Add model visitor, and allow bundles to have categories (as allowed in the spec)

hapi-fhir-base/examples/src/main/java/example/GenericClientExample.java

@@ -17,22 +17,19 @@ import ca.uhn.fhir.rest.method.SearchStyleEnum;
 
 public class GenericClientExample {
 
-@SuppressWarnings("unused")
 public static void simpleExample() {
 // START SNIPPET: simple
 FhirContext ctx = new FhirContext();
-String serverBase = "http://fhir.healthintersections.com.au/open";
+String serverBase = "http://fhirtest.uhn.ca/base";
 IGenericClient client = ctx.newRestfulGenericClient(serverBase);
 
-// Read a patient
+// Perform a search
-Patient patient = client.read(Patient.class, "1");
+Bundle results = client.search()
+      .forResource(Patient.class)
+      .where(Patient.FAMILY.matches().value("duck"))
+      .execute();
 
-// Change the patient and update it to the server
+System.out.println("Found " + results.size() + " patients named 'duck'");
-patient.getNameFirstRep().getFamilyFirstRep().setValue("Jones");
-client.update("1", patient);
-
-// Return the version history for that patient
-Bundle versions = client.history(Patient.class, "1",null,null);
 // END SNIPPET: simple	
 }
 
@@ -177,7 +174,7 @@ List<IResource> response = client.transaction()
 }
 
 	public static void main(String[] args) {
-		// nothing
+		simpleExample();
 	}
 
 }

hapi-fhir-base/src/changes/changes.xml

@@ -87,6 +87,10 @@
 				Transaction method in server can now have parameter type Bundle instead of
 				List<IResource>
 			</action>
+			<action type="add">
+				HAPI parsers now use field access to get/set values instead of method accessors and mutators.
+				This should give a small performance boost.
+			</action>
 		</release>
 		<release version="0.5" date="2014-Jul-30">
 			<action type="add">

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Bundle.java

@@ -44,11 +44,6 @@ public class Bundle extends BaseBundle /* implements IElement */{
 
 	private volatile transient Map<IdDt, IResource> myIdToEntries;
 
-	//@formatter:off
-	/* ****************************************************
-	 * NB: add any new fields to the isEmpty() method!!!
-	 *****************************************************/
-	//@formatter:on
 	private List<BundleEntry> myEntries;
 	private StringDt myBundleId;
 	private StringDt myLinkBase;
@@ -61,6 +56,7 @@ public class Bundle extends BaseBundle /* implements IElement */{
 	private StringDt myTitle;
 	private IntegerDt myTotalResults;
 	private InstantDt myUpdated;
+	private TagList myCategories;
 
 	/**
 	 * Returns true if this bundle contains zero entries
@@ -70,6 +66,16 @@ public class Bundle extends BaseBundle /* implements IElement */{
 		return getEntries().isEmpty();
 	}
 
