitcc_obs_bp_dia");
+		obsDiastolic.getSubject().setResource(patient);
+		obsDiastolic.setEffective(obsEffectiveTime);
+		obsParent.addRelated().setType(ObservationRelationshipType.HASMEMBER).setTarget(new Reference(obsDiastolic));
+
+		String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
+		ourLog.info(str);
+
+		assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
+		assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
+	}
+
+	@Test
+	public void testEncodeReferenceWithUuid() {
+
+		Practitioner pract = new Practitioner();
+		pract.setId(IdType.newRandomUuid());
+		pract.addName().setFamily("PRACT FAMILY");
+
+		Patient patient = new Patient();
+		patient.addGeneralPractitioner().setResource(pract);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		assertThat(pract.getId(), startsWith("urn:uuid:"));
+		assertThat(encoded, containsString("<reference value=\"" + pract.getId() + "\"/>"));
+	}
+
+	@Test
+	public void testEncodeSummary() {
+		Patient patient = new Patient();
+		patient.setId("Patient/1/_history/1");
+		patient.getText().setDivAsString("<div>THE DIV</div>");
+		patient.addName().setFamily("FAMILY");
+		patient.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode("D")));
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).setSummaryMode(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("<Patient"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, not(containsString("THE DIV")));
+		assertThat(encoded, containsString("family"));
+		assertThat(encoded, not(containsString("maritalStatus")));
+	}
+
+	@Test
+	public void testEncodeSummary2() {
+		Patient patient = new Patient();
+		patient.setId("Patient/1/_history/1");
+		patient.getText().setDivAsString("<div>THE DIV</div>");
+		patient.addName().setFamily("FAMILY");
+		patient.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode("D")));
+
+		patient.getMeta().addTag().setSystem("foo").setCode("bar");
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).setSummaryMode(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+
+		assertThat(encoded, containsString("<Patient"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"foo\"/>", "<code value=\"bar\"/>", "</tag>"));
+		assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
+		assertThat(encoded, not(containsString("THE DIV")));
+		assertThat(encoded, containsString("family"));
+		assertThat(encoded, not(containsString("maritalStatus")));
+	}
+
+	@Test
+	public void testEncodeUndeclaredBlock() throws Exception {
+		FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
+		source.getMessageHeaderApplicationId().setValue("APPID");
+		source.setName("NAME");
+
+		FooMessageHeader header = new FooMessageHeader();
+		header.setSource(source);
+
+		header.addDestination().setName("DEST");
+
+		Bundle bundle = new Bundle();
+		bundle.addEntry().setResource(header);
+
+		IParser p = ourCtx.newXmlParser();
+		p.setPrettyPrint(true);
+
+		String encode = p.encodeResourceToString(bundle);
+		ourLog.info(encode);
+
+		assertThat(encode, containsString("<value value=\"APPID\"/>"));
+		assertThat(encode, stringContainsInOrder("<dest", "<source"));
+	}
+
+	@Test
+	public void testEncodeUndeclaredExtensionWithEnumerationContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		Patient patient = new Patient();
+		patient.addAddress().setUse(AddressUse.HOME);
+		EnumFactory<AddressUse> fact = new AddressUseEnumFactory();
+		PrimitiveType<AddressUse> enumeration = new Enumeration<AddressUse>(fact).setValue(AddressUse.HOME);
+		patient.addExtension().setUrl("urn:foo").setValue(enumeration);
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueCode value=\"home\"/></extension>"));
+
+		MyPatientWithOneDeclaredEnumerationExtensionDstu3 actual = parser.parseResource(MyPatientWithOneDeclaredEnumerationExtensionDstu3.class, val);
+		assertEquals(AddressUse.HOME, patient.getAddress().get(0).getUse());
+		Enumeration<AddressUse> ref = actual.getFoo();
+		assertEquals("home", ref.getValue().toCode());
+
+	}
+
+	@Test
+	public void testEncodeWithContained() {
+		List<Resource> contained = new ArrayList<Resource>();
+
+		// Will be added by reference
+		Patient p = new Patient();
+		p.setId("#" + "1000");
+		contained.add(p);
+
+		// Will be added by direct resource object
+		Location l = new Location();
+		l.setId("#" + "1001");
+		contained.add(l);
+
+		// Will not be referred to (and therefore shouldn't appear in output)
+		Location l2 = new Location();
+		l2.setId("#1002");
+		contained.add(l2);
+
+		Appointment appointment = new Appointment();
+		appointment.setId("1234");
+		appointment.getContained().addAll(contained);
+
+		appointment.addParticipant().getActor().setReference("#1000");
+		appointment.addParticipant().getActor().setResource(l);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(appointment);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder(
+				"<Appointment xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"1234\"/>",
+				"<contained>",
+				"<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"1000\"/>",
+				"</Patient>",
+				"</contained>",
+				"<contained>",
+				"<Location xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"1001\"/>",
+				"</Location>",
+				"</contained>",
+				"<participant>",
+				"<actor>",
+				"<reference value=\"#1000\"/>",
+				"</actor>",
+				"</participant>",
+				"<participant>",
+				"<actor>",
+				"<reference value=\"#1001\"/>",
+				"</actor>",
+				"</participant>",
+				"</Appointment>"));
+
+		assertThat(encoded, not(containsString("#1002")));
+	}
+
+	@Test
+	public void testEncodeWithDontEncodeElements() throws Exception {
+		Patient patient = new Patient();
+		patient.setId("123");
+		patient.getMeta().addProfile("http://profile");
+		patient.addName().setFamily("FAMILY").addGiven("GIVEN");
+		patient.addAddress().addLine("LINE1");
+
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta", "Patient.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.name.family"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("GIVEN"));
+			assertThat(out, not(containsString("FAMILY")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("address"));
+			assertThat(out, not(containsString("id")));
+			assertThat(out, not(containsString("meta")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
+			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(patient);
+			ourLog.info(out);
+			assertThat(out, containsString("Patient"));
+			assertThat(out, containsString("name"));
+			assertThat(out, containsString("id"));
+			assertThat(out, not(containsString("address")));
+			assertThat(out, not(containsString("meta")));
+		}
+	}
+
+	@Test
+	public void testEncodeWithEncodeElements() throws Exception {
+		Patient patient = new Patient();
+		patient.getMeta().addProfile("http://profile");
+		patient.addName().setFamily("FAMILY");
+		patient.addAddress().addLine("LINE1");
+
+		Bundle bundle = new Bundle();
+		bundle.setTotal(100);
+		bundle.addEntry().setResource(patient);
+
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(bundle);
+			ourLog.info(out);
+			assertThat(out, not(containsString("total")));
+			assertThat(out, (containsString("Patient")));
+			assertThat(out, (containsString("name")));
+			assertThat(out, not(containsString("address")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(bundle);
+			ourLog.info(out);
+			assertThat(out, (containsString("total")));
+			assertThat(out, (containsString("Patient")));
+			assertThat(out, (containsString("name")));
+			assertThat(out, not(containsString("address")));
+		}
+		{
+			IParser p = ourCtx.newXmlParser();
+			p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
+			p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
+			p.setPrettyPrint(true);
+			String out = p.encodeResourceToString(bundle);
+			ourLog.info(out);
+			assertThat(out, (containsString("total")));
+			assertThat(out, (containsString("Patient")));
+			assertThat(out, (containsString("name")));
+			assertThat(out, (containsString("address")));
+		}
+
+	}
+
+	@Test
+	public void testEncodeWithNarrative() {
+		Patient p = new Patient();
+		p.addName().setFamily("Smith").addGiven("John");
+
+		ourCtx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
+
+		String output = ourCtx.newXmlParser().encodeResourceToString(p);
+		ourLog.info(output);
+
+		assertThat(output, containsString("<text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">John <b>SMITH </b>"));
+	}
+
+	/**
+	 * Test for the url generated based on the server config
+	 */
+	@Test
+	public void testGeneratedUrls() {
+		final IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
+		xmlParser.setServerBaseUrl("http://myserver.com");
+
+		final CustomPatientDstu3 patient = new CustomPatientDstu3();
+		patient.setHomeless(new BooleanType(true));
+
+		final String parsedPatient = xmlParser.encodeResourceToString(patient);
+
+		assertTrue(parsedPatient.contains("<profile value=\"http://myserver.com/StructureDefinition/Patient\"/>"));
+		assertTrue(parsedPatient.contains("<extension url=\"http://myserver.com/StructureDefinition/homeless\">"));
+	}
+
+	@Test
+	public void testMoreExtensions() throws Exception {
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setUse(IdentifierUse.OFFICIAL).setSystem("urn:example").setValue("7000135");
+
+		Extension ext = new Extension();
+		ext.setUrl("http://example.com/extensions#someext");
+		ext.setValue(new DateTimeType("2011-01-02T11:13:15"));
+
+		// Add the extension to the resource
+		patient.addExtension(ext);
+		// END SNIPPET: resourceExtension
+
+		// START SNIPPET: resourceStringExtension
+		HumanName name = patient.addName();
+		name.setFamily("Shmoe");
+		StringType given = name.addGivenElement();
+		given.setValue("Joe");
+		Extension ext2 = new Extension().setUrl("http://examples.com#givenext").setValue(new StringType("given"));
+		given.addExtension(ext2);
+
+		StringType given2 = name.addGivenElement();
+		given2.setValue("Shmoe");
+		Extension given2ext = new Extension().setUrl("http://examples.com#givenext_parent");
+		given2.addExtension(given2ext);
+		Extension givenExtChild = new Extension();
+		givenExtChild.setUrl("http://examples.com#givenext_child").setValue(new StringType("CHILD"));
+		given2ext.addExtension(givenExtChild);
+		// END SNIPPET: resourceStringExtension
+
+		// START SNIPPET: subExtension
+		Extension parent = new Extension().setUrl("http://example.com#parent");
+		patient.addExtension(parent);
+
+		Extension child1 = new Extension().setUrl("http://example.com#child").setValue(new StringType("value1"));
+		parent.addExtension(child1);
+
+		Extension child2 = new Extension().setUrl("http://example.com#child").setValue(new StringType("value1"));
+		parent.addExtension(child2);
+		// END SNIPPET: subExtension
+
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(output);
+
+		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
+		assertThat(enc, containsString(
+				"<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension></extension>"));
+		assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
+		assertThat(enc, containsString(
+				"<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
+	}
+
+	@Test
+	public void testOmitResourceId() {
+		Patient p = new Patient();
+		p.setId("123");
+		p.addName().setFamily("ABC");
+
+		assertThat(ourCtx.newXmlParser().encodeResourceToString(p), stringContainsInOrder("123", "ABC"));
+		assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), containsString("ABC"));
+		assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), not(containsString("123")));
+	}
 
-  @After
-  public void after() {
-    if (ourCtx == null) {
-      ourCtx = FhirContext.forDstu3();
-    }
-    ourCtx.setNarrativeGenerator(null);
-  }
-  
 	@Test
 	public void testOverrideResourceIdWithBundleEntryFullUrlDisabled_ConfiguredOnFhirContext() {
 		try {
@@ -100,7 +2000,7 @@ public class XmlParserDstu3Test {
 			ourCtx = null;
 		}
 	}
-	
+
 	@Test
 	public void testOverrideResourceIdWithBundleEntryFullUrlDisabled_ConfiguredOnParser() {
 		try {
@@ -121,3143 +2021,1261 @@ public class XmlParserDstu3Test {
 		}
 	}
 
-  /**
-   * See #551
-   */
-  @Test
-  public void testXmlLargeAttribute() {
-    String largeString = StringUtils.leftPad("", (int) FileUtils.ONE_MB, 'A');
-
-    Patient p = new Patient();
-    p.addName().setFamily(largeString);
-
-    String encoded = ourCtx.newXmlParser().encodeResourceToString(p);
-
-    p = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
-
-    assertEquals(largeString, p.getNameFirstRep().getFamily());
-  }
-
-  /**
-   * See #544
-   */
-  @Test
-  public void testBundleStitchReferencesByUuid() throws Exception {
-    Bundle bundle = new Bundle();
-
-    DocumentManifest dm = new DocumentManifest();
-    dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
-    bundle.addEntry().setResource(dm);
-
-    Patient patient = new Patient();
-    patient.addName().setFamily("FAMILY");
-    bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
-    ourLog.info(encoded);
-
-    bundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
-    dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
-
-    assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
-
-    Patient subject = (Patient) dm.getSubject().getResource();
-    assertNotNull(subject);
-    assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
-  }
-
-  @Test
-  public void testBundleWithBinary() {
-
-    String bundle = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <base value=\"http://localhost:52788\"/>\n" +
-        "   <total value=\"1\"/>\n" +
-        "   <link>\n" +
-        "      <relation value=\"self\"/>\n" +
-        "      <url value=\"http://localhost:52788/Binary?_pretty=true\"/>\n" +
-        "   </link>\n" +
-        "   <entry>\n" +
-        "      <resource>\n" +
-        "         <Binary xmlns=\"http://hl7.org/fhir\">\n" +
-        "            <id value=\"1\"/>\n" +
-        "            <meta/>\n" +
-        "            <contentType value=\"text/plain\"/>\n" +
-        "            <content value=\"AQIDBA==\"/>\n" +
-        "         </Binary>\n" +
-        "      </resource>\n" +
-        "   </entry>\n" +
-        "</Bundle>";
-
-    Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, bundle);
-    assertEquals(1, b.getEntry().size());
-
-    Binary bin = (Binary) b.getEntry().get(0).getResource();
-    assertArrayEquals(new byte[] { 1, 2, 3, 4 }, bin.getContent());
-
-  }
-
-  @Test
-  public void testContainedResourceInExtensionUndeclared() {
-    Patient p = new Patient();
-    p.addName().setFamily("PATIENT");
-
-    Organization o = new Organization();
-    o.setName("ORG");
-    p.addExtension(new Extension("urn:foo", new Reference(o)));
-
-    String str = ourCtx.newXmlParser().encodeResourceToString(p);
-    ourLog.info(str);
-
-    p = ourCtx.newXmlParser().parseResource(Patient.class, str);
-    assertEquals("PATIENT", p.getName().get(0).getFamily());
-
-    List<Extension> exts = p.getExtensionsByUrl("urn:foo");
-    assertEquals(1, exts.size());
-    Reference rr = (Reference) exts.get(0).getValue();
-    o = (Organization) rr.getResource();
-    assertEquals("ORG", o.getName());
-  }
-
-  @Test(expected = DataFormatException.class)
-  public void testContainedResourceWithNoId() throws IOException {
-    String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setParserErrorHandler(new StrictErrorHandler());
-    parser.parseResource(Bundle.class, string);
-  }
-
-  @Test()
-  public void testContainedResourceWithNoIdLenient() throws IOException {
-    String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setParserErrorHandler(new LenientErrorHandler());
-    parser.parseResource(Bundle.class, string);
-  }
-
-  @Test
-  public void testDuration() {
-    Encounter enc = new Encounter();
-    Duration duration = new Duration();
-    duration.setUnit("day").setValue(123L);
-    enc.setLength(duration);
-
-    String str = ourCtx.newXmlParser().encodeResourceToString(enc);
-    ourLog.info(str);
-
-    assertThat(str, not(containsString("meta")));
-    assertThat(str, containsString("<length><value value=\"123\"/><unit value=\"day\"/></length>"));
-  }
-
-  @Test
-  public void testEncodeAndParseBundleWithResourceRefs() {
-
-    Patient pt = new Patient();
-    pt.setId("patid");
-    pt.addName().setFamily("PATIENT");
-
-    Organization org = new Organization();
-    org.setId("orgid");
-    org.setName("ORG");
-    pt.getManagingOrganization().setResource(org);
-
-    Bundle bundle = new Bundle();
-    bundle.addEntry().setResource(pt);
-    bundle.addEntry().setResource(org);
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder(
-        "<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<managingOrganization>",
-        "<reference value=\"Organization/orgid\"/>",
-        "</managingOrganization>"));
-
-    bundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
-    pt = (Patient) bundle.getEntry().get(0).getResource();
-    org = (Organization) bundle.getEntry().get(1).getResource();
-
-    assertEquals("Organization/orgid", org.getIdElement().getValue());
-    assertEquals("Organization/orgid", pt.getManagingOrganization().getReferenceElement().getValue());
-    assertSame(org, pt.getManagingOrganization().getResource());
-  }
-
-  @Test
-  public void testEncodeAndParseCompositeExtension() {
-    PatientWithCustomCompositeExtension pat = new PatientWithCustomCompositeExtension();
-    pat.setId("123");
-    pat.setFooParentExtension(new FooParentExtension());
-    pat.getFooParentExtension().setChildA(new StringType("ValueA"));
-    pat.getFooParentExtension().setChildB(new StringType("ValueB"));
-
-    String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(pat);
-    ourLog.info(enc);
-
-    pat = ourCtx.newXmlParser().parseResource(PatientWithCustomCompositeExtension.class, enc);
-
-    assertEquals("ValueA", pat.getFooParentExtension().getChildA().getValue());
-    assertEquals("ValueB", pat.getFooParentExtension().getChildB().getValue());
-  }
-
-  @Test
-  public void testEncodeAndParseContained() {
-    IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
-
-    // Create an organization, note that the organization does not have an ID
-    Organization org = new Organization();
-    org.getNameElement().setValue("Contained Test Organization");
-
-    // Create a patient
-    Patient patient = new Patient();
-    patient.setId("Patient/1333");
-    patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
-
-    // Put the organization as a reference in the patient resource
-    patient.getManagingOrganization().setResource(org);
-
-    String encoded = xmlParser.encodeResourceToString(patient);
-    ourLog.info(encoded);
-    assertThat(encoded, containsString("<contained>"));
-    assertThat(encoded, containsString("<reference value=\"#1\"/>"));
-
-    // Create a bundle with just the patient resource
-    Bundle b = new Bundle();
-    b.addEntry().setResource(patient);
-
-    // Encode the bundle
-    encoded = xmlParser.encodeResourceToString(b);
-    ourLog.info(encoded);
-    assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<id value=\"1\"/>", "</contained>")));
-    assertThat(encoded, containsString("<reference value=\"#1\"/>"));
-    assertThat(encoded, stringContainsInOrder(Arrays.asList("<entry>", "</entry>")));
-    assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<entry>", "</entry>", "<entry>"))));
-
-    // Re-parse the bundle
-    patient = (Patient) xmlParser.parseResource(xmlParser.encodeResourceToString(patient));
-    assertEquals("#1", patient.getManagingOrganization().getReference());
-
-    assertNotNull(patient.getManagingOrganization().getResource());
-    org = (Organization) patient.getManagingOrganization().getResource();
-    assertEquals("#1", org.getIdElement().getValue());
-    assertEquals("Contained Test Organization", org.getName());
-
-    // And re-encode a second time
-    encoded = xmlParser.encodeResourceToString(patient);
-    ourLog.info(encoded);
-    assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<Organization ", "<id value=\"1\"/>", "</Organization", "</contained>", "<reference value=\"#1\"/>")));
-    assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<contained>", "<Org", "<contained>"))));
-    assertThat(encoded, containsString("<reference value=\"#1\"/>"));
-
-    // And re-encode once more, with the references cleared
-    patient.getContained().clear();
-    patient.getManagingOrganization().setReference((String) null);
-    encoded = xmlParser.encodeResourceToString(patient);
-    ourLog.info(encoded);
-    assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<Organization ", "<id value=\"1\"/>", "</Organization", "</contained>", "<reference value=\"#1\"/>")));
-    assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<contained>", "<Org", "<contained>"))));
-    assertThat(encoded, containsString("<reference value=\"#1\"/>"));
-
-    // And re-encode once more, with the references cleared and a manually set local ID
-    patient.getContained().clear();
-    patient.getManagingOrganization().setReference((String) null);
-    patient.getManagingOrganization().getResource().setId(("#333"));
-    encoded = xmlParser.encodeResourceToString(patient);
-    ourLog.info(encoded);
-    assertThat(encoded, stringContainsInOrder(Arrays.asList("<contained>", "<Organization ", "<id value=\"333\"/>", "</Organization", "</contained>", "<reference value=\"#333\"/>")));
-    assertThat(encoded, not(stringContainsInOrder(Arrays.asList("<contained>", "<Org", "<contained>"))));
-
-  }
-
-  @Test
-  public void testEncodeAndParseContainedCustomTypes() {
-    ourCtx = FhirContext.forDstu3();
-    ourCtx.setDefaultTypeForProfile(CustomObservation.PROFILE, CustomObservation.class);
-    ourCtx.setDefaultTypeForProfile(CustomDiagnosticReport.PROFILE, CustomDiagnosticReport.class);
-
-    CustomObservation obs = new CustomObservation();
-    obs.setStatus(ObservationStatus.FINAL);
-
-    CustomDiagnosticReport dr = new CustomDiagnosticReport();
-    dr.setStatus(DiagnosticReportStatus.FINAL);
-    dr.addResult().setResource(obs);
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setPrettyPrint(true);
-
-    String output = parser.encodeResourceToString(dr);
-    ourLog.info(output);
-
-    assertThat(output, stringContainsInOrder(
-        "<DiagnosticReport xmlns=\"http://hl7.org/fhir\">",
-        "<meta>",
-        "<profile value=\"http://custom_DiagnosticReport\"/>",
-        "</meta>",
-        "<contained>",
-        "<Observation xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"1\"/>",
-        "<meta>",
-        "<profile value=\"http://custom_Observation\"/>",
-        "</meta>",
-        "<status value=\"final\"/>",
-        "</Observation>",
-        "</contained>",
-        "<status value=\"final\"/>",
-        "<result>",
-        "<reference value=\"#1\"/>",
-        "</result>",
-        "</DiagnosticReport>"));
-
-    /*
-     * Now PARSE!
-     */
-
-    dr = (CustomDiagnosticReport) parser.parseResource(output);
-    assertEquals(DiagnosticReportStatus.FINAL, dr.getStatus());
-
-    assertEquals("#1", dr.getResult().get(0).getReference());
-    obs = (CustomObservation) dr.getResult().get(0).getResource();
-    assertEquals(ObservationStatus.FINAL, obs.getStatus());
-
-    ourCtx = null;
-  }
-
-  @Test
-  public void testEncodeAndParseContainedNonCustomTypes() {
-    ourCtx = FhirContext.forDstu3();
-
-    Observation obs = new Observation();
-    obs.setStatus(ObservationStatus.FINAL);
-
-    DiagnosticReport dr = new DiagnosticReport();
-    dr.setStatus(DiagnosticReportStatus.FINAL);
-    dr.addResult().setResource(obs);
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setPrettyPrint(true);
-
-    String output = parser.encodeResourceToString(dr);
-    ourLog.info(output);
-
-    assertThat(output, stringContainsInOrder(
-        "<DiagnosticReport xmlns=\"http://hl7.org/fhir\">",
-        "<contained>",
-        "<Observation xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"1\"/>",
-        "<status value=\"final\"/>",
-        "</Observation>",
-        "</contained>",
-        "<status value=\"final\"/>",
-        "<result>",
-        "<reference value=\"#1\"/>",
-        "</result>",
-        "</DiagnosticReport>"));
-
-    /*
-     * Now PARSE!
-     */
-
-    dr = (DiagnosticReport) parser.parseResource(output);
-    assertEquals(DiagnosticReportStatus.FINAL, dr.getStatus());
-
-    assertEquals("#1", dr.getResult().get(0).getReference());
-    obs = (Observation) dr.getResult().get(0).getResource();
-    assertEquals(ObservationStatus.FINAL, obs.getStatus());
-
-    ourCtx = null;
-  }
-
-  @Test
-  public void testEncodeAndParseExtensionOnCode() {
-    Organization o = new Organization();
-    o.setName("ORG");
-    o.addExtension(new Extension("urn:foo", new CodeType("acode")));
-
-    String str = ourCtx.newXmlParser().encodeResourceToString(o);
-    ourLog.info(str);
-    assertThat(str, containsString("<valueCode value=\"acode\"/>"));
-
-    o = ourCtx.newXmlParser().parseResource(Organization.class, str);
-
-    List<Extension> exts = o.getExtensionsByUrl("urn:foo");
-    assertEquals(1, exts.size());
-    CodeType code = (CodeType) exts.get(0).getValue();
-    assertEquals("acode", code.getValue());
-
-  }
-
-  @Test
-  public void testEncodeAndParseExtensionOnReference() {
-    DataElement de = new DataElement();
-    ElementDefinitionBindingComponent b = de.addElement().getBinding();
-    b.setDescription("BINDING");
-
-    Organization o = new Organization();
-    o.setName("ORG");
-    b.addExtension(new Extension("urn:foo", new Reference(o)));
-
-    String str = ourCtx.newXmlParser().encodeResourceToString(de);
-    ourLog.info(str);
-
-    de = ourCtx.newXmlParser().parseResource(DataElement.class, str);
-    b = de.getElement().get(0).getBinding();
-    assertEquals("BINDING", b.getDescription());
-
-    List<Extension> exts = b.getExtensionsByUrl("urn:foo");
-    assertEquals(1, exts.size());
-    Reference rr = (Reference) exts.get(0).getValue();
-    o = (Organization) rr.getResource();
-    assertEquals("ORG", o.getName());
-
-  }
-
-  @Test
-  public void testEncodeAndParseExtensions() throws Exception {
-
-    Patient patient = new Patient();
-    patient.addIdentifier().setUse(IdentifierUse.OFFICIAL).setSystem("urn:example").setValue("7000135");
-
-    Extension ext = new Extension();
-    ext.setUrl("http://example.com/extensions#someext");
-    ext.setValue(new DateTimeType("2011-01-02T11:13:15"));
-    patient.addExtension(ext);
-
-    Extension parent = new Extension().setUrl("http://example.com#parent");
-    patient.addExtension(parent);
-    Extension child1 = new Extension().setUrl("http://example.com#child").setValue(new StringType("value1"));
-    parent.addExtension(child1);
-    Extension child2 = new Extension().setUrl("http://example.com#child").setValue(new StringType("value2"));
-    parent.addExtension(child2);
-
-    Extension modExt = new Extension();
-    modExt.setUrl("http://example.com/extensions#modext");
-    modExt.setValue(new DateType("1995-01-02"));
-    patient.addModifierExtension(modExt);
-
-    HumanName name = patient.addName();
-    name.setFamily("Blah");
-    StringType given = name.addGivenElement();
-    given.setValue("Joe");
-    Extension ext2 = new Extension().setUrl("http://examples.com#givenext").setValue(new StringType("given"));
-    given.addExtension(ext2);
-
-    StringType given2 = name.addGivenElement();
-    given2.setValue("Shmoe");
-    Extension given2ext = new Extension().setUrl("http://examples.com#givenext_parent");
-    given2.addExtension(given2ext);
-    given2ext.addExtension(new Extension().setUrl("http://examples.com#givenext_child").setValue(new StringType("CHILD")));
-
-    String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-    ourLog.info(output);
-
-    String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
-    assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
-    assertThat(enc, containsString("<modifierExtension url=\"http://example.com/extensions#modext\"><valueDate value=\"1995-01-02\"/></modifierExtension>"));
-    assertThat(enc, containsString(
-        "<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
-    assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
-    assertThat(enc, containsString(
-        "<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
-
-    /*
-     * Now parse this back
-     */
-
-    Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, enc);
-    ext = parsed.getExtension().get(0);
-    assertEquals("http://example.com/extensions#someext", ext.getUrl());
-    assertEquals("2011-01-02T11:13:15", ((DateTimeType) ext.getValue()).getValueAsString());
-
-    parent = patient.getExtension().get(1);
-    assertEquals("http://example.com#parent", parent.getUrl());
-    assertNull(parent.getValue());
-    child1 = parent.getExtension().get(0);
-    assertEquals("http://example.com#child", child1.getUrl());
-    assertEquals("value1", ((StringType) child1.getValue()).getValueAsString());
-    child2 = parent.getExtension().get(1);
-    assertEquals("http://example.com#child", child2.getUrl());
-    assertEquals("value2", ((StringType) child2.getValue()).getValueAsString());
-
-    modExt = parsed.getModifierExtension().get(0);
-    assertEquals("http://example.com/extensions#modext", modExt.getUrl());
-    assertEquals("1995-01-02", ((DateType) modExt.getValue()).getValueAsString());
-
-    name = parsed.getName().get(0);
-
-    ext2 = name.getGiven().get(0).getExtension().get(0);
-    assertEquals("http://examples.com#givenext", ext2.getUrl());
-    assertEquals("given", ((StringType) ext2.getValue()).getValueAsString());
-
-    given2ext = name.getGiven().get(1).getExtension().get(0);
-    assertEquals("http://examples.com#givenext_parent", given2ext.getUrl());
-    assertNull(given2ext.getValue());
-    Extension given2ext2 = given2ext.getExtension().get(0);
-    assertEquals("http://examples.com#givenext_child", given2ext2.getUrl());
-    assertEquals("CHILD", ((StringType) given2ext2.getValue()).getValue());
-
-  }
-
-  /**
-   * See #216
-   */
-  @Test
-  public void testEncodeAndParseIdentifierDstu2() {
-    IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
-
-    Patient patient = new Patient();
-    patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(new CodeableConcept().addCoding(new Coding().setSystem("http://hl7.org/fhir/v2/0203").setCode("MR")));
-
-    String out = xmlParser.encodeResourceToString(patient);
-    ourLog.info(out);
-
-    assertThat(out, stringContainsInOrder("<identifier>",
-        "<type>",
-        "<coding>",
-        "<system value=\"http://hl7.org/fhir/v2/0203\"/>",
-        "<code value=\"MR\"/>",
-        "</coding>",
-        "</type>",
-        "<system value=\"SYS\"/>",
-        "<value value=\"VAL\"/>",
-        "</identifier>"));
-
-    patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
-    assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
-    assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
-  }
-
-  /**
-   * See #347
-   */
-  @Test
-  public void testEncodeAndParseMedicationRequest() {
-    MedicationRequest mo = new MedicationRequest();
-    mo.getAuthoredOnElement().setValueAsString("2015-10-05");
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(mo);
-    ourLog.info(encoded);
-
-    mo = ourCtx.newXmlParser().parseResource(MedicationRequest.class, encoded);
-    assertEquals("2015-10-05", mo.getAuthoredOnElement().getValueAsString());
-  }
-
-  @Test
-  public void testEncodeAndParseMetaProfileAndTags() {
-    Patient p = new Patient();
-    p.addName().setFamily("FAMILY");
-
-    p.getMeta().addProfile("http://foo/Profile1");
-    p.getMeta().addProfile("http://foo/Profile2");
-
-    p.getMeta().addTag().setSystem("scheme1").setCode("term1").setDisplay("label1");
-    p.getMeta().addTag().setSystem("scheme2").setCode("term2").setDisplay("label2");
-
-    p.getMeta().addSecurity().setSystem("sec_scheme1").setCode("sec_term1").setDisplay("sec_label1");
-    p.getMeta().addSecurity().setSystem("sec_scheme2").setCode("sec_term2").setDisplay("sec_label2");
-
-    String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
-    ourLog.info(enc);
-
-    assertThat(enc, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<meta>",
-        "<meta>",
-        "<profile value=\"http://foo/Profile1\"/>",
-        "<profile value=\"http://foo/Profile2\"/>",
-        "<tag>",
-        "<system value=\"scheme1\"/>",
-        "<code value=\"term1\"/>",
-        "<display value=\"label1\"/>",
-        "</tag>",
-        "<tag>",
-        "<system value=\"scheme2\"/>",
-        "<code value=\"term2\"/>",
-        "<display value=\"label2\"/>",
-        "</tag>",
-        "</meta>",
-        "</meta>",
-        "<name>",
-        "<family value=\"FAMILY\"/>",
-        "</name>",
-        "</Patient>"));
-
-    Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, enc);
-    List<UriType> gotLabels = parsed.getMeta().getProfile();
-    assertEquals(2, gotLabels.size());
-    UriType label = gotLabels.get(0);
-    assertEquals("http://foo/Profile1", label.getValue());
-    label = gotLabels.get(1);
-    assertEquals("http://foo/Profile2", label.getValue());
-
-    List<Coding> tagList = parsed.getMeta().getTag();
-    assertEquals(2, tagList.size());
-    assertEquals("scheme1", tagList.get(0).getSystem());
-    assertEquals("term1", tagList.get(0).getCode());
-    assertEquals("label1", tagList.get(0).getDisplay());
-    assertEquals("scheme2", tagList.get(1).getSystem());
-    assertEquals("term2", tagList.get(1).getCode());
-    assertEquals("label2", tagList.get(1).getDisplay());
-
-    tagList = parsed.getMeta().getSecurity();
-    assertEquals(2, tagList.size());
-    assertEquals("sec_scheme1", tagList.get(0).getSystem());
-    assertEquals("sec_term1", tagList.get(0).getCode());
-    assertEquals("sec_label1", tagList.get(0).getDisplay());
-    assertEquals("sec_scheme2", tagList.get(1).getSystem());
-    assertEquals("sec_term2", tagList.get(1).getCode());
-    assertEquals("sec_label2", tagList.get(1).getDisplay());
-  }
-
-  @Test
-  public void testEncodeAndParseMetaProfiles() {
-    Patient p = new Patient();
-    p.addName().setFamily("FAMILY");
-
-    p.getMeta().addTag().setSystem("scheme1").setCode("term1").setDisplay("label1");
-    p.getMeta().addTag().setSystem("scheme2").setCode("term2").setDisplay("label2");
-
-    String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
-    ourLog.info(enc);
-
-    assertThat(enc, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<meta>",
-        "<meta>",
-        "<tag>",
-        "<system value=\"scheme1\"/>",
-        "<code value=\"term1\"/>",
-        "<display value=\"label1\"/>",
-        "</tag>",
-        "<tag>",
-        "<system value=\"scheme2\"/>",
-        "<code value=\"term2\"/>",
-        "<display value=\"label2\"/>",
-        "</tag>",
-        "</meta>",
-        "</meta>",
-        "<name>",
-        "<family value=\"FAMILY\"/>",
-        "</name>",
-        "</Patient>"));
-
-    Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, enc);
-    assertThat(parsed.getMeta().getProfile(), empty());
-
-    List<Coding> tagList = parsed.getMeta().getTag();
-    assertEquals(2, tagList.size());
-    assertEquals("scheme1", tagList.get(0).getSystem());
-    assertEquals("term1", tagList.get(0).getCode());
-    assertEquals("label1", tagList.get(0).getDisplay());
-    assertEquals("scheme2", tagList.get(1).getSystem());
-    assertEquals("term2", tagList.get(1).getCode());
-    assertEquals("label2", tagList.get(1).getDisplay());
-  }
-
-  /**
-   * See #336
-   */
-  @Test
-  public void testEncodeAndParseNullPrimitiveWithExtensions() {
-
-    Patient p = new Patient();
-    p.setId("patid");
-    HumanName name = p.addName();
-    name.addGivenElement().setValue(null).setId("f0").addExtension(new Extension("http://foo", new StringType("FOOEXT0")));
-    name.addGivenElement().setValue("V1").setId("f1").addExtension((Extension) new Extension("http://foo", new StringType("FOOEXT1")).setId("ext1id"));
-    name.addGivenElement(); // this one shouldn't get encoded
-    name.addGivenElement().setValue(null).addExtension(new Extension("http://foo", new StringType("FOOEXT3")));
-    name.setId("nameid");
-
-    String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
-    ourLog.info(output);
-
-    output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
-    String expected = "<Patient xmlns=\"http://hl7.org/fhir\"><id value=\"patid\"/><name id=\"nameid\"><given id=\"f0\"><extension url=\"http://foo\"><valueString value=\"FOOEXT0\"/></extension></given><given id=\"f1\" value=\"V1\"><extension id=\"ext1id\" url=\"http://foo\"><valueString value=\"FOOEXT1\"/></extension></given><given><extension url=\"http://foo\"><valueString value=\"FOOEXT3\"/></extension></given></name></Patient>";
-
-    ourLog.info("Expected: {}", expected);
-    ourLog.info("Actual  : {}", output);
-
-    assertEquals(expected, output);
-
-    p = ourCtx.newXmlParser().parseResource(Patient.class, output);
-    assertEquals("patid", p.getIdElement().getIdPart());
-
-    name = p.getName().get(0);
-    assertEquals("nameid", name.getId());
-    assertEquals(3, name.getGiven().size());
-
-    assertEquals(null, name.getGiven().get(0).getValue());
-    assertEquals("V1", name.getGiven().get(1).getValue());
-    assertEquals(null, name.getGiven().get(2).getValue());
-
-    assertEquals("f0", name.getGiven().get(0).getId());
-    assertEquals("f1", name.getGiven().get(1).getId());
-    assertEquals(null, name.getGiven().get(2).getId());
-
-    assertEquals(1, name.getGiven().get(0).getExtension().size());
-    assertEquals("http://foo", name.getGiven().get(0).getExtension().get(0).getUrl());
-    assertEquals("FOOEXT0", ((StringType) name.getGiven().get(0).getExtension().get(0).getValue()).getValue());
-    assertEquals(null, name.getGiven().get(0).getExtension().get(0).getId());
-
-    assertEquals(1, name.getGiven().get(1).getExtension().size());
-    assertEquals("http://foo", name.getGiven().get(1).getExtension().get(0).getUrl());
-    assertEquals("FOOEXT1", ((StringType) name.getGiven().get(1).getExtension().get(0).getValue()).getValue());
-    assertEquals("ext1id", name.getGiven().get(1).getExtension().get(0).getId());
-
-    assertEquals(1, name.getGiven().get(2).getExtension().size());
-    assertEquals("http://foo", name.getGiven().get(2).getExtension().get(0).getUrl());
-    assertEquals("FOOEXT3", ((StringType) name.getGiven().get(2).getExtension().get(0).getValue()).getValue());
-    assertEquals(null, name.getGiven().get(2).getExtension().get(0).getId());
-
-  }
-
-  @Test
-  public void testEncodeAndParseProfiledDatatype() {
-    MedicationRequest mo = new MedicationRequest();
-    mo.addDosageInstruction().getTiming().getRepeat().setBounds(new Duration().setCode("code"));
-    String out = ourCtx.newXmlParser().encodeResourceToString(mo);
-    ourLog.info(out);
-    assertThat(out, containsString("</boundsDuration>"));
-
-    mo = ourCtx.newXmlParser().parseResource(MedicationRequest.class, out);
-    Duration duration = (Duration) mo.getDosageInstruction().get(0).getTiming().getRepeat().getBounds();
-    assertEquals("code", duration.getCode());
-  }
-
-  /**
-   * See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
-   */
-  @Test
-  public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
-    IParser xmlParser = ourCtx.newXmlParser();
-
-    MedicationStatement ms = new MedicationStatement();
-    ms.addDosage().setDose(new SimpleQuantity().setValue(123));
-
-    String output = xmlParser.encodeResourceToString(ms);
-    assertThat(output, containsString("<doseQuantity><value value=\"123\"/></doseQuantity>"));
-  }
-
-  @Test
-  public void testEncodeAndParseSecurityLabels() {
-    Patient p = new Patient();
-    p.addName().setFamily("FAMILY");
-
-    List<Coding> labels = new ArrayList<Coding>();
-    labels.add(new Coding().setSystem("SYSTEM1").setCode("CODE1").setDisplay("DISPLAY1").setVersion("VERSION1"));
-    labels.add(new Coding().setSystem("SYSTEM2").setCode("CODE2").setDisplay("DISPLAY2").setVersion("VERSION2"));
-    p.getMeta().getSecurity().addAll(labels);
-
-    String enc = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
-    ourLog.info(enc);
-
-    assertThat(enc, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<meta>",
-        "<security>",
-        "<system value=\"SYSTEM1\"/>",
-        "<version value=\"VERSION1\"/>",
-        "<code value=\"CODE1\"/>",
-        "<display value=\"DISPLAY1\"/>",
-        "</security>",
-        "<security>",
-        "<system value=\"SYSTEM2\"/>",
-        "<version value=\"VERSION2\"/>",
-        "<code value=\"CODE2\"/>",
-        "<display value=\"DISPLAY2\"/>",
-        "</security>",
-        "</meta>",
-        "<name>",
-        "<family value=\"FAMILY\"/>",
-        "</name>",
-        "</Patient>"));
-
-    Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, enc);
-    List<Coding> gotLabels = parsed.getMeta().getSecurity();
-
-    assertEquals(2, gotLabels.size());
-
-    Coding label = gotLabels.get(0);
-    assertEquals("SYSTEM1", label.getSystem());
-    assertEquals("CODE1", label.getCode());
-    assertEquals("DISPLAY1", label.getDisplay());
-    assertEquals("VERSION1", label.getVersion());
-
-    label = gotLabels.get(1);
-    assertEquals("SYSTEM2", label.getSystem());
-    assertEquals("CODE2", label.getCode());
-    assertEquals("DISPLAY2", label.getDisplay());
-    assertEquals("VERSION2", label.getVersion());
-  }
-
-  /**
-   * See #103
-   */
-  @Test
-  public void testEncodeAndReEncodeContainedJson() {
-    Composition comp = new Composition();
-    comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section0_Allergy0")));
-    comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section1_Allergy0")));
-    comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section2_Allergy0")));
-
-    IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
-
-    String string = parser.encodeResourceToString(comp);
-    ourLog.info(string);
-
-    Composition parsed = parser.parseResource(Composition.class, string);
-    parsed.getSection().remove(0);
-
-    string = parser.encodeResourceToString(parsed);
-    ourLog.info(string);
-
-    parsed = parser.parseResource(Composition.class, string);
-    assertEquals(2, parsed.getContained().size());
-  }
-
-  /**
-   * See #103
-   */
-  @Test
-  public void testEncodeAndReEncodeContainedXml() {
-    Composition comp = new Composition();
-    comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section0_Allergy0")));
-    comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section1_Allergy0")));
-    comp.addSection().addEntry().setResource(new AllergyIntolerance().addNote(new Annotation().setText("Section2_Allergy0")));
-
-    IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
-
-    String string = parser.encodeResourceToString(comp);
-    ourLog.info(string);
-
-    Composition parsed = parser.parseResource(Composition.class, string);
-    parsed.getSection().remove(0);
-
-    string = parser.encodeResourceToString(parsed);
-    ourLog.info(string);
-
-    parsed = parser.parseResource(Composition.class, string);
-    assertEquals(2, parsed.getContained().size());
-  }
-
-  @Test
-  public void testEncodeBinaryWithNoContentType() {
-    Binary b = new Binary();
-    b.setContent(new byte[] { 1, 2, 3, 4 });
-
-    String output = ourCtx.newXmlParser().encodeResourceToString(b);
-    ourLog.info(output);
-
-    assertEquals("<Binary xmlns=\"http://hl7.org/fhir\"><content value=\"AQIDBA==\"/></Binary>", output);
-  }
-
-  @Test
-  public void testEncodeBundleWithContained() {
-    DiagnosticReport rpt = new DiagnosticReport();
-    rpt.addResult().setResource(new Observation().setCode(new CodeableConcept().setText("Sharp1")).setId("#1"));
-    rpt.addResult().setResource(new Observation().setCode(new CodeableConcept().setText("Uuid1")).setId("urn:uuid:UUID1"));
-
-    Bundle b = new Bundle();
-    b.addEntry().setResource(rpt);
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder("<DiagnosticReport", "<contained", "<Observation", "<text value=\"Sharp1\"", "</DiagnosticReport"));
-    assertThat(encoded, not(stringContainsInOrder("<DiagnosticReport", "<contained", "<Observation", "<contained", "<Observation", "</DiagnosticReport")));
-  }
-
-  @Test
-  public void testEncodeChainedContainedResourcer() {
-    Organization gp = new Organization();
-    gp.setName("grandparent");
-
-    Organization parent = new Organization();
-    parent.setName("parent");
-    parent.getPartOf().setResource(gp);
-
-    Organization child = new Organization();
-    child.setName("child");
-    child.getPartOf().setResource(parent);
-
-    Patient patient = new Patient();
-    patient.getManagingOrganization().setResource(child);
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-    ourLog.info(encoded);
-
-    patient = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
-
-    child = (Organization) patient.getManagingOrganization().getResource();
-    assertEquals("child", child.getName());
-
-    parent = (Organization) child.getPartOf().getResource();
-    assertEquals("parent", parent.getName());
-
-    gp = (Organization) parent.getPartOf().getResource();
-    assertEquals("grandparent", gp.getName());
-  }
-
-  /**
-   * See #326
-   */
-  @Test
-  public void testEncodeContainedResource() {
-    Patient patient = new Patient();
-    patient.getBirthDateElement().setValueAsString("2016-04-05");
-    patient.addExtension().setUrl("test").setValue(new Reference(new Condition()));
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder(
-        "<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<contained>",
-        "<Condition xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"1\"/>",
-        "</Condition>",
-        "</contained>",
-        "<extension url=\"test\">",
-        "<valueReference>",
-        "<reference value=\"#1\"/>",
-        "</valueReference>",
-        "</extension>",
-        "<birthDate value=\"2016-04-05\"/>",
-        "</Patient>"));
-
-  }
-
-  /**
-   * See #113
-   */
-  @Test
-  public void testEncodeContainedResources() {
-
-    MedicationRequest medicationPrescript = new MedicationRequest();
-
-    String medId = "123";
-    CodeableConcept codeDt = new CodeableConcept().addCoding(new Coding().setSystem("urn:sys").setCode("code1"));
-
-    // Adding medication to Contained.