+	public Tag addCategory() {
+		Tag retVal = new Tag();
+		getCategories().add(retVal);
+		return retVal;
+	}
+
+	public void addCategory(Tag theTag) {
+		getCategories().add(theTag);
+	}
+
 	/**
 	 * Adds and returns a new bundle entry
 	 */
@@ -82,12 +88,15 @@ public class Bundle extends BaseBundle /* implements IElement */{
 	/**
 	 * Retrieves a resource from a bundle given its logical ID.
 	 * <p>
-	 * <b>Important usage notes</b>: This method ignores base URLs (so passing in an ID of <code>http://foo/Patient/123</code> will return a resource if it has the logical ID of
+	 * <b>Important usage notes</b>: This method ignores base URLs (so passing in an ID of
-	 * <code>http://bar/Patient/123</code>. Also, this method is intended to be used for bundles which have already been populated. It will cache its results for fast performance, but that means that
+	 * <code>http://foo/Patient/123</code> will return a resource if it has the logical ID of
-	 * modifications to the bundle after this method is called may not be accurately reflected.
+	 * <code>http://bar/Patient/123</code>. Also, this method is intended to be used for bundles which have already been
+	 * populated. It will cache its results for fast performance, but that means that modifications to the bundle after
+	 * this method is called may not be accurately reflected.
 	 * </p>
 	 * 
-	 * @param theId The resource ID
+	 * @param theId
+	 *            The resource ID
 	 * @return Returns the resource with the given ID, or <code>null</code> if none is found
 	 */
 	public IResource getResourceById(IdDt theId) {
@@ -129,6 +138,18 @@ public class Bundle extends BaseBundle /* implements IElement */{
 	// c.update().resource(txt).withId("1665").execute();
 	// }
 	//
+
+	public TagList getCategories() {
+		if (myCategories == null) {
+			myCategories = new TagList();
+		}
+		return myCategories;
+	}
+
+	public void setCategories(TagList theCategories) {
+		myCategories = theCategories;
+	}
+
 	public List<BundleEntry> getEntries() {
 		if (myEntries == null) {
 			myEntries = new ArrayList<BundleEntry>();

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java

@@ -167,6 +167,8 @@ public class JsonParser extends BaseParser implements IParser {
 			eventWriter.writeEnd();
 		}
 		
+		writeCategories(eventWriter, theBundle.getCategories());
+
 		writeOptionalTagWithTextNode(eventWriter, "totalResults", theBundle.getTotalResults());
 
 		writeAuthor(theBundle, eventWriter);
@@ -193,17 +195,7 @@ public class JsonParser extends BaseParser implements IParser {
 			writeOptionalTagWithTextNode(eventWriter, "updated", nextEntry.getUpdated());
 			writeOptionalTagWithTextNode(eventWriter, "published", nextEntry.getPublished());
 
-			if (nextEntry.getCategories() != null && nextEntry.getCategories().size() > 0) {
+			writeCategories(eventWriter, nextEntry.getCategories());
-				eventWriter.writeStartArray("category");
-				for (Tag next : nextEntry.getCategories()) {
-					eventWriter.writeStartObject();
-					eventWriter.write("term", defaultString(next.getTerm()));
-					eventWriter.write("label", defaultString(next.getLabel()));
-					eventWriter.write("scheme", defaultString(next.getScheme()));
-					eventWriter.writeEnd();
-				}
-				eventWriter.writeEnd();
-			}
 
 			writeAuthor(nextEntry, eventWriter);
 
@@ -221,6 +213,20 @@ public class JsonParser extends BaseParser implements IParser {
 		eventWriter.flush();
 	}
 
+	private void writeCategories(JsonGenerator eventWriter, TagList categories) {
+		if (categories != null && categories.size() > 0) {
+			eventWriter.writeStartArray("category");
+			for (Tag next : categories) {
+				eventWriter.writeStartObject();
+				eventWriter.write("term", defaultString(next.getTerm()));
+				eventWriter.write("label", defaultString(next.getLabel()));
+				eventWriter.write("scheme", defaultString(next.getScheme()));
+				eventWriter.writeEnd();
+			}
+			eventWriter.writeEnd();
+		}
+	}
+
 	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, JsonGenerator theWriter, IElement theValue, BaseRuntimeElementDefinition<?> theChildDef,
 			String theChildName) throws IOException {
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java

@@ -20,8 +20,7 @@ package ca.uhn.fhir.parser;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
+import static org.apache.commons.lang3.StringUtils.*;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -67,6 +66,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.util.IModelVisitor;
 