-    Medication medResource = new Medication();
-    medResource.setCode(codeDt);
-    medResource.setId("#" + String.valueOf(medId));
-    medicationPrescript.getContained().add(medResource);
-
-    // Medication reference. This should point to the contained resource.
-    Reference medRefDt = new Reference("#" + medId);
-    medRefDt.setDisplay("MedRef");
-    medicationPrescript.setMedication(medRefDt);
-
-    IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
-    String encoded = p.encodeResourceToString(medicationPrescript);
-    ourLog.info(encoded);
-
-    // @formatter:on
-    assertThat(encoded,
-        stringContainsInOrder("<MedicationRequest xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
-            "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
-            "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationRequest>"));
-
-  }
-
-  /**
-   * See #113
-   */
-  @Test
-  public void testEncodeContainedResourcesAutomatic() {
-
-    MedicationRequest medicationPrescript = new MedicationRequest();
-    String nameDisp = "MedRef";
-    CodeableConcept codeDt = new CodeableConcept().addCoding(new Coding("urn:sys", "code1", null));
-
-    // Adding medication to Contained.
-    Medication medResource = new Medication();
-    // No ID set
-    medResource.setCode(codeDt);
-
-    // Medication reference. This should point to the contained resource.
-    Reference medRefDt = new Reference();
-    medRefDt.setDisplay(nameDisp);
-    // Resource reference set, but no ID
-    medRefDt.setResource(medResource);
-    medicationPrescript.setMedication(medRefDt);
-
-    IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
-    String encoded = p.encodeResourceToString(medicationPrescript);
-    ourLog.info(encoded);
-
-    assertThat(encoded,
-        stringContainsInOrder("<MedicationRequest xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>",
-            "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>",
-            "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationRequest>"));
-
-  }
-
-  /**
-   * See #113
-   */
-  @Test
-  public void testEncodeContainedResourcesManualContainUsingNonLocalId() {
-
-    MedicationRequest medicationPrescript = new MedicationRequest();
-
-    String medId = "123";
-    CodeableConcept codeDt = new CodeableConcept().addCoding(new Coding("urn:sys", "code1", null));
-
-    // Adding medication to Contained.
-    Medication medResource = new Medication();
-    medResource.setCode(codeDt);
-    medResource.setId(String.valueOf(medId)); // ID does not start with '#'
-    medicationPrescript.getContained().add(medResource);
-
-    // Medication reference. This should point to the contained resource.
-    Reference medRefDt = new Reference("#" + medId);
-    medRefDt.setDisplay("MedRef");
-    medicationPrescript.setMedication(medRefDt);
-
-    IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
-    String encoded = p.encodeResourceToString(medicationPrescript);
-    ourLog.info(encoded);
-
-    assertThat(encoded,
-        stringContainsInOrder("<MedicationRequest xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
-            "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
-            "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationRequest>"));
-
-  }
-
-  @Test
-  public void testEncodeContainedWithNarrativeIsSuppresed() throws Exception {
-    IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
-
-    // Create an organization, note that the organization does not have an ID
-    Organization org = new Organization();
-    org.getNameElement().setValue("Contained Test Organization");
-    org.getText().setDivAsString("<div>FOOBAR</div>");
-
-    // Create a patient
-    Patient patient = new Patient();
-    patient.setId("Patient/1333");
-    patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
-    patient.getText().setDivAsString("<div>BARFOO</div>");
-    patient.getManagingOrganization().setResource(org);
-
-    String encoded = parser.encodeResourceToString(patient);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder("<Patient", "<text>", "<div xmlns=\"http://www.w3.org/1999/xhtml\">BARFOO</div>", "<contained>", "<Organization", "</Organization"));
-    assertThat(encoded, not(stringContainsInOrder("<Patient", "<text>", "<contained>", "<Organization", "<text", "</Organization")));
-
-    assertThat(encoded, not(containsString("FOOBAR")));
-    assertThat(encoded, (containsString("BARFOO")));
-
-  }
-
-  @Test
-  public void testEncodeContainedWithNonLocalId() throws Exception {
-
-    Patient p = new Patient();
-    p.setId("Patient1");
-    p.setBirthDate(new SimpleDateFormat("yyyy-mm-dd HH:mm:ss").parse("2016-04-15 10:15:30"));
-
-    ProcedureRequest pr = new ProcedureRequest();
-    pr.setId("1234567");
-    pr.setSubject(new Reference(p));
-    pr.setCode(new CodeableConcept().addCoding(new Coding("breastfeeding-readiness-assessment", "Breastfeeding Readiness Assessment", "Breastfeeding Readiness Assessment")));
-    // pr.setReason(new StringType("Single Live Birth"));
-    // pr.setScheduled(new DateType(new Date()));
-    pr.setContext(new Reference("Live Birth Encounter"));
-    pr.setPerformer(new Reference("Charge Nurse"));
-    pr.setStatus(ProcedureRequest.ProcedureRequestStatus.DRAFT);
-
-    GuidanceResponse.GuidanceResponseStatus status = GuidanceResponse.GuidanceResponseStatus.SUCCESS;
-
-    GuidanceResponse gr = new GuidanceResponse()
-        .setRequestId("123")
-        .setModule(new Reference("Evaluate Operation"))
-        .setStatus(status);
-
-    gr.setReason(new Reference(pr));
-    gr.getContained().add(p);
-    gr.getContained().add(pr);
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setPrettyPrint(true);
-    ourLog.info(parser.encodeResourceToString(gr));
-  }
-
-  @Test
-  public void testEncodeDeclaredBlock() throws Exception {
-    FooMessageSourceComponent source = new FooMessageHeaderWithExplicitField.FooMessageSourceComponent();
-    source.getMessageHeaderApplicationId().setValue("APPID");
-    source.setName("NAME");
-
-    FooMessageHeaderWithExplicitField header = new FooMessageHeaderWithExplicitField();
-    header.setSourceNew(source);
-
-    header.addDestination().setName("DEST");
-
-    Bundle bundle = new Bundle();
-    bundle.addEntry().setResource(header);
-
-    IParser p = ourCtx.newXmlParser();
-    p.setPrettyPrint(true);
-
-    String encode = p.encodeResourceToString(bundle);
-    ourLog.info(encode);
-
-    assertThat(encode, containsString("<value value=\"APPID\"/>"));
-    assertThat(encode, stringContainsInOrder("<dest","<source"));
-  }
-
-  /**
-   * Make sure whitespace is preserved for pre tags
-   */
-  @Test
-  public void testEncodeDivWithPreNonPrettyPrint() {
-
-    Patient p = new Patient();
-    p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
-
-    String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
-    ourLog.info(output);
-
-    assertThat(output, stringContainsInOrder(
-        "<text><div",
-        "<p>A P TAG</p><p>",
-        "<pre>line1\nline2\nline3  <b>BOLD</b></pre>"));
-
-  }
-
-  @Test
-  public void testEncodeDivWithPrePrettyPrint() {
-
-    Patient p = new Patient();
-    p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
-
-    String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
-    ourLog.info(output);
-
-    assertThat(output, stringContainsInOrder(
-        "   <text>",
-        "      <div",
-        "         <pre>line1\nline2\nline3  <b>BOLD</b></pre>"));
-
-  }
-
-  @Test
-  public void testEncodeDoesntIncludeUuidId() {
-    Patient p = new Patient();
-    p.setId(new IdType("urn:uuid:42795ed8-041f-4ebf-b6f4-78ef6f64c2f2"));
-    p.addIdentifier().setSystem("ACME");
-
-    String actual = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
-    assertThat(actual, not(containsString("78ef6f64c2f2")));
-  }
-
-  @Test
-  public void testEncodeEmptyBinary() {
-    String output = ourCtx.newXmlParser().encodeResourceToString(new Binary());
-    assertEquals("<Binary xmlns=\"http://hl7.org/fhir\"/>", output);
-  }
-
-  /**
-   * #158
-   */
-  @Test
-  public void testEncodeEmptyTag() {
-    ArrayList<Coding> tagList = new ArrayList<Coding>();
-    tagList.add(new Coding());
-    tagList.add(new Coding().setDisplay("Label"));
-
-    Patient p = new Patient();
-    p.getMeta().getTag().addAll(tagList);
-
-    String encoded = ourCtx.newXmlParser().encodeResourceToString(p);
-    assertThat(encoded, not(containsString("tag")));
-  }
-
-  /**
-   * #158
-   */
-  @Test
-  public void testEncodeEmptyTag2() {
-    ArrayList<Coding> tagList = new ArrayList<Coding>();
-    tagList.add(new Coding().setSystem("scheme").setCode("code"));
-    tagList.add(new Coding().setDisplay("Label"));
-
-    Patient p = new Patient();
-    p.getMeta().getTag().addAll(tagList);
-
-    String encoded = ourCtx.newXmlParser().encodeResourceToString(p);
-    assertThat(encoded, containsString("tag"));
-    assertThat(encoded, containsString("scheme"));
-    assertThat(encoded, not(containsString("Label")));
-  }
-
-  @Test
-  public void testEncodeExtensionUndeclaredNonModifier() {
-    Observation obs = new Observation();
-    obs.setId("1");
-    obs.getMeta().addProfile("http://profile");
-    Extension ext = obs.addExtension();
-    ext.setUrl("http://exturl").setValue(new StringType("ext_url_value"));
-
-    obs.getCode().setText("CODE");
-
-    IParser parser = ourCtx.newXmlParser();
-
-    String output = parser.setPrettyPrint(true).encodeResourceToString(obs);
-    ourLog.info(output);
-
-    assertThat(output, stringContainsInOrder(
-        "<id value=\"1\"/>",
-        "<meta>",
-        "<profile value=\"http://profile\"/>",
-        "<extension url=\"http://exturl\">",
-        "<valueString value=\"ext_url_value\"/>",
-        "<text value=\"CODE\"/>"));
-    assertThat(output, not(stringContainsInOrder(
-        "<url value=\"http://exturl\"/>")));
-
-    obs = parser.parseResource(Observation.class, output);
-    assertEquals(1, obs.getExtension().size());
-    assertEquals("http://exturl", obs.getExtension().get(0).getUrl());
-    assertEquals("ext_url_value", ((StringType) obs.getExtension().get(0).getValue()).getValue());
-  }
-
-  @Test
-  public void testEncodeExtensionUndeclaredNonModifierWithChildExtension() {
-    Observation obs = new Observation();
-    obs.setId("1");
-    obs.getMeta().addProfile("http://profile");
-    Extension ext = obs.addExtension();
-    ext.setUrl("http://exturl");
-
-    Extension subExt = ext.addExtension();
-    subExt.setUrl("http://subext").setValue(new StringType("sub_ext_value"));
-
-    obs.getCode().setText("CODE");
-
-    IParser parser = ourCtx.newXmlParser();
-
-    String output = parser.setPrettyPrint(true).encodeResourceToString(obs);
-    ourLog.info(output);
-
-    assertThat(output, stringContainsInOrder(
-        "<id value=\"1\"/>",
-        "<meta>",
-        "<profile value=\"http://profile\"/>",
-        "<extension url=\"http://exturl\">",
-        "<extension url=\"http://subext\">",
-        "<valueString value=\"sub_ext_value\"/>",
-        "<text value=\"CODE\"/>"));
-    assertThat(output, not(stringContainsInOrder(
-        "<url value=\"http://exturl\"/>")));
-
-    obs = parser.parseResource(Observation.class, output);
-    assertEquals(1, obs.getExtension().size());
-    assertEquals("http://exturl", obs.getExtension().get(0).getUrl());
-    assertEquals(1, obs.getExtension().get(0).getExtension().size());
-    assertEquals("http://subext", obs.getExtension().get(0).getExtension().get(0).getUrl());
-    assertEquals("sub_ext_value", ((StringType) obs.getExtension().get(0).getExtension().get(0).getValue()).getValue());
-  }
-
-  /**
-   * See #327
-   */
-  @Test
-  public void testEncodeExtensionWithContainedResource() {
-
-    TestPatientFor327 patient = new TestPatientFor327();
-    patient.setBirthDateElement(new DateType("2016-04-14"));
-
-    List<Reference> conditions = new ArrayList<Reference>();
-    Condition condition = new Condition();
-    condition.addBodySite().setText("BODY SITE");
-    conditions.add(new Reference(condition));
-    patient.setCondition(conditions);
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder(
-        "<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<contained>",
-        "<Condition xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"1\"/>",
-        "<bodySite>",
-        "<text value=\"BODY SITE\"/>",
-        "</bodySite>",
-        "</Condition>",
-        "</contained>",
-        "<extension url=\"testCondition\">",
-        "<valueReference>",
-        "<reference value=\"#1\"/>",
-        "</valueReference>",
-        "</extension>",
-        "<birthDate value=\"2016-04-14\"/>",
-        "</Patient>"));
-
-  }
-
-  @Test
-  public void testEncodeExtensionWithResourceContent() {
-    IParser parser = ourCtx.newXmlParser();
-
-    Patient patient = new Patient();
-    patient.addAddress().setUse(AddressUse.HOME);
-    patient.addExtension(new Extension("urn:foo", new Reference("Organization/123")));
-
-    String val = parser.encodeResourceToString(patient);
-    ourLog.info(val);
-    assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueReference><reference value=\"Organization/123\"/></valueReference></extension>"));
-
-    Patient actual = parser.parseResource(Patient.class, val);
-    assertEquals(AddressUse.HOME, patient.getAddress().get(0).getUse());
-    List<Extension> ext = actual.getExtension();
-    assertEquals(1, ext.size());
-    Reference ref = (Reference) ext.get(0).getValue();
-    assertEquals("Organization/123", ref.getReference());
-
-  }
-
-  @Test
-  public void testEncodeHistoryEncodeVersionsAtPath3() {
-    ourCtx = FhirContext.forDstu3();
-
-    assertNull(ourCtx.newXmlParser().getStripVersionsFromReferences());
-
-    AuditEvent auditEvent = new AuditEvent();
-    auditEvent.addEntity().setReference(new Reference("http://foo.com/Organization/2/_history/1"));
-
-    IParser parser = ourCtx.newXmlParser();
-
-    parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
-    String enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
-    ourLog.info(enc);
-    assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2/_history/1\"/>"));
-
-    parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<String>());
-    enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
-    ourLog.info(enc);
-    assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
-
-    parser.setDontStripVersionsFromReferencesAtPaths((String[]) null);
-    enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
-    ourLog.info(enc);
-    assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
-
-    parser.setDontStripVersionsFromReferencesAtPaths((List<String>) null);
-    enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
-    ourLog.info(enc);
-    assertThat(enc, containsString("<reference value=\"http://foo.com/Organization/2\"/>"));
-
-  }
-
-  @Test
-  public void testEncodeNarrativeSuppressed() {
-    Patient patient = new Patient();
-    patient.setId("Patient/1/_history/1");
-    patient.getText().setDivAsString("<div>THE DIV</div>");
-    patient.addName().setFamily("FAMILY");
-    patient.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode("D")));
-    patient.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode("D")));
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).setSuppressNarratives(true).encodeResourceToString(patient);
-    ourLog.info(encoded);
-
-    assertThat(encoded, containsString("<Patient"));
-    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
-    assertThat(encoded, not(containsString("text")));
-    assertThat(encoded, not(containsString("THE DIV")));
-    assertThat(encoded, containsString("family"));
-    assertThat(encoded, containsString("maritalStatus"));
-  }
-
-  @Test
-  public void testEncodeNonContained() {
-    // Create an organization
-    Organization org = new Organization();
-    org.setId("Organization/65546");
-    org.getNameElement().setValue("Contained Test Organization");
-
-    // Create a patient
-    Patient patient = new Patient();
-    patient.setId("Patient/1333");
-    patient.addIdentifier().setSystem("urn:mrns").setValue("253345");
-    patient.getManagingOrganization().setResource(org);
-
-    // Create a list containing both resources. In a server method, you might just
-    // return this list, but here we will create a bundle to encode.