 class ParserState<T> {
 
@@ -628,6 +628,8 @@ class ParserState<T> {
 				push(new AtomPrimitiveState(myInstance.getUpdated()));
 			} else if ("author".equals(theLocalPart)) {
 				push(new AtomAuthorState(myInstance));
+			} else if ("category".equals(theLocalPart)) {
+				push(new AtomCategoryState(myInstance.getCategories().addTag()));
 			} else if ("deleted-entry".equals(theLocalPart) && verifyNamespace(XmlParser.TOMBSTONES_NS, theNamespaceURI)) {
 				push(new AtomDeletedEntryState(myInstance, myResourceType));
 			} else {
@@ -908,7 +910,7 @@ class ParserState<T> {
 		public void attributeValue(String theName, String theValue) throws DataFormatException {
 			if ("id".equals(theName)) {
 				if (myInstance instanceof IIdentifiableElement) {
-					((IIdentifiableElement) myInstance).setId(new IdDt(theValue));
+					((IIdentifiableElement) myInstance).setElementSpecificId((theValue));
 				} else if (myInstance instanceof IResource) {
 					((IResource) myInstance).setId(new IdDt(theValue));
 				}
@@ -1255,7 +1257,17 @@ class ParserState<T> {
 				myObject = (T) myInstance;
 			}
 
-			for (ResourceReferenceDt nextRef : myResourceReferences) {
+			myContext.newTerser().visit(myInstance, new IModelVisitor() {
+				
+				@Override
+				public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
+					acceptElement(theNextExt.getValue(), null, null);
+				}
+				
+				@Override
+				public void acceptElement(IElement theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
+					if (theElement instanceof ResourceReferenceDt) {
+						ResourceReferenceDt nextRef = (ResourceReferenceDt)theElement;
 						String ref = nextRef.getReference().getValue();
 						if (isNotBlank(ref)) {
 							if (ref.startsWith("#")) {
@@ -1268,6 +1280,8 @@ class ParserState<T> {
 							}
 						}
 					}
+				}
+			});
 			
 		}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java

@@ -144,6 +144,8 @@ public class XmlParser extends BaseParser implements IParser {
 				eventWriter.writeEndElement();
 			}
 
+			writeCategories(eventWriter, theBundle.getCategories());
+
 			for (BundleEntry nextEntry : theBundle.getEntries()) {
 				boolean deleted = false;
 				if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
@@ -182,15 +184,7 @@ public class XmlParser extends BaseParser implements IParser {
 				writeOptionalTagWithTextNode(eventWriter, "updated", nextEntry.getUpdated());
 				writeOptionalTagWithTextNode(eventWriter, "published", nextEntry.getPublished());
 
-				if (nextEntry.getCategories() != null) {
+				writeCategories(eventWriter, nextEntry.getCategories());
-					for (Tag next : nextEntry.getCategories()) {
-						eventWriter.writeStartElement("category");
-						eventWriter.writeAttribute("term", defaultString(next.getTerm()));
-						eventWriter.writeAttribute("label", defaultString(next.getLabel()));
-						eventWriter.writeAttribute("scheme", defaultString(next.getScheme()));
-						eventWriter.writeEndElement();
-					}
-				}
 
 				if (!nextEntry.getLinkSelf().isEmpty()) {
 					writeAtomLink(eventWriter, "self", nextEntry.getLinkSelf());
@@ -224,6 +218,18 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 	}
 
+	private void writeCategories(XMLStreamWriter eventWriter,  TagList categories) throws XMLStreamException {
+		if (categories != null) {
+			for (Tag next : categories) {
+				eventWriter.writeStartElement("category");
+				eventWriter.writeAttribute("term", defaultString(next.getTerm()));
+				eventWriter.writeAttribute("label", defaultString(next.getLabel()));
+				eventWriter.writeAttribute("scheme", defaultString(next.getScheme()));
+				eventWriter.writeEndElement();
+			}
+		}
+	}
+
 	@Override
 	public String encodeResourceToString(IResource theResource) throws DataFormatException {
 		if (theResource == null) {