-    List<IBaseResource> resources = new ArrayList<IBaseResource>();
-    resources.add(org);
-    resources.add(patient);
-
-    // Create a bundle with both
-    Bundle b = new Bundle();
-    b.addEntry().setResource(org);
-    b.addEntry().setResource(patient);
-
-    // Encode the buntdle
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b);
-    ourLog.info(encoded);
-    assertThat(encoded, not(containsString("<contained>")));
-    assertThat(encoded, stringContainsInOrder("<Organization", "<id value=\"65546\"/>", "</Organization>"));
-    assertThat(encoded, containsString("<reference value=\"Organization/65546\"/>"));
-    assertThat(encoded, stringContainsInOrder("<Patient", "<id value=\"1333\"/>", "</Patient>"));
-
-    encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-    ourLog.info(encoded);
-    assertThat(encoded, not(containsString("<contained>")));
-    assertThat(encoded, containsString("<reference value=\"Organization/65546\"/>"));
-
-  }
-
-  /**
-   * See #312
-   */
-  @Test
-  public void testEncodeNullElement() {
-    Patient patient = new Patient();
-    patient.addName().getGiven().add(null);
-
-    IParser parser = ourCtx.newXmlParser();
-    String xml = parser.encodeResourceToString(patient);
-
-    ourLog.info(xml);
-    assertEquals("<Patient xmlns=\"http://hl7.org/fhir\"/>", xml);
-  }
-
-  /**
-   * See #312
-   */
-  @Test
-  public void testEncodeNullExtension() {
-    Patient patient = new Patient();
-    patient.getExtension().add(null); // Purposely add null
-    patient.getModifierExtension().add(null); // Purposely add null
-    patient.getExtension().add(new Extension("http://hello.world", new StringType("Hello World")));
-    patient.getName().add(null);
-    patient.addName().getGiven().add(null);
-
-    IParser parser = ourCtx.newXmlParser();
-    String xml = parser.encodeResourceToString(patient);
-
-    ourLog.info(xml);
-    assertEquals("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://hello.world\"><valueString value=\"Hello World\"/></extension></Patient>", xml);
-  }
-
-  @Test
-  public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
-
-    Patient patient = new Patient();
-    patient.setId("phitcc_pat_normal");
-    patient.addName().addGiven("Patty").setUse(NameUse.NICKNAME);
-    patient.addTelecom().setSystem(ContactPointSystem.EMAIL).setValue("patpain@ehealthinnovation.org");
-    patient.setGender(AdministrativeGender.FEMALE);
-    patient.setBirthDateElement(new DateType("2001-10-13"));
-
-    DateTimeType obsEffectiveTime = new DateTimeType("2015-04-11T12:22:01-04:00");
-
-    Observation obsParent = new Observation();
-    obsParent.setId("phitcc_obs_bp_parent");
-    obsParent.getSubject().setResource(patient);
-    obsParent.setStatus(ObservationStatus.FINAL);
-    obsParent.setEffective(obsEffectiveTime);
-
-    Observation obsSystolic = new Observation();
-    obsSystolic.setId("phitcc_obs_bp_dia");
-    obsSystolic.getSubject().setResource(patient);
-    obsSystolic.setEffective(obsEffectiveTime);
-    obsParent.addRelated().setType(ObservationRelationshipType.HASMEMBER).setTarget(new Reference(obsSystolic));
-
-    Observation obsDiastolic = new Observation();
-    obsDiastolic.setId("phitcc_obs_bp_dia");
-    obsDiastolic.getSubject().setResource(patient);
-    obsDiastolic.setEffective(obsEffectiveTime);
-    obsParent.addRelated().setType(ObservationRelationshipType.HASMEMBER).setTarget(new Reference(obsDiastolic));
-
-    String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
-    ourLog.info(str);
-
-    assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
-    assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
-  }
-
-  @Test
-  public void testEncodeReferenceWithUuid() {
-
-    Practitioner pract = new Practitioner();
-    pract.setId(IdType.newRandomUuid());
-    pract.addName().setFamily("PRACT FAMILY");
-
-    Patient patient = new Patient();
-    patient.addGeneralPractitioner().setResource(pract);
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-    ourLog.info(encoded);
-
-    assertThat(pract.getId(), startsWith("urn:uuid:"));
-    assertThat(encoded, containsString("<reference value=\"" + pract.getId() + "\"/>"));
-  }
-
-  @Test
-  public void testEncodeSummary() {
-    Patient patient = new Patient();
-    patient.setId("Patient/1/_history/1");
-    patient.getText().setDivAsString("<div>THE DIV</div>");
-    patient.addName().setFamily("FAMILY");
-    patient.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode("D")));
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).setSummaryMode(true).encodeResourceToString(patient);
-    ourLog.info(encoded);
-
-    assertThat(encoded, containsString("<Patient"));
-    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
-    assertThat(encoded, not(containsString("THE DIV")));
-    assertThat(encoded, containsString("family"));
-    assertThat(encoded, not(containsString("maritalStatus")));
-  }
-
-  @Test
-  public void testEncodeSummary2() {
-    Patient patient = new Patient();
-    patient.setId("Patient/1/_history/1");
-    patient.getText().setDivAsString("<div>THE DIV</div>");
-    patient.addName().setFamily("FAMILY");
-    patient.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode("D")));
-
-    patient.getMeta().addTag().setSystem("foo").setCode("bar");
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).setSummaryMode(true).encodeResourceToString(patient);
-    ourLog.info(encoded);
-
-    assertThat(encoded, containsString("<Patient"));
-    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"foo\"/>", "<code value=\"bar\"/>", "</tag>"));
-    assertThat(encoded, stringContainsInOrder("<tag>", "<system value=\"" + Constants.TAG_SUBSETTED_SYSTEM + "\"/>", "<code value=\"" + Constants.TAG_SUBSETTED_CODE + "\"/>", "</tag>"));
-    assertThat(encoded, not(containsString("THE DIV")));
-    assertThat(encoded, containsString("family"));
-    assertThat(encoded, not(containsString("maritalStatus")));
-  }
-
-  @Test
-  public void testEncodeUndeclaredBlock() throws Exception {
-    FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
-    source.getMessageHeaderApplicationId().setValue("APPID");
-    source.setName("NAME");
-
-    FooMessageHeader header = new FooMessageHeader();
-    header.setSource(source);
-
-    header.addDestination().setName("DEST");
-
-    Bundle bundle = new Bundle();
-    bundle.addEntry().setResource(header);
-
-    IParser p = ourCtx.newXmlParser();
-    p.setPrettyPrint(true);
-
-    String encode = p.encodeResourceToString(bundle);
-    ourLog.info(encode);
-
-    assertThat(encode, containsString("<value value=\"APPID\"/>"));
-    assertThat(encode, stringContainsInOrder("<dest","<source"));
-  }
-
-  @Test
-  public void testEncodeUndeclaredExtensionWithEnumerationContent() {
-    IParser parser = ourCtx.newXmlParser();
-
-    Patient patient = new Patient();
-    patient.addAddress().setUse(AddressUse.HOME);
-    EnumFactory<AddressUse> fact = new AddressUseEnumFactory();
-    PrimitiveType<AddressUse> enumeration = new Enumeration<AddressUse>(fact).setValue(AddressUse.HOME);
-    patient.addExtension().setUrl("urn:foo").setValue(enumeration);
-
-    String val = parser.encodeResourceToString(patient);
-    ourLog.info(val);
-    assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueCode value=\"home\"/></extension>"));
-
-    MyPatientWithOneDeclaredEnumerationExtensionDstu3 actual = parser.parseResource(MyPatientWithOneDeclaredEnumerationExtensionDstu3.class, val);
-    assertEquals(AddressUse.HOME, patient.getAddress().get(0).getUse());
-    Enumeration<AddressUse> ref = actual.getFoo();
-    assertEquals("home", ref.getValue().toCode());
-
-  }
-
-  @Test
-  public void testEncodeWithContained() {
-    List<Resource> contained = new ArrayList<Resource>();
-
-    // Will be added by reference
-    Patient p = new Patient();
-    p.setId("#" + "1000");
-    contained.add(p);
-
-    // Will be added by direct resource object
-    Location l = new Location();
-    l.setId("#" + "1001");
-    contained.add(l);
-
-    // Will not be referred to (and therefore shouldn't appear in output)
-    Location l2 = new Location();
-    l2.setId("#1002");
-    contained.add(l2);
-
-    Appointment appointment = new Appointment();
-    appointment.setId("1234");
-    appointment.getContained().addAll(contained);
-
-    appointment.addParticipant().getActor().setReference("#1000");
-    appointment.addParticipant().getActor().setResource(l);
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(appointment);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder(
-        "<Appointment xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"1234\"/>",
-        "<contained>",
-        "<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"1000\"/>",
-        "</Patient>",
-        "</contained>",
-        "<contained>",
-        "<Location xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"1001\"/>",
-        "</Location>",
-        "</contained>",
-        "<participant>",
-        "<actor>",
-        "<reference value=\"#1000\"/>",
-        "</actor>",
-        "</participant>",
-        "<participant>",
-        "<actor>",
-        "<reference value=\"#1001\"/>",
-        "</actor>",
-        "</participant>",
-        "</Appointment>"));
-
-    assertThat(encoded, not(containsString("#1002")));
-  }
-
-  @Test
-  public void testEncodeWithDontEncodeElements() throws Exception {
-    Patient patient = new Patient();
-    patient.setId("123");
-    patient.getMeta().addProfile("http://profile");
-    patient.addName().setFamily("FAMILY").addGiven("GIVEN");
-    patient.addAddress().addLine("LINE1");
-
-    {
-      IParser p = ourCtx.newXmlParser();
-      p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
-      p.setPrettyPrint(true);
-      String out = p.encodeResourceToString(patient);
-      ourLog.info(out);
-      assertThat(out, containsString("Patient"));
-      assertThat(out, containsString("name"));
-      assertThat(out, containsString("address"));
-      assertThat(out, not(containsString("id")));
-      assertThat(out, not(containsString("meta")));
-    }
-    {
-      IParser p = ourCtx.newXmlParser();
-      p.setDontEncodeElements(Sets.newHashSet("Patient.meta", "Patient.id"));
-      p.setPrettyPrint(true);
-      String out = p.encodeResourceToString(patient);
-      ourLog.info(out);
-      assertThat(out, containsString("Patient"));
-      assertThat(out, containsString("name"));
-      assertThat(out, containsString("address"));
-      assertThat(out, not(containsString("id")));
-      assertThat(out, not(containsString("meta")));
-    }
-    {
-      IParser p = ourCtx.newXmlParser();
-      p.setDontEncodeElements(Sets.newHashSet("Patient.name.family"));
-      p.setPrettyPrint(true);
-      String out = p.encodeResourceToString(patient);
-      ourLog.info(out);
-      assertThat(out, containsString("GIVEN"));
-      assertThat(out, not(containsString("FAMILY")));
-    }
-    {
-      IParser p = ourCtx.newXmlParser();
-      p.setDontEncodeElements(Sets.newHashSet("*.meta", "*.id"));
-      p.setPrettyPrint(true);
-      String out = p.encodeResourceToString(patient);
-      ourLog.info(out);
-      assertThat(out, containsString("Patient"));
-      assertThat(out, containsString("name"));
-      assertThat(out, containsString("address"));
-      assertThat(out, not(containsString("id")));
-      assertThat(out, not(containsString("meta")));
-    }
-    {
-      IParser p = ourCtx.newXmlParser();
-      p.setDontEncodeElements(Sets.newHashSet("Patient.meta"));
-      p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
-      p.setPrettyPrint(true);
-      String out = p.encodeResourceToString(patient);
-      ourLog.info(out);
-      assertThat(out, containsString("Patient"));
-      assertThat(out, containsString("name"));
-      assertThat(out, containsString("id"));
-      assertThat(out, not(containsString("address")));
-      assertThat(out, not(containsString("meta")));
-    }
-  }
-
-  @Test
-  public void testEncodeWithEncodeElements() throws Exception {
-    Patient patient = new Patient();
-    patient.getMeta().addProfile("http://profile");
-    patient.addName().setFamily("FAMILY");
-    patient.addAddress().addLine("LINE1");
-
-    Bundle bundle = new Bundle();
-    bundle.setTotal(100);
-    bundle.addEntry().setResource(patient);
-
-    {
-      IParser p = ourCtx.newXmlParser();
-      p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
-      p.setPrettyPrint(true);
-      String out = p.encodeResourceToString(bundle);
-      ourLog.info(out);
-      assertThat(out, not(containsString("total")));
-      assertThat(out, (containsString("Patient")));
-      assertThat(out, (containsString("name")));
-      assertThat(out, not(containsString("address")));
-    }
-    {
-      IParser p = ourCtx.newXmlParser();
-      p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
-      p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
-      p.setPrettyPrint(true);
-      String out = p.encodeResourceToString(bundle);
-      ourLog.info(out);
-      assertThat(out, (containsString("total")));
-      assertThat(out, (containsString("Patient")));
-      assertThat(out, (containsString("name")));
-      assertThat(out, not(containsString("address")));
-    }
-    {
-      IParser p = ourCtx.newXmlParser();
-      p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
-      p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
-      p.setPrettyPrint(true);
-      String out = p.encodeResourceToString(bundle);
-      ourLog.info(out);
-      assertThat(out, (containsString("total")));
-      assertThat(out, (containsString("Patient")));
-      assertThat(out, (containsString("name")));
-      assertThat(out, (containsString("address")));
-    }
-
-  }
-
-  @Test
-  public void testEncodeWithNarrative() {
-    Patient p = new Patient();
-    p.addName().setFamily("Smith").addGiven("John");
-
-    ourCtx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
-
-    String output = ourCtx.newXmlParser().encodeResourceToString(p);
-    ourLog.info(output);
-
-    assertThat(output, containsString("<text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">John <b>SMITH </b>"));
-  }
-
-  @Test
-  public void testMoreExtensions() throws Exception {
-
-    Patient patient = new Patient();
-    patient.addIdentifier().setUse(IdentifierUse.OFFICIAL).setSystem("urn:example").setValue("7000135");
-
-    Extension ext = new Extension();
-    ext.setUrl("http://example.com/extensions#someext");
-    ext.setValue(new DateTimeType("2011-01-02T11:13:15"));
-
-    // Add the extension to the resource
-    patient.addExtension(ext);
-    // END SNIPPET: resourceExtension
-
-    // START SNIPPET: resourceStringExtension
-    HumanName name = patient.addName();
-    name.setFamily("Shmoe");
-    StringType given = name.addGivenElement();
-    given.setValue("Joe");
-    Extension ext2 = new Extension().setUrl("http://examples.com#givenext").setValue(new StringType("given"));
-    given.addExtension(ext2);
-
-    StringType given2 = name.addGivenElement();
-    given2.setValue("Shmoe");
-    Extension given2ext = new Extension().setUrl("http://examples.com#givenext_parent");
-    given2.addExtension(given2ext);
-    Extension givenExtChild = new Extension();
-    givenExtChild.setUrl("http://examples.com#givenext_child").setValue(new StringType("CHILD"));
-    given2ext.addExtension(givenExtChild);
-    // END SNIPPET: resourceStringExtension
-
-    // START SNIPPET: subExtension
-    Extension parent = new Extension().setUrl("http://example.com#parent");
-    patient.addExtension(parent);
-
-    Extension child1 = new Extension().setUrl("http://example.com#child").setValue(new StringType("value1"));
-    parent.addExtension(child1);
-
-    Extension child2 = new Extension().setUrl("http://example.com#child").setValue(new StringType("value1"));
-    parent.addExtension(child2);
-    // END SNIPPET: subExtension
-
-    String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-    ourLog.info(output);
-
-    String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
-    assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
-    assertThat(enc, containsString(
-        "<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension></extension>"));
-    assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
-    assertThat(enc, containsString(
-        "<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
-  }
-
-  @Test
-  public void testOmitResourceId() {
-    Patient p = new Patient();
-    p.setId("123");
-    p.addName().setFamily("ABC");
-
-    assertThat(ourCtx.newXmlParser().encodeResourceToString(p), stringContainsInOrder("123", "ABC"));
-    assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), containsString("ABC"));
-    assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), not(containsString("123")));
-  }
-
-  @Test
-  @Ignore
-  public void testParseAndEncodeBundle() throws Exception {
-    String content = IOUtils.toString(XmlParserDstu3Test.class.getResourceAsStream("/bundle-example.xml"), StandardCharsets.UTF_8);
-
-    Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, content);
-    assertEquals("Bundle/example/_history/1", parsed.getIdElement().getValue());
-    assertEquals("1", parsed.getMeta().getVersionId());
-    assertEquals("1", parsed.getIdElement().getVersionIdPart());
-    assertEquals(("2014-08-18T01:43:30Z"), parsed.getMeta().getLastUpdatedElement().getValueAsString());
-    assertEquals("searchset", parsed.getType().toCode());
-    assertEquals(3, parsed.getTotal());
-    assertEquals("https://example.com/base/MedicationRequest?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLink("next").getUrl());
-    assertEquals("https://example.com/base/MedicationRequest?patient=347&_include=MedicationRequest.medication", parsed.getLink("self").getUrl());
-
-    assertEquals(2, parsed.getEntry().size());
-    assertEquals("http://foo?search", parsed.getEntry().get(0).getLink("search").getUrl());
-
-    assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", parsed.getEntry().get(0).getLink("alternate").getUrl());
-    MedicationRequest p = (MedicationRequest) parsed.getEntry().get(0).getResource();
-    assertEquals("Patient/347", p.getSubject().getReference());
-    assertEquals("2014-08-16T05:31:17Z", p.getMeta().getLastUpdatedElement().getValueAsString());
-    assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", p.getId());
-
-    Medication m = (Medication) parsed.getEntry().get(1).getResource();
-    assertEquals("http://example.com/base/Medication/example", m.getId());
-    assertSame(((Reference) p.getMedication()).getResource(), m);
-
-    String reencoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parsed);
-    ourLog.info(reencoded);
-
-    Diff d = new Diff(new StringReader(content), new StringReader(reencoded));
-    assertTrue(d.toString(), d.identical());
-
-  }
-
-  @Test
-  @Ignore
-  public void testParseAndEncodeBundleNewStyle() throws Exception {
-    String content = IOUtils.toString(XmlParserDstu3Test.class.getResourceAsStream("/bundle-example.xml"), StandardCharsets.UTF_8);
-
-    IParser newXmlParser = ourCtx.newXmlParser();
-    Bundle parsed = newXmlParser.parseResource(Bundle.class, content);
-    assertEquals("Bundle/example/_history/1", parsed.getIdElement().getValue());
-    assertEquals("1", parsed.getIdElement().getVersionIdPart());
-    assertEquals("2014-08-18T01:43:30Z", parsed.getMeta().getLastUpdatedElement().getValueAsString());
-    assertEquals("searchset", parsed.getType());
-    assertEquals(3, parsed.getTotal());
-    assertEquals("https://example.com/base/MedicationRequest?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLink().get(0).getUrlElement().getValueAsString());
-    assertEquals("https://example.com/base/MedicationRequest?patient=347&_include=MedicationRequest.medication", parsed.getLink().get(1).getUrlElement().getValueAsString());
-
-    assertEquals(2, parsed.getEntry().size());
-    assertEquals("alternate", parsed.getEntry().get(0).getLink().get(0).getRelation());
-    assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", parsed.getEntry().get(0).getLink().get(0).getUrl());
-    assertEquals("http://foo?search", parsed.getEntry().get(0).getRequest().getUrlElement().getValueAsString());
-
-    MedicationRequest p = (MedicationRequest) parsed.getEntry().get(0).getResource();
-    assertEquals("Patient/347", p.getSubject().getReference());
-    assertEquals("2014-08-16T05:31:17Z", p.getMeta().getLastUpdatedElement().getValueAsString());
-    assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", p.getId());
-    // assertEquals("3123", p.getId());
-
-    Medication m = (Medication) parsed.getEntry().get(1).getResource();
-    assertEquals("http://example.com/base/Medication/example", m.getId());
-    assertSame(((Reference) p.getMedication()).getResource(), m);
-
-    String reencoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parsed);
-    ourLog.info(reencoded);
-
-    Diff d = new Diff(new StringReader(content), new StringReader(reencoded));
-    assertTrue(d.toString(), d.identical());
-
-  }
-
-  @Test
-  public void testParseAndEncodeComments() {
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "  <!--pre resource comment-->" +
-        "  <id value=\"pat1\"/>\n" +
-        "  <text>\n" +
-        "    <status value=\"generated\"/>\n" +
-        "    <div xmlns=\"http://www.w3.org/1999/xhtml\">\n" +
-        "\n" +
-        "      <p>Patient Donald DUCK @ Acme Healthcare, Inc. MR = 654321</p>\n" +
-        "\n" +
-        "    </div>\n" +
-        "  </text>\n" +
-        "  <!--identifier comment 1-->\n" +
-        "  <!--identifier comment 2-->\n" +
-        "  <identifier>\n" +
-        "    <!--use comment 1-->\n" +
-        "    <!--use comment 2-->\n" +
-        "    <use value=\"usual\"/>\n" +
-        "    <type>\n" +
-        "      <coding>\n" +
-        "        <system value=\"http://hl7.org/fhir/v2/0203\"/>\n" +
-        "        <code value=\"MR\"/>\n" +
-        "      </coding>\n" +
-        "    </type>\n" +
-        "    <system value=\"urn:oid:0.1.2.3.4.5.6.7\"/>\n" +
-        "    <value value=\"654321\"/>\n" +