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

@@ -108,30 +108,64 @@ public class FhirTerser {
 	}
 
 	/**
-	 * Returns a list containing all child elements (including the resource itself) which are <b>non-empty</b>
+	 * Visit all elements in a given resource
-	 * and are either of the exact type specified, or are a subclass of that type.
+	 * 
-	 * <p>
+	 * @param theResource The resource to visit
-	 * For example, specifying a type of {@link StringDt} would return all non-empty string instances within
+	 * @param theVisitor The visitor
-	 * the message. Specifying a type of {@link IResource} would return the resource itself, as well as any contained resources. 
-	 * </p>  
-	 * @param theResourceT The resource instance to search. Must not be null.
-	 * @param theType The type to search for. Must not be null.
-	 * @return
 	 */
-	public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(IResource theResource, Class<T> theType) {
+	public void visit(IResource theResource, IModelVisitor theVisitor) {
-		ArrayList<T> retVal = new ArrayList<T>();
 		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
-		getAllChildElementsOfType(theResource, def, theType, retVal);
+		visit(theResource, null, def, theVisitor);
-		return retVal;
 	}
 
-	private <T extends IElement> void getAllChildElementsOfType(IElement theElement, BaseRuntimeElementDefinition<?> theDefinition, Class<T> theType, ArrayList<T> theList) {
+	/**
+	 * Returns a list containing all child elements (including the resource itself) which are <b>non-empty</b> and are
+	 * either of the exact type specified, or are a subclass of that type.
+	 * <p>
+	 * For example, specifying a type of {@link StringDt} would return all non-empty string instances within the
+	 * message. Specifying a type of {@link IResource} would return the resource itself, as well as any contained
+	 * resources.
+	 * </p>
+	 * 
+	 * @param theResourceT
+	 *            The resource instance to search. Must not be null.
+	 * @param theType
+	 *            The type to search for. Must not be null.
+	 * @return
+	 */
+	public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(IResource theResource, final Class<T> theType) {
+		final ArrayList<T> retVal = new ArrayList<T>();
+		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
+		visit(theResource, null, def, new IModelVisitor() {
+			@SuppressWarnings("unchecked")
+			@Override
+			public void acceptElement(IElement theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
 				if (theElement.isEmpty()) {
 					return;
 				}
 
-		addIfCorrectType(theElement, theType, theList);
+				if (theElement != null && theType.isAssignableFrom(theElement.getClass())) {
-		addUndeclaredExtensions(theElement, theType, theList);
+					retVal.add((T) theElement);
+				}
+			}
+
+			@SuppressWarnings("unchecked")
+			@Override
+			public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
+				if (theType.isAssignableFrom(theNextExt.getClass())) {
+					retVal.add((T) theNextExt);
+				}
+				if (theNextExt.getValue() != null && theType.isAssignableFrom(theNextExt.getValue().getClass())) {
+					retVal.add((T) theNextExt.getValue());
+				}
+			}
+		});
+		return retVal;
+	}
+
+	private <T extends IElement> void visit(IElement theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
+		theCallback.acceptElement(theElement, theChildDefinition, theDefinition);
+		addUndeclaredExtensions(theElement, theDefinition, theChildDefinition, theCallback);
 
 		switch (theDefinition.getChildType()) {
 		case PRIMITIVE_XHTML:
@@ -171,7 +205,7 @@ public class FhirTerser {
 							}
 							throw new DataFormatException(b.toString());
 						}
-						getAllChildElementsOfType(nextValue, childElementDef, theType, theList);
+						visit(nextValue, nextChild, childElementDef, theCallback);
 					}
 				}
 			}
@@ -181,7 +215,7 @@ public class FhirTerser {
 			ContainedDt value = (ContainedDt) theElement;
 			for (IResource next : value.getContainedResources()) {
 				BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(next);
-				getAllChildElementsOfType(next, def, theType, theList);
+				visit(next, null, def, theCallback);
 			}
 			break;
 		}
@@ -192,22 +226,14 @@ public class FhirTerser {
 		}
 	}
 