-        "  </identifier>\n" +
-        "  <active value=\"true\"/>" +
-        "  <!--post resource comment-->" +
-        "</Patient>";
-
-    Patient res = ourCtx.newXmlParser().parseResource(Patient.class, input);
-    res.getFormatCommentsPre();
-    assertEquals("Patient/pat1", res.getId());
-    assertEquals("654321", res.getIdentifier().get(0).getValue());
-    assertEquals(true, res.getActive());
-
-    assertThat(res.getIdElement().getFormatCommentsPre(), contains("pre resource comment"));
-    assertThat(res.getIdentifier().get(0).getFormatCommentsPre(), contains("identifier comment 1", "identifier comment 2"));
-    assertThat(res.getIdentifier().get(0).getUseElement().getFormatCommentsPre(), contains("use comment 1", "use comment 2"));
-    assertThat(res.getActiveElement().getFormatCommentsPost(), contains("post resource comment"));
-
-    String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(res);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder(
-        "\"identifier\": [",
-        "{",
-        "\"fhir_comments\":",
-        "[",
-        "\"identifier comment 1\"",
-        ",",
-        "\"identifier comment 2\"",
-        "]",
-        "\"use\": \"usual\",",
-        "\"_use\": {",
-        "\"fhir_comments\":",
-        "[",
-        "\"use comment 1\"",
-        ",",
-        "\"use comment 2\"",
-        "]",
-        "},",
-        "\"type\""));
-
-    encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(res);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder(
-        "<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"pat1\"/>",
-        "<text>",
-        "<status value=\"generated\"/>",
-        "<div xmlns=\"http://www.w3.org/1999/xhtml\"> ",
-        "<p>Patient Donald DUCK @ Acme Healthcare, Inc. MR = 654321</p> ",
-        "</div>",
-        "</text>",
-        " <!--identifier comment 1-->\n",
-        " <!--identifier comment 2-->",
-        "<identifier>",
-        "<!--use comment 1-->",
-        "<!--use comment 2-->",
-        "<use value=\"usual\"/>",
-        "<type>",
-        "<coding>",
-        "<system value=\"http://hl7.org/fhir/v2/0203\"/>",
-        "<code value=\"MR\"/>",
-        "</coding>",
-        "</type>",
-        "<system value=\"urn:oid:0.1.2.3.4.5.6.7\"/>",
-        "<value value=\"654321\"/>",
-        "</identifier>",
-        "<active value=\"true\"/>",
-        "</Patient>"));
-
-  }
-
-  @Test
-  public void testParseAndEncodeCommentsOnExtensions() {
-
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "  <!-- comment 1 -->\n" +
-        "  <id value=\"someid\"/>\n" +
-        "  <!-- comment 2 -->\n" +
-        "  <extension url=\"urn:patientext:att\">\n" +
-        "    <!-- comment 3 -->\n" +
-        "    <valueAttachment>\n" +
-        "      <!-- comment 4 -->\n" +
-        "      <contentType value=\"aaaa\"/>\n" +
-        "      <data value=\"AAAA\"/>\n" +
-        "      <!-- comment 5 -->\n" +
-        "    </valueAttachment>\n" +
-        "    <!-- comment 6 -->\n" +
-        "  </extension>\n" +
-        "  <!-- comment 7 -->\n" +
-        "</Patient>";
-
-    Patient pat = ourCtx.newXmlParser().parseResource(Patient.class, input);
-    String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(pat);
-    ourLog.info(output);
-
-    assertThat(output, stringContainsInOrder(
-        "<Patient xmlns=\"http://hl7.org/fhir\">",
-        "  <!-- comment 1 -->",
-        "  <id value=\"someid\"/>",
-        "  <!-- comment 2 -->",
-        "  <extension url=\"urn:patientext:att\">",
-        "    <!-- comment 3 -->",
-        "    <valueAttachment>",
-        "      <!-- comment 4 -->",
-        "      <contentType value=\"aaaa\"/>",
-        "      <data value=\"AAAA\"/>",
-        "      <!-- comment 5 -->",
-        "    </valueAttachment>",
-        "    <!-- comment 6 -->",
-        "  </extension>",
-        "  <!-- comment 7 -->",
-        "</Patient>"));
-
-    output = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(pat);
-    ourLog.info(output);
-
-    assertThat(output, stringContainsInOrder(
-        "{",
-        "  \"resourceType\": \"Patient\",",
-        "  \"id\": \"someid\",",
-        "  \"_id\": {",
-        "    \"fhir_comments\": [",
-        "      \" comment 1 \"",
-        "    ]",
-        "  },",
-        "  \"extension\": [",
-        "    {",
-        "      \"fhir_comments\": [",
-        "        \" comment 2 \",",
-        "        \" comment 7 \"",
-        "      ],",
-        "      \"url\": \"urn:patientext:att\",",
-        "      \"valueAttachment\": {",
-        "        \"fhir_comments\": [",
-        "          \" comment 3 \",",
-        "          \" comment 6 \"",
-        "        ],",
-        "        \"contentType\": \"aaaa\",",
-        "        \"_contentType\": {",
-        "          \"fhir_comments\": [",
-        "            \" comment 4 \"",
-        "          ]",
-        "        },",
-        "        \"data\": \"AAAA\",",
-        "        \"_data\": {",
-        "          \"fhir_comments\": [",
-        "            \" comment 5 \"",
-        "          ]",
-        "        }",
-        "      }",
-        "    }",
-        "  ]",
-        "}"));
-
-  }
-
-  @Test
-  public void testParseAndEncodeExtensionOnReference() {
-
-    String input = "<DataElement>" +
-        "<id value=\"gender\"/>" +
-        "<contained>" +
-        "<ValueSet>" +
-        "<id value=\"2179414\"/>" +
-        "<url value=\"2179414\"/>" +
-        "<version value=\"1.0\"/>" +
-        "<status value=\"active\"/>" +
-        "<description value=\"All codes representing the gender of a person.\"/>" +
-        "<compose>" +
-        "<include>" +
-        "<system value=\"http://ncit.nci.nih.gov\"/>" +
-        "<concept>" +
-        "<code value=\"C17998\"/>" +
-        "<display value=\"Unknown\"/>" +
-        "</concept>" +
-        "<concept>" +
-        "<code value=\"C20197\"/>" +
-        "<display value=\"Male\"/>" +
-        "</concept>" +
-        "<concept>" +
-        "<code value=\"C16576\"/>" +
-        "<display value=\"Female\"/>" +
-        "</concept>" +
-        "<concept>" +
-        "<code value=\"C38046\"/>" +
-        "<display value=\"Not specified\"/>" +
-        "</concept>" +
-        "</include>" +
-        "</compose>" +
-        "</ValueSet>" +
-        "</contained>" +
-        "<contained>" +
-        "<ValueSet>" +
-        "<id value=\"2179414-permitted\"/>" +
-        "<status value=\"active\"/>" +
-        "<codeSystem>" +
-        "<system value=\"http://example.org/fhir/2179414\"/>" +
-        "<caseSensitive value=\"true\"/>" +
-        "<concept>" +
-        "<code value=\"0\"/>" +
-        "</concept>" +
-        "<concept>" +
-        "<code value=\"1\"/>" +
-        "</concept>" +
-        "<concept>" +
-        "<code value=\"2\"/>" +
-        "</concept>" +
-        "<concept>" +
-        "<code value=\"3\"/>" +
-        "</concept>" +
-        "</codeSystem>" +
-        "</ValueSet>" +
-        "</contained>" +
-        "<contained>" +
-        "<ConceptMap>" +
-        "<id value=\"2179414-cm\"/>" +
-        "<status value=\"active\"/>" +
-        "<sourceReference>" +
-        "<reference value=\"#2179414\"/>" +
-        "</sourceReference>" +
-        "<targetReference>" +
-        "<reference value=\"#2179414-permitted\"/>" +
-        "</targetReference>" +
-        "<element>" +
-        "<code value=\"C17998\"/>" +
-        "<target>" +
-        "<code value=\"0\"/>" +
-        "<equivalence value=\"equal\"/>" +
-        "</target>" +
-        "</element>" +
-        "<element>" +
-        "<code value=\"C20197\"/>" +
-        "<target>" +
-        "<code value=\"1\"/>" +
-        "<equivalence value=\"equal\"/>" +
-        "</target>" +
-        "</element>" +
-        "<element>" +
-        "<code value=\"C16576\"/>" +
-        "<target>" +
-        "<code value=\"2\"/>" +
-        "<equivalence value=\"equal\"/>" +
-        "</target>" +
-        "</element>" +
-        "<element>" +
-        "<code value=\"C38046\"/>" +
-        "<target>" +
-        "<code value=\"3\"/>" +
-        "<equivalence value=\"equal\"/>" +
-        "</target>" +
-        "</element>" +
-        "</ConceptMap>" +
-        "</contained>" +
-        "<identifier>" +
-        "<value value=\"2179650\"/>" +
-        "</identifier>" +
-        "<version value=\"1.0\"/>" +
-        "<name value=\"Gender Code\"/>" +
-        "<status value=\"active\"/>" +
-        "<publisher value=\"DCP\"/>" +
-        "<useContext>" +
-        "<coding>" +
-        "<system value=\"http://example.org/FBPP\"/>" +
-        "<display value=\"FBPP Pooled Database\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/PhenX\"/>" +
-        "<display value=\"Demographics\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/EligibilityCriteria\"/>" +
-        "<display value=\"Pt. Administrative\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/UAMSClinicalResearch\"/>" +
-        "<display value=\"UAMS New CDEs\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/PhenX\"/>" +
-        "<display value=\"Substance Abuse and \"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/Category\"/>" +
-        "<display value=\"CSAERS Adverse Event\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/PhenX\"/>" +
-        "<display value=\"Core: Tier 1\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/Category\"/>" +
-        "<display value=\"Case Report Forms\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/Category\"/>" +
-        "<display value=\"CSAERS Review Set\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/Demonstration%20Applications\"/>" +
-        "<display value=\"CIAF\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/NIDA%20CTN%20Usage\"/>" +
-        "<display value=\"Clinical Research\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/NIDA%20CTN%20Usage\"/>" +
-        "<display value=\"Electronic Health Re\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/Condition\"/>" +
-        "<display value=\"Barretts Esophagus\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/Condition\"/>" +
-        "<display value=\"Bladder Cancer\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/Condition\"/>" +
-        "<display value=\"Oral Leukoplakia\"/>" +
-        "</coding>" +
-        "<coding>" +
-        "<system value=\"http://example.org/Condition\"/>" +
-        "<display value=\"Sulindac for Breast\"/>" +
-        "</coding>" +
-        "</useContext>" +
-        "<element>" +
-        "<extension url=\"http://hl7.org/fhir/StructureDefinition/minLength\">" +
-        "<valueInteger value=\"1\"/>" +
-        "</extension>" +
-        "<extension url=\"http://hl7.org/fhir/StructureDefinition/elementdefinition-question\">" +
-        "<valueString value=\"Gender\"/>" +
-        "</extension>" +
-        "<path value=\"Gender\"/>" +
-        "<definition value=\"The code representing the gender of a person.\"/>" +
-        "<type>" +
-        "<code value=\"CodeableConcept\"/>" +
-        "</type>" +
-        "<maxLength value=\"13\"/>" +
-        "<binding>" +
-        "<strength value=\"required\"/>" +
-        "<valueSetReference>" +
-        "<extension url=\"http://hl7.org/fhir/StructureDefinition/11179-permitted-value-valueset\">" +
-        "<valueReference>" +
-        "<reference value=\"#2179414-permitted\"/>" +
-        "</valueReference>" +
-        "</extension>" +
-        "<extension url=\"http://hl7.org/fhir/StructureDefinition/11179-permitted-value-conceptmap\">" +
-        "<valueReference>" +
-        "<reference value=\"#2179414-cm\"/>" +
-        "</valueReference>" +
-        "</extension>" +
-        "<reference value=\"#2179414\"/>" +
-        "</valueSetReference>" +
-        "</binding>" +
-        "</element>" +
-        "</DataElement>";
-
-    DataElement de = ourCtx.newXmlParser().parseResource(DataElement.class, input);
-    String output = ourCtx.newXmlParser().encodeResourceToString(de).replace(" xmlns=\"http://hl7.org/fhir\"", "");
-
-    ElementDefinition elem = de.getElement().get(0);
-    ElementDefinitionBindingComponent b = elem.getBinding();
-    // assertEquals("All codes representing the gender of a person.", b.getDescription());
-
-    Reference ref = (Reference) b.getValueSet();
-    assertEquals("#2179414", ref.getReference());
-
-    assertEquals(2, ref.getExtension().size());
-    Extension ext = ref.getExtension().get(0);
-    assertEquals("http://hl7.org/fhir/StructureDefinition/11179-permitted-value-valueset", ext.getUrl());
-    assertEquals(Reference.class, ext.getValue().getClass());
-    assertEquals("#2179414-permitted", ((Reference) ext.getValue()).getReference());
-    assertEquals(ValueSet.class, ((Reference) ext.getValue()).getResource().getClass());
-
-    ext = ref.getExtension().get(1);
-    assertEquals("http://hl7.org/fhir/StructureDefinition/11179-permitted-value-conceptmap", ext.getUrl());
-    assertEquals(Reference.class, ext.getValue().getClass());
-    assertEquals("#2179414-cm", ((Reference) ext.getValue()).getReference());
-    assertEquals(ConceptMap.class, ((Reference) ext.getValue()).getResource().getClass());
-
-    ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(de));
-
-    assertThat(output, containsString("http://hl7.org/fhir/StructureDefinition/11179-permitted-value-valueset"));
-
-  }
-
-  @Test
-  public void testParseAndEncodeNestedExtensions() {
-
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <birthDate value=\"2005-03-04\">\n" +
-        "      <extension url=\"http://my.fancy.extension.url\">\n" +
-        "         <extension url=\"http://my.fancy.extension.url\">\n" +
-        "            <valueString value=\"myNestedValue\"/>\n" +
-        "         </extension>\n" +
-        "      </extension>\n" +
-        "   </birthDate>\n" +
-        "</Patient>";
-
-    Patient p = ourCtx.newXmlParser().parseResource(Patient.class, input);
-    DateType bd = p.getBirthDateElement();
-    assertEquals("2005-03-04", bd.getValueAsString());
-
-    List<Extension> exts = bd.getExtensionsByUrl("http://my.fancy.extension.url");
-    assertEquals(1, exts.size());
-    Extension ext = exts.get(0);
-    assertEquals(null, ext.getValue());
-
-    exts = ext.getExtensionsByUrl("http://my.fancy.extension.url");
-    assertEquals(1, exts.size());
-    ext = exts.get(0);
-    assertEquals("myNestedValue", ((StringType) ext.getValue()).getValue());
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
-    ourLog.info(encoded);
-
-    assertThat(encoded, stringContainsInOrder(
-        "<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<birthDate value=\"2005-03-04\">",
-        "<extension url=\"http://my.fancy.extension.url\">",
-        "<extension url=\"http://my.fancy.extension.url\">",
-        "<valueString value=\"myNestedValue\"/>",
-        "</extension>",
-        "</extension>",
-        "</birthDate>",
-        "</Patient>"));
-
-  }
-
-  @Test
-  public void testParseBundleNewWithPlaceholderIds() {
-
-    String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "    <id value=\"ringholm1430996763590912\"/>\n" +
-        "    <entry>\n" +
-        "        <fullUrl value=\"urn:oid:0.1.2.3\"/>\n" +
-        "        <resource>\n" +
-        "            <Provenance>\n" +
-        "                <id value=\"0.1.2.3\"/>\n" +
-        "            </Provenance>\n" +
-        "        </resource>\n" +
-        "    </entry>\n" +
-        "</Bundle>\n";
-
-    Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
-    assertEquals("urn:oid:0.1.2.3", parsed.getEntry().get(0).getResource().getIdElement().getValue());
-
-  }
-
-  @Test
-  public void testParseBundleNewWithPlaceholderIdsInBase1() {
-
-    String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "    <id value=\"ringholm1430996763590912\"/>\n" +
-        "    <entry>\n" +
-        "        <fullUrl value=\"urn:oid:0.1.2.3\"/>\n" +
-        "        <resource>\n" +
-        "            <Provenance>\n" +
-        "                <id value=\"0.1.2.3\"/>\n" +
-        "            </Provenance>\n" +
-        "        </resource>\n" +
-        "    </entry>\n" +
-        "</Bundle>\n";
-
-    Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
-    assertEquals("urn:oid:0.1.2.3", parsed.getEntry().get(0).getResource().getIdElement().getValue());
-  }
-
-  @Test
-  public void testParseBundleNewWithPlaceholderIdsInBase2() {
-
-    String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "    <id value=\"ringholm1430996763590912\"/>\n" +
-        "    <entry>\n" +
-        "        <fullUrl value=\"urn:uuid:0.1.2.3\"/>\n" +
-        "        <resource>\n" +
-        "            <Provenance>\n" +
-        "                <id value=\"0.1.2.3\"/>\n" +
-        "            </Provenance>\n" +
-        "        </resource>\n" +
-        "    </entry>\n" +
-        "</Bundle>\n";
-
-    Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
-    assertEquals("urn:uuid:0.1.2.3", parsed.getEntry().get(0).getResource().getIdElement().getValue());
-
-    input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "    <id value=\"ringholm1430996763590912\"/>\n" +
-        "    <entry>\n" +
-        "        <fullUrl value=\"urn:uuid:0.1.2.3\"/>\n" +
-        "        <resource>\n" +
-        "            <Provenance>\n" +
-        "                <id value=\"0.1.2.3\"/>\n" +
-        "            </Provenance>\n" +
-        "        </resource>\n" +
-        "    </entry>\n" +
-        "</Bundle>\n";
-
-    parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
-    assertEquals("urn:uuid:0.1.2.3", parsed.getEntry().get(0).getResource().getIdElement().getValue());
-
-  }
-
-  @Test
-  public void testParseBundleOldStyleWithUnknownLinks() throws Exception {
-
-    String bundle = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <base value=\"http://foo/fhirBase1\"/>\n" +
-        "   <total value=\"1\"/>\n" +
-        "   <link>\n" +
-        "      <relation value=\"foo\"/>\n" +
-        "      <url value=\"http://localhost:52788/Binary?_pretty=true\"/>\n" +
-        "   </link>\n" +
-        "   <entry>\n" +
-        "   <link>\n" +
-        "      <relation value=\"bar\"/>\n" +
-        "      <url value=\"http://localhost:52788/Binary?_pretty=true\"/>\n" +
-        "   </link>\n" +
-        "      <resource>\n" +
-        "         <Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "            <id value=\"1\"/>\n" +
-        "            <meta>\n" +
-        "               <versionId value=\"2\"/>\n" +
-        "               <lastUpdated value=\"2001-02-22T11:22:33-05:00\"/>\n" +
-        "            </meta>\n" +
-        "            <birthDate value=\"2012-01-02\"/>\n" +
-        "         </Patient>\n" +
-        "      </resource>\n" +
-        "   </entry>\n" +
-        "</Bundle>";
-
-    Bundle b = (Bundle) ourCtx.newXmlParser().parseResource(bundle);
-    assertEquals(1, b.getEntry().size());
-
-  }
-
-  @Test
-  public void testParseBundleOldWithPlaceholderIds() {
-
-    String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "    <id value=\"ringholm1430996763590912\"/>\n" +
-        "    <entry>\n" +
-        "        <fullUrl value=\"urn:oid:0.1.2.3\"/>\n" +
-        "        <resource>\n" +
-        "            <Provenance>\n" +
-        "                <id value=\"0.1.2.3\"/>\n" +
-        "            </Provenance>\n" +
-        "        </resource>\n" +
-        "    </entry>\n" +
-        "</Bundle>\n";
-
-    Bundle parsed = (Bundle) ourCtx.newXmlParser().parseResource(input);
-    assertEquals("urn:oid:0.1.2.3", parsed.getEntry().get(0).getResource().getId());
-
-  }
-
-  @Test
-  public void testParseBundleWithBinary() {
-    // TODO: implement this test, make sure we handle ID and meta correctly in Binary
-  }
-
-  /**
-   * See #191
-   */
-  @Test
-  public void testParseBundleWithLinksOfUnknownRelation() throws Exception {
-    String input = IOUtils.toString(XmlParserDstu3Test.class.getResourceAsStream("/bundle_orion.xml"), StandardCharsets.UTF_8);
-    Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
-
-    BundleLinkComponent link = parsed.getLink().get(0);
-    assertEquals("just trying add link", link.getRelation());
-    assertEquals("blarion", link.getUrl());
-
-    BundleEntryComponent entry = parsed.getEntry().get(0);
-    link = entry.getLink().get(0);
-    assertEquals("orionhealth.edit", link.getRelation());
-    assertEquals("Observation", link.getUrl());
-  }
-
-  @Test
-  public void testParseBundleWithResourceId() {
-
-    String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
-        + "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
-        + "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
-        + "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
-        + "</Bundle>\n";
-
-    Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, input);
-    assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getIdElement().getValue());
-    assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getIdElement().getValue());
-    assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getIdElement().getValue());
-  }
-
-  /**
-   * see #144 and #146
-   */
-  @Test
-  @Ignore
-  public void testParseContained() {
-
-    FhirContext c = FhirContext.forDstu3();
-    IParser parser = c.newXmlParser().setPrettyPrint(true);
-
-    Observation o = new Observation();
-    o.getCode().setText("obs text");
-
-    Patient p = new Patient();
-    p.addName().setFamily("patient family");
-    o.getSubject().setResource(p);
-
-    String enc = parser.encodeResourceToString(o);
-    ourLog.info(enc);
-
-    assertThat(enc, stringContainsInOrder(
-        "<Observation xmlns=\"http://hl7.org/fhir\">",
-        "<contained>",
-        "<Patient xmlns=\"http://hl7.org/fhir\">",
-        "<id value=\"1\"/>",
-        "</contained>",
-        "<reference value=\"#1\"/>"));
-
-    o = parser.parseResource(Observation.class, enc);
-    assertEquals("obs text", o.getCode().getText());
-
-    assertNotNull(o.getSubject().getResource());
-    p = (Patient) o.getSubject().getResource();
-    assertEquals("patient family", p.getName().get(0).getFamily());
-  }
-
-  /**
-   * Thanks to Alexander Kley!
-   */
-  @Test
-  public void testParseContainedBinaryResource() {
-    byte[] bin = new byte[] { 0, 1, 2, 3, 4 };
-    final Binary binary = new Binary();
-    binary.setContentType("PatientConsent").setContent(bin);
-
-    DocumentManifest manifest = new DocumentManifest();
-    CodeableConcept cc = new CodeableConcept();
-    cc.addCoding().setSystem("mySystem").setCode("PatientDocument");
-    manifest.setType(cc);
-    manifest.setMasterIdentifier(new Identifier().setSystem("mySystem").setValue(UUID.randomUUID().toString()));
-    manifest.addContent().setP(new Reference(binary));
-    manifest.setStatus(DocumentReferenceStatus.CURRENT);
-
-    String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(manifest);
-    ourLog.info(encoded);
-    assertThat(encoded, StringContainsInOrder.stringContainsInOrder(Arrays.asList("contained>", "<Binary", "</contained>")));
-
-    DocumentManifest actual = ourCtx.newXmlParser().parseResource(DocumentManifest.class, encoded);
-    assertEquals(1, actual.getContained().size());
-    assertEquals(1, actual.getContent().size());
-
-    /*
-     * If this fails, it's possibe the DocumentManifest structure is wrong: It should be
-     * 
-     * @Child(name = "p", type = {Attachment.class, ValueSet.class}, order=1, min=1, max=1, modifier=false, summary=true)
-     */
-    assertNotNull(((Reference) actual.getContent().get(0).getP()).getResource());
-  }
-
-  /**
-   * See #426
-   */
-  @Test
-  public void testParseExtensionWithIdType() {
-
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "    <extension url=\"http://aaa.ch/fhir/Patient#mangedcare\">\n" +
-        "        <extension url=\"http://aaa.ch/fhir/Patient#mangedcare-aaa-id\">\n" +
-        "           <valueId value=\"mc1\"/>\n" +
-        "        </extension>\n" +
-        "    </extension>\n" +
-        "    <identifier>\n" +
-        "        <value value=\"ais111\"/>\n" +
-        "    </identifier>\n" +
-        "</Patient>";
-
-    Patient pt = ourCtx.newXmlParser().parseResource(Patient.class, input);
-
-    List<Extension> extList = pt.getExtensionsByUrl("http://aaa.ch/fhir/Patient#mangedcare");
-    extList = extList.get(0).getExtensionsByUrl("http://aaa.ch/fhir/Patient#mangedcare-aaa-id");
-    Extension ext = extList.get(0);
-    IdType value = (IdType) ext.getValue();
-    assertEquals("mc1", value.getValueAsString());
-  }
-
-  /**
-   * See #426
-   * 
-   * Value type of FOO isn't a valid datatype
-   */
-  @Test
-  public void testParseExtensionWithInvalidType() {
-
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "    <extension url=\"http://aaa.ch/fhir/Patient#mangedcare\">\n" +
-        "        <extension url=\"http://aaa.ch/fhir/Patient#mangedcare-aaa-id\">\n" +
-        "           <valueFOO value=\"mc1\"/>\n" +
-        "        </extension>\n" +
-        "    </extension>\n" +
-        "    <identifier>\n" +
-        "        <value value=\"ais111\"/>\n" +
-        "    </identifier>\n" +
-        "</Patient>";
-
-    Patient pt = ourCtx.newXmlParser().parseResource(Patient.class, input);
-
-    List<Extension> extList = pt.getExtensionsByUrl("http://aaa.ch/fhir/Patient#mangedcare");
-    extList = extList.get(0).getExtensionsByUrl("http://aaa.ch/fhir/Patient#mangedcare-aaa-id");
-    Extension ext = extList.get(0);
-    IdType value = (IdType) ext.getValue();
-    assertEquals(null, value);
-  }
-
-  /**
-   * See #342
-   */
-  @Test(expected = DataFormatException.class)
-  public void testParseInvalid() {
-    ourCtx.newXmlParser().parseResource("FOO");
-  }
-
-  /**
-   * See #366
-   */
-  @Test()
-  public void testParseInvalidBoolean() {
-
-    String resource = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <active value=\"1\"/>\n" +
-        "</Patient>";
-
-    IParser p = ourCtx.newXmlParser();
-
-    try {
-      p.parseResource(resource);
-      fail();
-    } catch (DataFormatException e) {
-      assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"1\": Invalid boolean string: '1'", e.getMessage());
-    }
-
-    LenientErrorHandler errorHandler = new LenientErrorHandler();
-    assertEquals(true, errorHandler.isErrorOnInvalidValue());
-    errorHandler.setErrorOnInvalidValue(false);
-    p.setParserErrorHandler(errorHandler);
-  }
-
-  @Test
-  public void testParseInvalidTextualNumber() {
-    Observation obs = new Observation();
-    obs.setValue(new Quantity().setValue(1234));
-    String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs);
-    encoded = encoded.replace("1234", "\"1234\"");
-    ourLog.info(encoded);
-    ourCtx.newJsonParser().parseResource(encoded);
-  }
-
-  /**
-   * See #216
-   */
-  @Test
-  public void testParseMalformedIdentifierDstu2() {
-
-    // This was changed from 0.5 to 1.0.0
-
-    String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <identifier>\n" +
-        "      <type value=\"MRN\"/>\n" +
-        "      <system value=\"SYS\"/>\n" +
-        "      <value value=\"VAL\"/>\n" +
-        "   </identifier>\n" +
-        "</Patient>";
-
-    IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
-
-    IParser p = ourCtx.newXmlParser();
-    p.setParserErrorHandler(errorHandler);
-
-    Patient patient = p.parseResource(Patient.class, out);
-    assertThat(patient.getIdentifier().get(0).getType().getCoding(), IsEmptyCollection.empty());
-
-    ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
-    verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
-
-    assertEquals("value", capt.getValue());
-  }
-
-  @Test
-  public void testParseMetadata() throws Exception {
-
-    String bundle = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <total value=\"1\"/>\n" +
-        "   <link>\n" +
-        "      <relation value=\"self\"/>\n" +
-        "      <url value=\"http://localhost:52788/Binary?_pretty=true\"/>\n" +
-        "   </link>\n" +
-        "   <entry>\n" +
-        "      <fullUrl value=\"http://foo/fhirBase2/Patient/1/_history/2\"/>\n" +
-        "      <resource>\n" +
-        "         <Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "            <id value=\"1\"/>\n" +
-        "            <meta>\n" +
-        "               <versionId value=\"2\"/>\n" +
-        "               <lastUpdated value=\"2001-02-22T09:22:33-07:00\"/>\n" +
-        "            </meta>\n" +
-        "            <birthDate value=\"2012-01-02\"/>\n" +
-        "         </Patient>\n" +
-        "      </resource>\n" +
-        "      <search>\n" +
-        "         <mode value=\"match\"/>\n" +
-        "         <score value=\"0.123\"/>\n" +
-        "      </search>\n" +
-        "      <request>\n" +
-        "         <method value=\"POST\"/>\n" +
-        "         <url value=\"http://foo/Patient?identifier=value\"/>\n" +
-        "      </request>\n" +
-        "   </entry>\n" +
-        "</Bundle>";
-
-    Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, bundle);
-    assertEquals(1, b.getEntry().size());
-
-    BundleEntryComponent entry = b.getEntry().get(0);
-    Patient pt = (Patient) entry.getResource();
-    assertEquals("http://foo/fhirBase2/Patient/1/_history/2", pt.getIdElement().getValue());
-    assertEquals("2012-01-02", pt.getBirthDateElement().getValueAsString());
-    assertEquals("0.123", entry.getSearch().getScore().toString());
-    assertEquals("match", entry.getSearch().getMode().toCode());
-    assertEquals("POST", entry.getRequest().getMethod().toCode());
-    assertEquals("http://foo/Patient?identifier=value", entry.getRequest().getUrl());
-    assertEquals("2001-02-22T09:22:33-07:00", pt.getMeta().getLastUpdatedElement().getValueAsString());
-
-    IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
-    String reEncoded = p.encodeResourceToString(b);
-    ourLog.info(reEncoded);
-
-    Diff d = new Diff(new StringReader(bundle), new StringReader(reEncoded));
-    assertTrue(d.toString(), d.identical());
-
-  }
-
-  @Test
-  public void testParseMetaUpdatedDate() {
-
-    String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <id value=\"e2ee823b-ee4d-472d-b79d-495c23f16b99\"/>\n" +
-        "   <meta>\n" +
-        "      <lastUpdated value=\"2015-06-22T15:48:57.554-04:00\"/>\n" +
-        "   </meta>\n" +
-        "   <type value=\"searchset\"/>\n" +
-        "   <base value=\"http://localhost:58109/fhir/context\"/>\n" +
-        "   <total value=\"0\"/>\n" +
-        "   <link>\n" +
-        "      <relation value=\"self\"/>\n" +
-        "      <url value=\"http://localhost:58109/fhir/context/Patient?_pretty=true\"/>\n" +
-        "   </link>\n" +
-        "</Bundle>";
-
-    Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, input);
-
-    InstantType updated = b.getMeta().getLastUpdatedElement();
-    assertEquals("2015-06-22T15:48:57.554-04:00", updated.getValueAsString());
-
-  }
-
-  // TODO: this should work
-  @Test
-  @Ignore
-  public void testParseNarrative() throws Exception {
-
-    String htmlNoNs = "<div>AAA<b>BBB</b>CCC</div>";
-    String htmlNs = htmlNoNs.replace("<div>", "<div xmlns=\"http://www.w3.org/1999/xhtml\">");
-    String res = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <id value=\"1333\"/>\n" +
-        "   <text>\n" +
-        "      " + htmlNs + "\n" +
-        "   </text>\n" +
-        "</Patient>";
-
-    Patient p = ourCtx.newXmlParser().parseResource(Patient.class, res);
-    assertEquals(htmlNs, p.getText().getDiv().getValueAsString());
-  }
-
-  @Test
-  public void testParseNestedExtensionsInvalid() {
-
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "   <birthDate value=\"2005-03-04\">\n" +
-        "      <extension url=\"http://my.fancy.extension.url\">\n" +
-        "         <valueString value=\"myvalue\"/>\n" +
-        "         <extension url=\"http://my.fancy.extension.url\">\n" +
-        "            <valueString value=\"myNestedValue\"/>\n" +
-        "         </extension>\n" +
-        "      </extension>\n" +
-        "   </birthDate>\n" +
-        "</Patient>";
-
-    try {
-      ourCtx.newXmlParser().parseResource(Patient.class, input);
-      fail();
-    } catch (DataFormatException e) {
-      assertThat(e.getMessage(), containsString("Extension (URL='http://my.fancy.extension.url') must not have both a value and other contained extensions"));
-    }
-  }
-
-  /**
-   * See #163
-   */
-  @Test
-  public void testParseResourceType() {
-    IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
-
-    // Patient
-    Patient patient = new Patient();
-    String patientId = UUID.randomUUID().toString();
-    patient.setId(new IdType("Patient", patientId));
-    patient.addName().addGiven("John").setFamily("Smith");
-    patient.setGender(AdministrativeGender.MALE);
-    patient.setBirthDateElement(new DateType("1987-04-16"));
-
-    // Bundle
-    Bundle bundle = new Bundle();
-    bundle.setType(BundleType.COLLECTION);
-    bundle.addEntry().setResource(patient);
-
-    String bundleText = xmlParser.encodeResourceToString(bundle);
-    ourLog.info(bundleText);
-
-    Bundle reincarnatedBundle = xmlParser.parseResource(Bundle.class, bundleText);
-    Patient reincarnatedPatient = (Patient) reincarnatedBundle.getEntry().get(0).getResource();
-
-    assertEquals("Patient", patient.getIdElement().getResourceType());
-    assertEquals("Patient", reincarnatedPatient.getIdElement().getResourceType());
-  }
-
-  /**
-   * See #344
-   */
-  @Test
-  public void testParserIsCaseSensitive() {
-    Observation obs = new Observation();
-    SampledData data = new SampledData();
-    data.setData("1 2 3");
-    data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
-    data.setPeriod(1000L);
-    obs.setValue(data);
-
-    IParser p = ourCtx.newXmlParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
-    String encoded = p.encodeResourceToString(obs);
-    ourLog.info(encoded);
-
-    p.parseResource(encoded);
-
-    try {
-      p.parseResource(encoded.replace("Observation", "observation"));
-      fail();
-    } catch (DataFormatException e) {
-      assertEquals("DataFormatException at [[row,col {unknown-source}]: [1,1]]: Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'",
-          e.getMessage());
-    }
-
-    try {
-      p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
-      fail();
-    } catch (DataFormatException e) {
-      assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Unknown element 'valueSampleddata' found during parse", e.getMessage());
-    }
-  }
-
-  @Test(expected = DataFormatException.class)
-  public void testParseWithInvalidLocalRef() throws IOException {
-    String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setParserErrorHandler(new StrictErrorHandler());
-    parser.parseResource(Bundle.class, string);
-  }
-
-  @Test()
-  public void testParseWithInvalidLocalRefLenient() throws IOException {
-    String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setParserErrorHandler(new LenientErrorHandler());
-    parser.parseResource(Bundle.class, string);
-  }
-
-  /**
-   * If a contained resource refers to a contained resource that comes after it, it should still be successfully
-   * woven together.
-   */
-  @Test
-  public void testParseWovenContainedResources() throws IOException {
-    String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setParserErrorHandler(new StrictErrorHandler());
-    org.hl7.fhir.dstu3.model.Bundle bundle = parser.parseResource(Bundle.class, string);
-
-    DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
-    Observation obs = (Observation) resource.getResult().get(1).getResource();
-    assertEquals("#2", obs.getId());
-    Reference performerFirstRep = obs.getPerformerFirstRep();
-    Practitioner performer = (Practitioner) performerFirstRep.getResource();
-    assertEquals("#3", performer.getId());
-  }
-
-  /**
-   * See #414
-   */
-  @Test
-  public void testParseXmlExtensionWithoutUrl() {
-
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "        <extension>\n" +
-        "          <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
-        "        </extension>\n" +
-        "</Patient>";
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setParserErrorHandler(new LenientErrorHandler());
-    Patient parsed = (Patient) parser.parseResource(input);
-    assertEquals(1, parsed.getExtension().size());
-    assertEquals(null, parsed.getExtension().get(0).getUrl());
-    assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
-
-    try {
-      parser = ourCtx.newXmlParser();
-      parser.setParserErrorHandler(new StrictErrorHandler());
-      parser.parseResource(input);
-      fail();
-    } catch (DataFormatException e) {
-      assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getCause().getMessage());
-    }
-
-  }
-
-  /**
-   * See #414
-   */
-  @Test
-  public void testParseXmlModifierExtensionWithoutUrl() {
-
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
-        "        <modifierExtension>\n" +
-        "          <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
-        "        </modifierExtension>\n" +
-        "</Patient>";
-
-    IParser parser = ourCtx.newXmlParser();
-    parser.setParserErrorHandler(new LenientErrorHandler());
-    Patient parsed = (Patient) parser.parseResource(input);
-    assertEquals(1, parsed.getModifierExtension().size());
-    assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
-    assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
-
-    try {
-      parser = ourCtx.newXmlParser();
-      parser.setParserErrorHandler(new StrictErrorHandler());
-      parser.parseResource(input);
-      fail();
-    } catch (DataFormatException e) {
-      assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getCause().getMessage());
-    }
-
-  }
-
-  /**
-   * See #339
-   * 
-   * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
-   */
-  @Test
-  public void testXxe() {
-
-    String input = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" +
-        "<!DOCTYPE foo [  " +
-        "<!ELEMENT foo ANY >" +
-        "<!ENTITY xxe SYSTEM \"file:///etc/passwd\" >]>" +
-        "<Patient xmlns=\"http://hl7.org/fhir\">" +
-        "<text>" +
-        "<div xmlns=\"http://www.w3.org/1999/xhtml\">TEXT &xxe; TEXT</div>" +
-        "</text>" +
-        "<address>" +
-        "<line value=\"FOO\"/>" +
-        "</address>" +
-        "</Patient>";
-
-    ourLog.info(input);
-
-    try {
-      ourCtx.newXmlParser().parseResource(Patient.class, input);
-      fail();
-    } catch (DataFormatException e) {
-      assertThat(e.toString(), containsString("Undeclared general entity"));
-    }
-
-  }
-
-  /**
-   * Test for the url generated based on the server config
-   */
-  @Test
-  public void testGeneratedUrls() {
-    final IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
-    xmlParser.setServerBaseUrl("http://myserver.com");
-
-    final CustomPatientDstu3 patient = new CustomPatientDstu3();
-    patient.setHomeless(new BooleanType(true));
-
-    final String parsedPatient = xmlParser.encodeResourceToString(patient);
-
-    assertTrue(parsedPatient.contains("<profile value=\"http://myserver.com/StructureDefinition/Patient\"/>"));
-    assertTrue(parsedPatient.contains("<extension url=\"http://myserver.com/StructureDefinition/homeless\">"));
-  }
-
-  /**
-   * Test for the url generated based on the server config
-   */
-  @Test
-  public void testCustomUrlExtension() {
-    final String expected = "<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://www.example.com/petname\"><valueString value=\"myName\"/></extension></Patient>";
-
-    final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
-    patient.setPetName(new StringType("myName"));
-
-    final IParser xmlParser = ourCtx.newXmlParser();
-    xmlParser.setServerBaseUrl("http://www.example.com");
-
-    final String parsedPatient = xmlParser.encodeResourceToString(patient);
-    System.out.println(parsedPatient);
-    assertEquals(expected, parsedPatient);
-
-    // Parse with string
-    MyPatientWithCustomUrlExtension newPatient = xmlParser.parseResource(MyPatientWithCustomUrlExtension.class, parsedPatient);
-    assertEquals("myName", newPatient.getPetName().getValue());
-
-    // Parse with stream
-    newPatient = xmlParser.parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
-    assertEquals("myName", newPatient.getPetName().getValue());
-
-    // Check no NPE if base server not configure
-    newPatient = ourCtx.newXmlParser().parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
-    assertNull("myName", newPatient.getPetName().getValue());
-    assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
-  }
-
-  @Test
-  public void testCustomUrlExtensioninBundle() {
-    final String expected = "<Bundle xmlns=\"http://hl7.org/fhir\"><entry><resource><Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://www.example.com/petname\"><valueString value=\"myName\"/></extension></Patient></resource></entry></Bundle>";
-
-    final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
-    patient.setPetName(new StringType("myName"));
-
-    final Bundle bundle = new Bundle();
-    final BundleEntryComponent entry = new BundleEntryComponent();
-    entry.setResource(patient);
-    bundle.addEntry(entry);
-
-    final IParser xmlParser = ourCtx.newXmlParser();
-    xmlParser.setServerBaseUrl("http://www.example.com");
-
-    final String parsedBundle = xmlParser.encodeResourceToString(bundle);
-    System.out.println(parsedBundle);
-    assertEquals(expected, parsedBundle);
-
-    // Parse with string
-    Bundle newBundle = xmlParser.parseResource(Bundle.class, parsedBundle);
-    assertNotNull(newBundle);
-    assertEquals(1, newBundle.getEntry().size());
-    Patient newPatient = (Patient) newBundle.getEntry().get(0).getResource();
-    assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
-
-    // Parse with stream
-    newBundle = xmlParser.parseResource(Bundle.class, new StringReader(parsedBundle));
-    assertNotNull(newBundle);
-    assertEquals(1, newBundle.getEntry().size());
-    newPatient = (Patient) newBundle.getEntry().get(0).getResource();
-    assertEquals("myName", ((StringType) newPatient.getExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
-
-  }
-
-  @AfterClass
-  public static void afterClassClearContext() {
-    TestUtil.clearAllStaticFieldsForUnitTest();
-  }
-
-  @BeforeClass
-  public static void beforeClass() {
-    XMLUnit.setIgnoreAttributeOrder(true);
-    XMLUnit.setIgnoreComments(true);
-    XMLUnit.setIgnoreWhitespace(true);
-  }
-
-  public static void main(String[] args) {
-    IGenericClient c = ourCtx.newRestfulGenericClient("http://fhir-dev.healthintersections.com.au/open");
-    // c.registerInterceptor(new LoggingInterceptor(true));
-    c.read().resource("Patient").withId("324").execute();
-  }
-
-  @ResourceDef(name = "Patient")
-  public static class TestPatientFor327 extends Patient {
-
-    private static final long serialVersionUID = 1L;
-
-    @Child(name = "testCondition")
-    @ca.uhn.fhir.model.api.annotation.Extension(url = "testCondition", definedLocally = true, isModifier = false)
-    private List<Reference> testConditions = null;
-
-    public List<Reference> getConditions() {
-      return this.testConditions;
-    }
-
-    public void setCondition(List<Reference> ref) {
-      this.testConditions = ref;
-    }
-  }
+	@Test
+	@Ignore
+	public void testParseAndEncodeBundle() throws Exception {
+		String content = IOUtils.toString(XmlParserDstu3Test.class.getResourceAsStream("/bundle-example.xml"), StandardCharsets.UTF_8);
+
+		Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, content);
+		assertEquals("Bundle/example/_history/1", parsed.getIdElement().getValue());
+		assertEquals("1", parsed.getMeta().getVersionId());
+		assertEquals("1", parsed.getIdElement().getVersionIdPart());
+		assertEquals(("2014-08-18T01:43:30Z"), parsed.getMeta().getLastUpdatedElement().getValueAsString());
+		assertEquals("searchset", parsed.getType().toCode());
+		assertEquals(3, parsed.getTotal());
+		assertEquals("https://example.com/base/MedicationRequest?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLink("next").getUrl());
+		assertEquals("https://example.com/base/MedicationRequest?patient=347&_include=MedicationRequest.medication", parsed.getLink("self").getUrl());
+
+		assertEquals(2, parsed.getEntry().size());
+		assertEquals("http://foo?search", parsed.getEntry().get(0).getLink("search").getUrl());
+
+		assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", parsed.getEntry().get(0).getLink("alternate").getUrl());
+		MedicationRequest p = (MedicationRequest) parsed.getEntry().get(0).getResource();
+		assertEquals("Patient/347", p.getSubject().getReference());
+		assertEquals("2014-08-16T05:31:17Z", p.getMeta().getLastUpdatedElement().getValueAsString());
+		assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", p.getId());
+
+		Medication m = (Medication) parsed.getEntry().get(1).getResource();
+		assertEquals("http://example.com/base/Medication/example", m.getId());
+		assertSame(((Reference) p.getMedication()).getResource(), m);
+
+		String reencoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parsed);
+		ourLog.info(reencoded);
+
+		Diff d = new Diff(new StringReader(content), new StringReader(reencoded));
+		assertTrue(d.toString(), d.identical());
+
+	}
+
+	@Test
+	@Ignore
+	public void testParseAndEncodeBundleNewStyle() throws Exception {