-	private <T extends IElement> void addUndeclaredExtensions(IElement theElement, Class<T> theType, ArrayList<T> theList) {
+	private <T extends IElement> void addUndeclaredExtensions(IElement theElement, BaseRuntimeElementDefinition<?> theDefinition, BaseRuntimeChildDefinition theChildDefinition, IModelVisitor theCallback) {
 		if (theElement instanceof ISupportsUndeclaredExtensions) {
-			ISupportsUndeclaredExtensions elem = (ISupportsUndeclaredExtensions) theElement;
+			ISupportsUndeclaredExtensions containingElement = (ISupportsUndeclaredExtensions) theElement;
-			for (ExtensionDt nextExt : elem.getUndeclaredExtensions()) {
+			for (ExtensionDt nextExt : containingElement.getUndeclaredExtensions()) {
-				addIfCorrectType(nextExt, theType, theList);
+				theCallback.acceptUndeclaredExtension(containingElement, theChildDefinition, theDefinition, nextExt);
-				addIfCorrectType(nextExt.getValue(), theType, theList);
+				addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
-				addUndeclaredExtensions(nextExt, theType, theList);
 			}
 		}
 	}
 
-	@SuppressWarnings("unchecked")
-	private <T extends IElement> void addIfCorrectType(IElement theElement, Class<T> theType, ArrayList<T> theList) {
-		if (theElement != null && theType.isAssignableFrom(theElement.getClass())) {
-			theList.add((T) theElement);
-		}
-	}
-
 }

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

@@ -0,0 +1,33 @@
+package ca.uhn.fhir.util;
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.api.IElement;
+import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
+
+/**
+ * @see FhirTerser#visit(ca.uhn.fhir.model.api.IResource, IModelVisitor)
+ */
+public interface IModelVisitor {
+
+	/**
+	 * 
+	 * @param theElement
+	 * @param theChildDefinition May be null if this is a root element
+	 * @param theDefinition
+	 */
+	void acceptElement(IElement theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition);
+
+	/**
+	 * 
+	 * @param theContainingElement
+	 * @param theChildDefinition May be null if this is a root element
+	 * @param theDefinition
+	 * @param theNextExt
+	 */
+	void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt);
+
+	
+	
+}

hapi-fhir-base/src/site/xdoc/doc_rest_client.xml

@@ -27,8 +27,9 @@
 				There are two types of clients provided by HAPI: Generic and Annotation-driven.
 				The generic client (introduced in HAPI-FHIR 0.3) is much simpler to create
 				and generally provides the faster way to get started. The annotation-driven
-				client is more powerful and can rely on code generation to give better
+				client can rely on code generation and static binding to specific operations to 
-				compile-time checking. 
+				give better	compile-time checking against servers with a specific set of capabilities
+				exposed. 
 			</p>
 
 		</section>
@@ -76,20 +77,12 @@
 				</p>
 			</subsection>
 						
-			<subsection name="Type - Create">
-				<p>
-					The following example shows how to perform a create
-					operation using the generic client:
-				</p>
-				<macro name="snippet">
-					<param name="id" value="create" />
-					<param name="file"
-						value="examples/src/main/java/example/GenericClientExample.java" />
-				</macro>
-			</subsection>			
-						
 			<subsection name="Type - Search/Query">
 				
+				<p>
+					Searching for resources is probably the most common initial scenario for
+					client applications, so we'll start the demonstration there.
+				</p>
 				<p>
 					The following example shows how to query using the generic client:
 				</p>
@@ -173,6 +166,18 @@
 				
 			</subsection>			
 
+			<subsection name="Type - Create">
+				<p>
+					The following example shows how to perform a create
+					operation using the generic client:
+				</p>
+				<macro name="snippet">
+					<param name="id" value="create" />
+					<param name="file"
+						value="examples/src/main/java/example/GenericClientExample.java" />
+				</macro>
+			</subsection>			
+
 			<subsection name="Instance - Delete">
 				<p>
 					The following example shows how to perform a delete

hapi-fhir-base/src/test/java/ca/uhn/fhir/context/ModelExtensionTest.java

@@ -30,6 +30,9 @@ public class ModelExtensionTest {
 		MyPatient parsed = ourCtx.newXmlParser().parseResource(MyPatient.class, str);
 		assertEquals("foo", parsed.getIdentifierFirstRep().getSystem().getValueAsString());
 