+		String content = IOUtils.toString(XmlParserDstu3Test.class.getResourceAsStream("/bundle-example.xml"), StandardCharsets.UTF_8);
+
+		IParser newXmlParser = ourCtx.newXmlParser();
+		Bundle parsed = newXmlParser.parseResource(Bundle.class, content);
+		assertEquals("Bundle/example/_history/1", parsed.getIdElement().getValue());
+		assertEquals("1", parsed.getIdElement().getVersionIdPart());
+		assertEquals("2014-08-18T01:43:30Z", parsed.getMeta().getLastUpdatedElement().getValueAsString());
+		assertEquals("searchset", parsed.getType());
+		assertEquals(3, parsed.getTotal());
+		assertEquals("https://example.com/base/MedicationRequest?patient=347&searchId=ff15fd40-ff71-4b48-b366-09c706bed9d0&page=2", parsed.getLink().get(0).getUrlElement().getValueAsString());
+		assertEquals("https://example.com/base/MedicationRequest?patient=347&_include=MedicationRequest.medication", parsed.getLink().get(1).getUrlElement().getValueAsString());
+
+		assertEquals(2, parsed.getEntry().size());
+		assertEquals("alternate", parsed.getEntry().get(0).getLink().get(0).getRelation());
+		assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", parsed.getEntry().get(0).getLink().get(0).getUrl());
+		assertEquals("http://foo?search", parsed.getEntry().get(0).getRequest().getUrlElement().getValueAsString());
+
+		MedicationRequest p = (MedicationRequest) parsed.getEntry().get(0).getResource();
+		assertEquals("Patient/347", p.getSubject().getReference());
+		assertEquals("2014-08-16T05:31:17Z", p.getMeta().getLastUpdatedElement().getValueAsString());
+		assertEquals("http://example.com/base/MedicationRequest/3123/_history/1", p.getId());
+		// assertEquals("3123", p.getId());
+
+		Medication m = (Medication) parsed.getEntry().get(1).getResource();
+		assertEquals("http://example.com/base/Medication/example", m.getId());
+		assertSame(((Reference) p.getMedication()).getResource(), m);
+
+		String reencoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parsed);
+		ourLog.info(reencoded);
+
+		Diff d = new Diff(new StringReader(content), new StringReader(reencoded));
+		assertTrue(d.toString(), d.identical());
+
+	}
+
+	@Test
+	public void testParseAndEncodeComments() {
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"  <!--pre resource comment-->" +
+				"  <id value=\"pat1\"/>\n" +
+				"  <text>\n" +
+				"    <status value=\"generated\"/>\n" +
+				"    <div xmlns=\"http://www.w3.org/1999/xhtml\">\n" +
+				"\n" +
+				"      <p>Patient Donald DUCK @ Acme Healthcare, Inc. MR = 654321</p>\n" +
+				"\n" +
+				"    </div>\n" +
+				"  </text>\n" +
+				"  <!--identifier comment 1-->\n" +
+				"  <!--identifier comment 2-->\n" +
+				"  <identifier>\n" +
+				"    <!--use comment 1-->\n" +
+				"    <!--use comment 2-->\n" +
+				"    <use value=\"usual\"/>\n" +
+				"    <type>\n" +
+				"      <coding>\n" +
+				"        <system value=\"http://hl7.org/fhir/v2/0203\"/>\n" +
+				"        <code value=\"MR\"/>\n" +
+				"      </coding>\n" +
+				"    </type>\n" +
+				"    <system value=\"urn:oid:0.1.2.3.4.5.6.7\"/>\n" +
+				"    <value value=\"654321\"/>\n" +
+				"  </identifier>\n" +
+				"  <active value=\"true\"/>" +
+				"  <!--post resource comment-->" +
+				"</Patient>";
+
+		Patient res = ourCtx.newXmlParser().parseResource(Patient.class, input);
+		res.getFormatCommentsPre();
+		assertEquals("Patient/pat1", res.getId());
+		assertEquals("654321", res.getIdentifier().get(0).getValue());
+		assertEquals(true, res.getActive());
+
+		assertThat(res.getIdElement().getFormatCommentsPre(), contains("pre resource comment"));
+		assertThat(res.getIdentifier().get(0).getFormatCommentsPre(), contains("identifier comment 1", "identifier comment 2"));
+		assertThat(res.getIdentifier().get(0).getUseElement().getFormatCommentsPre(), contains("use comment 1", "use comment 2"));
+		assertThat(res.getActiveElement().getFormatCommentsPost(), contains("post resource comment"));
+
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(res);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder(
+				"\"identifier\": [",
+				"{",
+				"\"fhir_comments\":",
+				"[",
+				"\"identifier comment 1\"",
+				",",
+				"\"identifier comment 2\"",
+				"]",
+				"\"use\": \"usual\",",
+				"\"_use\": {",
+				"\"fhir_comments\":",
+				"[",
+				"\"use comment 1\"",
+				",",
+				"\"use comment 2\"",
+				"]",
+				"},",
+				"\"type\""));
+
+		encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(res);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder(
+				"<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"pat1\"/>",
+				"<text>",
+				"<status value=\"generated\"/>",
+				"<div xmlns=\"http://www.w3.org/1999/xhtml\"> ",
+				"<p>Patient Donald DUCK @ Acme Healthcare, Inc. MR = 654321</p> ",
+				"</div>",
+				"</text>",
+				" <!--identifier comment 1-->\n",
+				" <!--identifier comment 2-->",
+				"<identifier>",
+				"<!--use comment 1-->",
+				"<!--use comment 2-->",
+				"<use value=\"usual\"/>",
+				"<type>",
+				"<coding>",
+				"<system value=\"http://hl7.org/fhir/v2/0203\"/>",
+				"<code value=\"MR\"/>",
+				"</coding>",
+				"</type>",
+				"<system value=\"urn:oid:0.1.2.3.4.5.6.7\"/>",
+				"<value value=\"654321\"/>",
+				"</identifier>",
+				"<active value=\"true\"/>",
+				"</Patient>"));
+
+	}
+
+	@Test
+	public void testParseAndEncodeCommentsOnExtensions() {
+
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"  <!-- comment 1 -->\n" +
+				"  <id value=\"someid\"/>\n" +
+				"  <!-- comment 2 -->\n" +
+				"  <extension url=\"urn:patientext:att\">\n" +
+				"    <!-- comment 3 -->\n" +
+				"    <valueAttachment>\n" +
+				"      <!-- comment 4 -->\n" +
+				"      <contentType value=\"aaaa\"/>\n" +
+				"      <data value=\"AAAA\"/>\n" +
+				"      <!-- comment 5 -->\n" +
+				"    </valueAttachment>\n" +
+				"    <!-- comment 6 -->\n" +
+				"  </extension>\n" +
+				"  <!-- comment 7 -->\n" +
+				"</Patient>";
+
+		Patient pat = ourCtx.newXmlParser().parseResource(Patient.class, input);
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(pat);
+		ourLog.info(output);
+
+		assertThat(output, stringContainsInOrder(
+				"<Patient xmlns=\"http://hl7.org/fhir\">",
+				"  <!-- comment 1 -->",
+				"  <id value=\"someid\"/>",
+				"  <!-- comment 2 -->",
+				"  <extension url=\"urn:patientext:att\">",
+				"    <!-- comment 3 -->",
+				"    <valueAttachment>",
+				"      <!-- comment 4 -->",
+				"      <contentType value=\"aaaa\"/>",
+				"      <data value=\"AAAA\"/>",
+				"      <!-- comment 5 -->",
+				"    </valueAttachment>",
+				"    <!-- comment 6 -->",
+				"  </extension>",
+				"  <!-- comment 7 -->",
+				"</Patient>"));
+
+		output = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(pat);
+		ourLog.info(output);
+
+		assertThat(output, stringContainsInOrder(
+				"{",
+				"  \"resourceType\": \"Patient\",",
+				"  \"id\": \"someid\",",
+				"  \"_id\": {",
+				"    \"fhir_comments\": [",
+				"      \" comment 1 \"",
+				"    ]",
+				"  },",
+				"  \"extension\": [",
+				"    {",
+				"      \"fhir_comments\": [",
+				"        \" comment 2 \",",
+				"        \" comment 7 \"",
+				"      ],",
+				"      \"url\": \"urn:patientext:att\",",
+				"      \"valueAttachment\": {",
+				"        \"fhir_comments\": [",
+				"          \" comment 3 \",",
+				"          \" comment 6 \"",
+				"        ],",
+				"        \"contentType\": \"aaaa\",",
+				"        \"_contentType\": {",
+				"          \"fhir_comments\": [",
+				"            \" comment 4 \"",
+				"          ]",
+				"        },",
+				"        \"data\": \"AAAA\",",
+				"        \"_data\": {",
+				"          \"fhir_comments\": [",
+				"            \" comment 5 \"",
+				"          ]",
+				"        }",
+				"      }",
+				"    }",
+				"  ]",
+				"}"));
+
+	}
+
+	@Test
+	public void testParseAndEncodeExtensionOnReference() {
+
+		String input = "<DataElement>" +
+				"<id value=\"gender\"/>" +
+				"<contained>" +
+				"<ValueSet>" +
+				"<id value=\"2179414\"/>" +
+				"<url value=\"2179414\"/>" +
+				"<version value=\"1.0\"/>" +
+				"<status value=\"active\"/>" +
+				"<description value=\"All codes representing the gender of a person.\"/>" +
+				"<compose>" +
+				"<include>" +
+				"<system value=\"http://ncit.nci.nih.gov\"/>" +
+				"<concept>" +
+				"<code value=\"C17998\"/>" +
+				"<display value=\"Unknown\"/>" +
+				"</concept>" +
+				"<concept>" +
+				"<code value=\"C20197\"/>" +
+				"<display value=\"Male\"/>" +
+				"</concept>" +
+				"<concept>" +
+				"<code value=\"C16576\"/>" +
+				"<display value=\"Female\"/>" +
+				"</concept>" +
+				"<concept>" +
+				"<code value=\"C38046\"/>" +
+				"<display value=\"Not specified\"/>" +
+				"</concept>" +
+				"</include>" +
+				"</compose>" +
+				"</ValueSet>" +
+				"</contained>" +
+				"<contained>" +
+				"<ValueSet>" +
+				"<id value=\"2179414-permitted\"/>" +
+				"<status value=\"active\"/>" +
+				"<codeSystem>" +
+				"<system value=\"http://example.org/fhir/2179414\"/>" +
+				"<caseSensitive value=\"true\"/>" +
+				"<concept>" +
+				"<code value=\"0\"/>" +
+				"</concept>" +
+				"<concept>" +
+				"<code value=\"1\"/>" +
+				"</concept>" +
+				"<concept>" +
+				"<code value=\"2\"/>" +
+				"</concept>" +
+				"<concept>" +
+				"<code value=\"3\"/>" +
+				"</concept>" +
+				"</codeSystem>" +
+				"</ValueSet>" +
+				"</contained>" +
+				"<contained>" +
+				"<ConceptMap>" +
+				"<id value=\"2179414-cm\"/>" +
+				"<status value=\"active\"/>" +
+				"<sourceReference>" +
+				"<reference value=\"#2179414\"/>" +
+				"</sourceReference>" +
+				"<targetReference>" +
+				"<reference value=\"#2179414-permitted\"/>" +
+				"</targetReference>" +
+				"<element>" +
+				"<code value=\"C17998\"/>" +
+				"<target>" +
+				"<code value=\"0\"/>" +
+				"<equivalence value=\"equal\"/>" +
+				"</target>" +
+				"</element>" +
+				"<element>" +
+				"<code value=\"C20197\"/>" +
+				"<target>" +
+				"<code value=\"1\"/>" +
+				"<equivalence value=\"equal\"/>" +
+				"</target>" +
+				"</element>" +
+				"<element>" +
+				"<code value=\"C16576\"/>" +
+				"<target>" +
+				"<code value=\"2\"/>" +
+				"<equivalence value=\"equal\"/>" +
+				"</target>" +
+				"</element>" +
+				"<element>" +
+				"<code value=\"C38046\"/>" +
+				"<target>" +
+				"<code value=\"3\"/>" +
+				"<equivalence value=\"equal\"/>" +
+				"</target>" +
+				"</element>" +
+				"</ConceptMap>" +
+				"</contained>" +
+				"<identifier>" +
+				"<value value=\"2179650\"/>" +
+				"</identifier>" +
+				"<version value=\"1.0\"/>" +
+				"<name value=\"Gender Code\"/>" +
+				"<status value=\"active\"/>" +
+				"<publisher value=\"DCP\"/>" +
+				"<useContext>" +
+				"<coding>" +
+				"<system value=\"http://example.org/FBPP\"/>" +
+				"<display value=\"FBPP Pooled Database\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/PhenX\"/>" +
+				"<display value=\"Demographics\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/EligibilityCriteria\"/>" +
+				"<display value=\"Pt. Administrative\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/UAMSClinicalResearch\"/>" +
+				"<display value=\"UAMS New CDEs\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/PhenX\"/>" +
+				"<display value=\"Substance Abuse and \"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/Category\"/>" +
+				"<display value=\"CSAERS Adverse Event\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/PhenX\"/>" +
+				"<display value=\"Core: Tier 1\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/Category\"/>" +
+				"<display value=\"Case Report Forms\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/Category\"/>" +
+				"<display value=\"CSAERS Review Set\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/Demonstration%20Applications\"/>" +
+				"<display value=\"CIAF\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/NIDA%20CTN%20Usage\"/>" +
+				"<display value=\"Clinical Research\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/NIDA%20CTN%20Usage\"/>" +
+				"<display value=\"Electronic Health Re\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/Condition\"/>" +
+				"<display value=\"Barretts Esophagus\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/Condition\"/>" +
+				"<display value=\"Bladder Cancer\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/Condition\"/>" +
+				"<display value=\"Oral Leukoplakia\"/>" +
+				"</coding>" +
+				"<coding>" +
+				"<system value=\"http://example.org/Condition\"/>" +
+				"<display value=\"Sulindac for Breast\"/>" +
+				"</coding>" +
+				"</useContext>" +
+				"<element>" +
+				"<extension url=\"http://hl7.org/fhir/StructureDefinition/minLength\">" +
+				"<valueInteger value=\"1\"/>" +
+				"</extension>" +
+				"<extension url=\"http://hl7.org/fhir/StructureDefinition/elementdefinition-question\">" +
+				"<valueString value=\"Gender\"/>" +
+				"</extension>" +
+				"<path value=\"Gender\"/>" +
+				"<definition value=\"The code representing the gender of a person.\"/>" +
+				"<type>" +
+				"<code value=\"CodeableConcept\"/>" +
+				"</type>" +
+				"<maxLength value=\"13\"/>" +
+				"<binding>" +
+				"<strength value=\"required\"/>" +
+				"<valueSetReference>" +
+				"<extension url=\"http://hl7.org/fhir/StructureDefinition/11179-permitted-value-valueset\">" +
+				"<valueReference>" +
+				"<reference value=\"#2179414-permitted\"/>" +
+				"</valueReference>" +
+				"</extension>" +
+				"<extension url=\"http://hl7.org/fhir/StructureDefinition/11179-permitted-value-conceptmap\">" +
+				"<valueReference>" +
+				"<reference value=\"#2179414-cm\"/>" +
+				"</valueReference>" +
+				"</extension>" +
+				"<reference value=\"#2179414\"/>" +
+				"</valueSetReference>" +
+				"</binding>" +
+				"</element>" +
+				"</DataElement>";
+
+		DataElement de = ourCtx.newXmlParser().parseResource(DataElement.class, input);
+		String output = ourCtx.newXmlParser().encodeResourceToString(de).replace(" xmlns=\"http://hl7.org/fhir\"", "");
+
+		ElementDefinition elem = de.getElement().get(0);
+		ElementDefinitionBindingComponent b = elem.getBinding();
+		// assertEquals("All codes representing the gender of a person.", b.getDescription());
+
+		Reference ref = (Reference) b.getValueSet();
+		assertEquals("#2179414", ref.getReference());
+
+		assertEquals(2, ref.getExtension().size());
+		Extension ext = ref.getExtension().get(0);
+		assertEquals("http://hl7.org/fhir/StructureDefinition/11179-permitted-value-valueset", ext.getUrl());
+		assertEquals(Reference.class, ext.getValue().getClass());
+		assertEquals("#2179414-permitted", ((Reference) ext.getValue()).getReference());
+		assertEquals(ValueSet.class, ((Reference) ext.getValue()).getResource().getClass());
+
+		ext = ref.getExtension().get(1);
+		assertEquals("http://hl7.org/fhir/StructureDefinition/11179-permitted-value-conceptmap", ext.getUrl());
+		assertEquals(Reference.class, ext.getValue().getClass());
+		assertEquals("#2179414-cm", ((Reference) ext.getValue()).getReference());
+		assertEquals(ConceptMap.class, ((Reference) ext.getValue()).getResource().getClass());
+
+		ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(de));
+
+		assertThat(output, containsString("http://hl7.org/fhir/StructureDefinition/11179-permitted-value-valueset"));
+
+	}
+
+	@Test
+	public void testParseAndEncodeNestedExtensions() {
+
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <birthDate value=\"2005-03-04\">\n" +
+				"      <extension url=\"http://my.fancy.extension.url\">\n" +
+				"         <extension url=\"http://my.fancy.extension.url\">\n" +
+				"            <valueString value=\"myNestedValue\"/>\n" +
+				"         </extension>\n" +
+				"      </extension>\n" +
+				"   </birthDate>\n" +
+				"</Patient>";
+
+		Patient p = ourCtx.newXmlParser().parseResource(Patient.class, input);
+		DateType bd = p.getBirthDateElement();
+		assertEquals("2005-03-04", bd.getValueAsString());
+
+		List<Extension> exts = bd.getExtensionsByUrl("http://my.fancy.extension.url");
+		assertEquals(1, exts.size());
+		Extension ext = exts.get(0);
+		assertEquals(null, ext.getValue());
+
+		exts = ext.getExtensionsByUrl("http://my.fancy.extension.url");
+		assertEquals(1, exts.size());
+		ext = exts.get(0);
+		assertEquals("myNestedValue", ((StringType) ext.getValue()).getValue());
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(encoded);
+
+		assertThat(encoded, stringContainsInOrder(
+				"<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<birthDate value=\"2005-03-04\">",
+				"<extension url=\"http://my.fancy.extension.url\">",
+				"<extension url=\"http://my.fancy.extension.url\">",
+				"<valueString value=\"myNestedValue\"/>",
+				"</extension>",
+				"</extension>",
+				"</birthDate>",
+				"</Patient>"));
+
+	}
+
+	@Test
+	public void testParseBundleNewWithPlaceholderIds() {
+
+		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"    <id value=\"ringholm1430996763590912\"/>\n" +
+				"    <entry>\n" +
+				"        <fullUrl value=\"urn:oid:0.1.2.3\"/>\n" +
+				"        <resource>\n" +
+				"            <Provenance>\n" +
+				"                <id value=\"0.1.2.3\"/>\n" +
+				"            </Provenance>\n" +
+				"        </resource>\n" +
+				"    </entry>\n" +
+				"</Bundle>\n";
+
+		Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
+		assertEquals("urn:oid:0.1.2.3", parsed.getEntry().get(0).getResource().getIdElement().getValue());
+
+	}
+
+	@Test
+	public void testParseBundleNewWithPlaceholderIdsInBase1() {
+
+		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"    <id value=\"ringholm1430996763590912\"/>\n" +
+				"    <entry>\n" +
+				"        <fullUrl value=\"urn:oid:0.1.2.3\"/>\n" +
+				"        <resource>\n" +
+				"            <Provenance>\n" +
+				"                <id value=\"0.1.2.3\"/>\n" +
+				"            </Provenance>\n" +
+				"        </resource>\n" +
+				"    </entry>\n" +
+				"</Bundle>\n";
+
+		Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
+		assertEquals("urn:oid:0.1.2.3", parsed.getEntry().get(0).getResource().getIdElement().getValue());
+	}
+
+	@Test
+	public void testParseBundleNewWithPlaceholderIdsInBase2() {
+
+		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"    <id value=\"ringholm1430996763590912\"/>\n" +
+				"    <entry>\n" +
+				"        <fullUrl value=\"urn:uuid:0.1.2.3\"/>\n" +
+				"        <resource>\n" +
+				"            <Provenance>\n" +
+				"                <id value=\"0.1.2.3\"/>\n" +
+				"            </Provenance>\n" +
+				"        </resource>\n" +
+				"    </entry>\n" +
+				"</Bundle>\n";
+
+		Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
+		assertEquals("urn:uuid:0.1.2.3", parsed.getEntry().get(0).getResource().getIdElement().getValue());
+
+		input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"    <id value=\"ringholm1430996763590912\"/>\n" +
+				"    <entry>\n" +
+				"        <fullUrl value=\"urn:uuid:0.1.2.3\"/>\n" +
+				"        <resource>\n" +
+				"            <Provenance>\n" +
+				"                <id value=\"0.1.2.3\"/>\n" +
+				"            </Provenance>\n" +
+				"        </resource>\n" +
+				"    </entry>\n" +
+				"</Bundle>\n";
+
+		parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
+		assertEquals("urn:uuid:0.1.2.3", parsed.getEntry().get(0).getResource().getIdElement().getValue());
+
+	}
+
+	@Test
+	public void testParseBundleOldStyleWithUnknownLinks() throws Exception {
+
+		String bundle = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <base value=\"http://foo/fhirBase1\"/>\n" +
+				"   <total value=\"1\"/>\n" +
+				"   <link>\n" +
+				"      <relation value=\"foo\"/>\n" +
+				"      <url value=\"http://localhost:52788/Binary?_pretty=true\"/>\n" +
+				"   </link>\n" +
+				"   <entry>\n" +
+				"   <link>\n" +
+				"      <relation value=\"bar\"/>\n" +
+				"      <url value=\"http://localhost:52788/Binary?_pretty=true\"/>\n" +
+				"   </link>\n" +
+				"      <resource>\n" +
+				"         <Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"            <id value=\"1\"/>\n" +
+				"            <meta>\n" +
+				"               <versionId value=\"2\"/>\n" +
+				"               <lastUpdated value=\"2001-02-22T11:22:33-05:00\"/>\n" +
+				"            </meta>\n" +
+				"            <birthDate value=\"2012-01-02\"/>\n" +
+				"         </Patient>\n" +
+				"      </resource>\n" +
+				"   </entry>\n" +
+				"</Bundle>";
+
+		Bundle b = (Bundle) ourCtx.newXmlParser().parseResource(bundle);
+		assertEquals(1, b.getEntry().size());
+
+	}
+
+	@Test
+	public void testParseBundleOldWithPlaceholderIds() {
+
+		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"    <id value=\"ringholm1430996763590912\"/>\n" +
+				"    <entry>\n" +
+				"        <fullUrl value=\"urn:oid:0.1.2.3\"/>\n" +
+				"        <resource>\n" +
+				"            <Provenance>\n" +
+				"                <id value=\"0.1.2.3\"/>\n" +
+				"            </Provenance>\n" +
+				"        </resource>\n" +
+				"    </entry>\n" +
+				"</Bundle>\n";
+
+		Bundle parsed = (Bundle) ourCtx.newXmlParser().parseResource(input);
+		assertEquals("urn:oid:0.1.2.3", parsed.getEntry().get(0).getResource().getId());
+
+	}
+
+	@Test
+	public void testParseBundleWithBinary() {
+		// TODO: implement this test, make sure we handle ID and meta correctly in Binary
+	}
+
+	/**
+	 * See #191
+	 */
+	@Test
+	public void testParseBundleWithLinksOfUnknownRelation() throws Exception {
+		String input = IOUtils.toString(XmlParserDstu3Test.class.getResourceAsStream("/bundle_orion.xml"), StandardCharsets.UTF_8);
+		Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
+
+		BundleLinkComponent link = parsed.getLink().get(0);
+		assertEquals("just trying add link", link.getRelation());
+		assertEquals("blarion", link.getUrl());
+
+		BundleEntryComponent entry = parsed.getEntry().get(0);
+		link = entry.getLink().get(0);
+		assertEquals("orionhealth.edit", link.getRelation());
+		assertEquals("Observation", link.getUrl());
+	}
+
+	@Test
+	public void testParseBundleWithResourceId() {
+
+		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
+				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+				+ "</Bundle>\n";
+
+		Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, input);
+		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getIdElement().getValue());
+		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getIdElement().getValue());
+		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getIdElement().getValue());
+	}
+
+	/**
+	 * see #144 and #146
+	 */
+	@Test
+	@Ignore
+	public void testParseContained() {
+
+		FhirContext c = FhirContext.forDstu3();
+		IParser parser = c.newXmlParser().setPrettyPrint(true);
+
+		Observation o = new Observation();
+		o.getCode().setText("obs text");
+
+		Patient p = new Patient();
+		p.addName().setFamily("patient family");
+		o.getSubject().setResource(p);
+
+		String enc = parser.encodeResourceToString(o);
+		ourLog.info(enc);
+
+		assertThat(enc, stringContainsInOrder(
+				"<Observation xmlns=\"http://hl7.org/fhir\">",
+				"<contained>",
+				"<Patient xmlns=\"http://hl7.org/fhir\">",
+				"<id value=\"1\"/>",
+				"</contained>",
+				"<reference value=\"#1\"/>"));
+
+		o = parser.parseResource(Observation.class, enc);
+		assertEquals("obs text", o.getCode().getText());
+
+		assertNotNull(o.getSubject().getResource());
+		p = (Patient) o.getSubject().getResource();
+		assertEquals("patient family", p.getName().get(0).getFamily());
+	}
+
+	/**
+	 * Thanks to Alexander Kley!
+	 */
+	@Test
+	public void testParseContainedBinaryResource() {
+		byte[] bin = new byte[] { 0, 1, 2, 3, 4 };
+		final Binary binary = new Binary();
+		binary.setContentType("PatientConsent").setContent(bin);
+
+		DocumentManifest manifest = new DocumentManifest();
+		CodeableConcept cc = new CodeableConcept();
+		cc.addCoding().setSystem("mySystem").setCode("PatientDocument");
+		manifest.setType(cc);
+		manifest.setMasterIdentifier(new Identifier().setSystem("mySystem").setValue(UUID.randomUUID().toString()));
+		manifest.addContent().setP(new Reference(binary));
+		manifest.setStatus(DocumentReferenceStatus.CURRENT);
+
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(manifest);
+		ourLog.info(encoded);
+		assertThat(encoded, StringContainsInOrder.stringContainsInOrder(Arrays.asList("contained>", "<Binary", "</contained>")));
+
+		DocumentManifest actual = ourCtx.newXmlParser().parseResource(DocumentManifest.class, encoded);
+		assertEquals(1, actual.getContained().size());
+		assertEquals(1, actual.getContent().size());
+
+		/*
+		 * If this fails, it's possibe the DocumentManifest structure is wrong: It should be
+		 * 
+		 * @Child(name = "p", type = {Attachment.class, ValueSet.class}, order=1, min=1, max=1, modifier=false, summary=true)
+		 */
+		assertNotNull(((Reference) actual.getContent().get(0).getP()).getResource());
+	}
+
+	/**
+	 * See #426
+	 */
+	@Test
+	public void testParseExtensionWithIdType() {
+
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"    <extension url=\"http://aaa.ch/fhir/Patient#mangedcare\">\n" +
+				"        <extension url=\"http://aaa.ch/fhir/Patient#mangedcare-aaa-id\">\n" +
+				"           <valueId value=\"mc1\"/>\n" +
+				"        </extension>\n" +
+				"    </extension>\n" +
+				"    <identifier>\n" +
+				"        <value value=\"ais111\"/>\n" +
+				"    </identifier>\n" +
+				"</Patient>";
+
+		Patient pt = ourCtx.newXmlParser().parseResource(Patient.class, input);
+
+		List<Extension> extList = pt.getExtensionsByUrl("http://aaa.ch/fhir/Patient#mangedcare");
+		extList = extList.get(0).getExtensionsByUrl("http://aaa.ch/fhir/Patient#mangedcare-aaa-id");
+		Extension ext = extList.get(0);
+		IdType value = (IdType) ext.getValue();
+		assertEquals("mc1", value.getValueAsString());
+	}
+
+	/**
+	 * See #426
+	 * 
+	 * Value type of FOO isn't a valid datatype
+	 */
+	@Test
+	public void testParseExtensionWithInvalidType() {
+
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"    <extension url=\"http://aaa.ch/fhir/Patient#mangedcare\">\n" +
+				"        <extension url=\"http://aaa.ch/fhir/Patient#mangedcare-aaa-id\">\n" +
+				"           <valueFOO value=\"mc1\"/>\n" +
+				"        </extension>\n" +
+				"    </extension>\n" +
+				"    <identifier>\n" +
+				"        <value value=\"ais111\"/>\n" +
+				"    </identifier>\n" +
+				"</Patient>";
+
+		Patient pt = ourCtx.newXmlParser().parseResource(Patient.class, input);
+
+		List<Extension> extList = pt.getExtensionsByUrl("http://aaa.ch/fhir/Patient#mangedcare");
+		extList = extList.get(0).getExtensionsByUrl("http://aaa.ch/fhir/Patient#mangedcare-aaa-id");
+		Extension ext = extList.get(0);
+		IdType value = (IdType) ext.getValue();
+		assertEquals(null, value);
+	}
+
+	/**
+	 * See #342
+	 */
+	@Test(expected = DataFormatException.class)
+	public void testParseInvalid() {
+		ourCtx.newXmlParser().parseResource("FOO");
+	}
+
+	/**
+	 * See #366
+	 */
+	@Test()
+	public void testParseInvalidBoolean() {
+
+		String resource = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <active value=\"1\"/>\n" +
+				"</Patient>";
+
+		IParser p = ourCtx.newXmlParser();
+
+		try {
+			p.parseResource(resource);
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"1\": Invalid boolean string: '1'", e.getMessage());
+		}
+
+		LenientErrorHandler errorHandler = new LenientErrorHandler();
+		assertEquals(true, errorHandler.isErrorOnInvalidValue());
+		errorHandler.setErrorOnInvalidValue(false);
+		p.setParserErrorHandler(errorHandler);
+	}
+
+	@Test
+	public void testParseInvalidTextualNumber() {
+		Observation obs = new Observation();
+		obs.setValue(new Quantity().setValue(1234));
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs);
+		encoded = encoded.replace("1234", "\"1234\"");
+		ourLog.info(encoded);
+		ourCtx.newJsonParser().parseResource(encoded);
+	}
+
+	/**
+	 * See #216
+	 */
+	@Test
+	public void testParseMalformedIdentifierDstu2() {
+
+		// This was changed from 0.5 to 1.0.0
+
+		String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <identifier>\n" +
+				"      <type value=\"MRN\"/>\n" +
+				"      <system value=\"SYS\"/>\n" +
+				"      <value value=\"VAL\"/>\n" +
+				"   </identifier>\n" +
+				"</Patient>";
+
+		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
+
+		IParser p = ourCtx.newXmlParser();
+		p.setParserErrorHandler(errorHandler);
+
+		Patient patient = p.parseResource(Patient.class, out);
+		assertThat(patient.getIdentifier().get(0).getType().getCoding(), IsEmptyCollection.empty());
+
+		ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
+		verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
+
+		assertEquals("value", capt.getValue());
+	}
+
+	@Test
+	public void testParseMetadata() throws Exception {
+
+		String bundle = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <total value=\"1\"/>\n" +
+				"   <link>\n" +
+				"      <relation value=\"self\"/>\n" +
+				"      <url value=\"http://localhost:52788/Binary?_pretty=true\"/>\n" +
+				"   </link>\n" +
+				"   <entry>\n" +
+				"      <fullUrl value=\"http://foo/fhirBase2/Patient/1/_history/2\"/>\n" +
+				"      <resource>\n" +
+				"         <Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"            <id value=\"1\"/>\n" +
+				"            <meta>\n" +
+				"               <versionId value=\"2\"/>\n" +
+				"               <lastUpdated value=\"2001-02-22T09:22:33-07:00\"/>\n" +
+				"            </meta>\n" +
+				"            <birthDate value=\"2012-01-02\"/>\n" +
+				"         </Patient>\n" +
+				"      </resource>\n" +
+				"      <search>\n" +
+				"         <mode value=\"match\"/>\n" +
+				"         <score value=\"0.123\"/>\n" +
+				"      </search>\n" +
+				"      <request>\n" +
+				"         <method value=\"POST\"/>\n" +
+				"         <url value=\"http://foo/Patient?identifier=value\"/>\n" +
+				"      </request>\n" +
+				"   </entry>\n" +
+				"</Bundle>";
+
+		Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, bundle);
+		assertEquals(1, b.getEntry().size());
+
+		BundleEntryComponent entry = b.getEntry().get(0);
+		Patient pt = (Patient) entry.getResource();
+		assertEquals("http://foo/fhirBase2/Patient/1/_history/2", pt.getIdElement().getValue());
+		assertEquals("2012-01-02", pt.getBirthDateElement().getValueAsString());
+		assertEquals("0.123", entry.getSearch().getScore().toString());
+		assertEquals("match", entry.getSearch().getMode().toCode());
+		assertEquals("POST", entry.getRequest().getMethod().toCode());
+		assertEquals("http://foo/Patient?identifier=value", entry.getRequest().getUrl());
+		assertEquals("2001-02-22T09:22:33-07:00", pt.getMeta().getLastUpdatedElement().getValueAsString());
+
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String reEncoded = p.encodeResourceToString(b);
+		ourLog.info(reEncoded);
+
+		Diff d = new Diff(new StringReader(bundle), new StringReader(reEncoded));
+		assertTrue(d.toString(), d.identical());
+
+	}
+
+	@Test
+	public void testParseMetaUpdatedDate() {
+
+		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <id value=\"e2ee823b-ee4d-472d-b79d-495c23f16b99\"/>\n" +
+				"   <meta>\n" +
+				"      <lastUpdated value=\"2015-06-22T15:48:57.554-04:00\"/>\n" +
+				"   </meta>\n" +
+				"   <type value=\"searchset\"/>\n" +
+				"   <base value=\"http://localhost:58109/fhir/context\"/>\n" +
+				"   <total value=\"0\"/>\n" +
+				"   <link>\n" +
+				"      <relation value=\"self\"/>\n" +
+				"      <url value=\"http://localhost:58109/fhir/context/Patient?_pretty=true\"/>\n" +
+				"   </link>\n" +
+				"</Bundle>";
+
+		Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, input);
+
+		InstantType updated = b.getMeta().getLastUpdatedElement();
+		assertEquals("2015-06-22T15:48:57.554-04:00", updated.getValueAsString());
+
+	}
+
+	// TODO: this should work
+	@Test
+	@Ignore
+	public void testParseNarrative() throws Exception {
+
+		String htmlNoNs = "<div>AAA<b>BBB</b>CCC</div>";
+		String htmlNs = htmlNoNs.replace("<div>", "<div xmlns=\"http://www.w3.org/1999/xhtml\">");
+		String res = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <id value=\"1333\"/>\n" +
+				"   <text>\n" +
+				"      " + htmlNs + "\n" +
+				"   </text>\n" +
+				"</Patient>";
+
+		Patient p = ourCtx.newXmlParser().parseResource(Patient.class, res);
+		assertEquals(htmlNs, p.getText().getDiv().getValueAsString());
+	}
+
+	@Test
+	public void testParseNestedExtensionsInvalid() {
+
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"   <birthDate value=\"2005-03-04\">\n" +
+				"      <extension url=\"http://my.fancy.extension.url\">\n" +
+				"         <valueString value=\"myvalue\"/>\n" +
+				"         <extension url=\"http://my.fancy.extension.url\">\n" +
+				"            <valueString value=\"myNestedValue\"/>\n" +
+				"         </extension>\n" +
+				"      </extension>\n" +
+				"   </birthDate>\n" +
+				"</Patient>";
+
+		try {
+			ourCtx.newXmlParser().parseResource(Patient.class, input);
+			fail();
+		} catch (DataFormatException e) {
+			assertThat(e.getMessage(), containsString("Extension (URL='http://my.fancy.extension.url') must not have both a value and other contained extensions"));
+		}
+	}
+
+	/**
+	 * See #163
+	 */
+	@Test
+	public void testParseResourceType() {
+		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
+
+		// Patient
+		Patient patient = new Patient();
+		String patientId = UUID.randomUUID().toString();
+		patient.setId(new IdType("Patient", patientId));
+		patient.addName().addGiven("John").setFamily("Smith");
+		patient.setGender(AdministrativeGender.MALE);
+		patient.setBirthDateElement(new DateType("1987-04-16"));
+
+		// Bundle
+		Bundle bundle = new Bundle();
+		bundle.setType(BundleType.COLLECTION);
+		bundle.addEntry().setResource(patient);
+
+		String bundleText = xmlParser.encodeResourceToString(bundle);
+		ourLog.info(bundleText);
+
+		Bundle reincarnatedBundle = xmlParser.parseResource(Bundle.class, bundleText);
+		Patient reincarnatedPatient = (Patient) reincarnatedBundle.getEntry().get(0).getResource();
+
+		assertEquals("Patient", patient.getIdElement().getResourceType());
+		assertEquals("Patient", reincarnatedPatient.getIdElement().getResourceType());
+	}
+
+	/**
+	 * See #344
+	 */
+	@Test
+	public void testParserIsCaseSensitive() {
+		Observation obs = new Observation();
+		SampledData data = new SampledData();
+		data.setData("1 2 3");
+		data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
+		data.setPeriod(1000L);
+		obs.setValue(data);
+
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
+		String encoded = p.encodeResourceToString(obs);
+		ourLog.info(encoded);
+
+		p.parseResource(encoded);
+
+		try {
+			p.parseResource(encoded.replace("Observation", "observation"));
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("DataFormatException at [[row,col {unknown-source}]: [1,1]]: Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'",
+					e.getMessage());
+		}
+
+		try {
+			p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Unknown element 'valueSampleddata' found during parse", e.getMessage());
+		}
+	}
+
+	@Test(expected = DataFormatException.class)
+	public void testParseWithInvalidLocalRef() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+		parser.parseResource(Bundle.class, string);
+	}
+
+	@Test()
+	public void testParseWithInvalidLocalRefLenient() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new LenientErrorHandler());
+		parser.parseResource(Bundle.class, string);
+	}
+
+	/**
+	 * If a contained resource refers to a contained resource that comes after it, it should still be successfully
+	 * woven together.
+	 */
+	@Test
+	public void testParseWovenContainedResources() throws IOException {
+		String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+		org.hl7.fhir.dstu3.model.Bundle bundle = parser.parseResource(Bundle.class, string);
+
+		DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
+		Observation obs = (Observation) resource.getResult().get(1).getResource();
+		assertEquals("#2", obs.getId());
+		Reference performerFirstRep = obs.getPerformerFirstRep();
+		Practitioner performer = (Practitioner) performerFirstRep.getResource();
+		assertEquals("#3", performer.getId());
+	}
+
+	/**
+	 * See #414
+	 */
+	@Test
+	public void testParseXmlExtensionWithoutUrl() {
+
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"        <extension>\n" +
+				"          <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
+				"        </extension>\n" +
+				"</Patient>";
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new LenientErrorHandler());
+		Patient parsed = (Patient) parser.parseResource(input);
+		assertEquals(1, parsed.getExtension().size());
+		assertEquals(null, parsed.getExtension().get(0).getUrl());
+		assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
+
+		try {
+			parser = ourCtx.newXmlParser();
+			parser.setParserErrorHandler(new StrictErrorHandler());
+			parser.parseResource(input);
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getCause().getMessage());
+		}
+
+	}
+
+	/**
+	 * See #414
+	 */
+	@Test
+	public void testParseXmlModifierExtensionWithoutUrl() {
+
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+				"        <modifierExtension>\n" +
+				"          <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
+				"        </modifierExtension>\n" +
+				"</Patient>";
+
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new LenientErrorHandler());
+		Patient parsed = (Patient) parser.parseResource(input);
+		assertEquals(1, parsed.getModifierExtension().size());
+		assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
+		assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
+
+		try {
+			parser = ourCtx.newXmlParser();
+			parser.setParserErrorHandler(new StrictErrorHandler());
+			parser.parseResource(input);
+			fail();
+		} catch (DataFormatException e) {
+			assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getCause().getMessage());
+		}
+
+	}
+
+	/**
+	 * See #551
+	 */
+	@Test
+	public void testXmlLargeAttribute() {
+		String largeString = StringUtils.leftPad("", (int) FileUtils.ONE_MB, 'A');
+
+		Patient p = new Patient();
+		p.addName().setFamily(largeString);
+
+		String encoded = ourCtx.newXmlParser().encodeResourceToString(p);
+
+		p = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
+
+		assertEquals(largeString, p.getNameFirstRep().getFamily());
+	}
+
+	/**
+	 * See #339
+	 * 
+	 * https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
+	 */
+	@Test
+	public void testXxe() {
+
+		String input = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" +
+				"<!DOCTYPE foo [  " +
+				"<!ELEMENT foo ANY >" +
+				"<!ENTITY xxe SYSTEM \"file:///etc/passwd\" >]>" +
+				"<Patient xmlns=\"http://hl7.org/fhir\">" +
+				"<text>" +
+				"<div xmlns=\"http://www.w3.org/1999/xhtml\">TEXT &xxe; TEXT</div>" +
+				"</text>" +
+				"<address>" +
+				"<line value=\"FOO\"/>" +
+				"</address>" +
+				"</Patient>";
+
+		ourLog.info(input);
+
+		try {
+			ourCtx.newXmlParser().parseResource(Patient.class, input);
+			fail();
+		} catch (DataFormatException e) {
+			assertThat(e.toString(), containsString("Undeclared general entity"));
+		}
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() {
+		XMLUnit.setIgnoreAttributeOrder(true);
+		XMLUnit.setIgnoreComments(true);
+		XMLUnit.setIgnoreWhitespace(true);
+	}
+
+	public static void main(String[] args) {
+		IGenericClient c = ourCtx.newRestfulGenericClient("http://fhir-dev.healthintersections.com.au/open");
+		// c.registerInterceptor(new LoggingInterceptor(true));
+		c.read().resource("Patient").withId("324").execute();
+	}
+
+	@ResourceDef(name = "Patient")
+	public static class TestPatientFor327 extends Patient {
+
+		private static final long serialVersionUID = 1L;
+
+		@Child(name = "testCondition")
+		@ca.uhn.fhir.model.api.annotation.Extension(url = "testCondition", definedLocally = true, isModifier = false)
+		private List<Reference> testConditions = null;
+
+		public List<Reference> getConditions() {
+			return this.testConditions;
+		}
+
+		public void setCondition(List<Reference> ref) {
+			this.testConditions = ref;
+		}
+	}
 
 }
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 88a4e8edbdc..70397ab8923 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -97,6 +97,10 @@
 				JPA server did not correctly support searching on a custom search parameter whose
 				path pointed to an extension, where the client used a chained value.
 			</action>
+			<action type="fix">
+				Fix issue where the JSON parser sometimes did not encode DSTU3 extensions on the root of a 
+				resource which have a value of type reference.
+			</action>
 		</release>
 		<release version="2.4" date="2017-04-19">
 			<action type="add">