+//		assertEquals(MyOrganization.class, parsed.getManagingOrganization().getResource().getClass());
+//		MyOrganization parsedOrg = (MyOrganization) parsed.getManagingOrganization().getResource();
+//		assertEquals("arg0", parsedOrg.getName().getValue());
 	}
 
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java

@@ -363,6 +363,29 @@ public class JsonParserTest {
 	@Test
 	public void testEncodeBundleCategory() {
 
+		Bundle b = new Bundle();
+		BundleEntry e = b.addEntry();
+		e.setResource(new Patient());
+		b.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
+		
+		String val = new FhirContext().newJsonParser().setPrettyPrint(false).encodeBundleToString(b);
+		ourLog.info(val);
+
+		assertThat(val, StringContains.containsString("\"category\":[{\"term\":\"term\",\"label\":\"label\",\"scheme\":\"scheme\"}]"));
+		
+		b = new FhirContext().newJsonParser().parseBundle(val);
+		assertEquals(1,b.getEntries().size());
+		assertEquals(1,b.getCategories().size());
+		assertEquals("term", b.getCategories().get(0).getTerm());
+		assertEquals("label", b.getCategories().get(0).getLabel());
+		assertEquals("scheme", b.getCategories().get(0).getScheme());
+		assertNull(b.getEntries().get(0).getResource());
+
+	}
+
+	@Test
+	public void testEncodeBundleEntryCategory() {
+
 		Bundle b = new Bundle();
 		BundleEntry e = b.addEntry();
 		e.setResource(new Patient());
@@ -383,7 +406,6 @@ public class JsonParserTest {
 
 	}
 	
-	
 	@Test
 	public void testEncodeContainedResources() throws IOException {
 
@@ -671,6 +693,11 @@ public class JsonParserTest {
 		IParser p = ourCtx.newJsonParser();
 		Bundle bundle = p.parseBundle(msg);
 
+		assertEquals(1, bundle.getCategories().size());
+		assertEquals("http://scheme", bundle.getCategories().get(0).getScheme());
+		assertEquals("http://term", bundle.getCategories().get(0).getTerm());
+		assertEquals("label", bundle.getCategories().get(0).getLabel());
+		
 		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(bundle);
 		ourLog.info(encoded);
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/XmlParserTest.java

@@ -63,16 +63,19 @@ import ca.uhn.fhir.parser.JsonParserTest.MyPatientWithOneDeclaredExtension;
 
 public class XmlParserTest {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserTest.class);
 	private static FhirContext ourCtx;
-
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserTest.class);
 
 	@Test
-	public void testParseLanguage() {
+	public void testEncodeBinaryResource() {
-		String input = "<Patient xmlns=\"http://hl7.org/fhir\"><language value=\"zh-CN\"/><text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> 海生 <b>王 </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>URNo</td></tr><tr><td>Address</td><td><span>99 Houston Road </span><br/><span>BENTLEIGH </span><span>Victoria </span></td></tr><tr><td>Date of birth</td><td><span>01 January 1997</span></td></tr></tbody></table></div></text><identifier><use value=\"usual\"/><label value=\"URNo\"/><value value=\"89532\"/></identifier><name><text value=\"王海生\"/><family value=\"王\"/><given value=\"海生\"/></name><telecom><system value=\"phone\"/><value value=\"9899 9878\"/><use value=\"home\"/></telecom><telecom><system value=\"email\"/><value value=\"zimmerman@datacorp.com.au\"/><use value=\"home\"/></telecom><gender><coding><system value=\"http://hl7.org/fhir/v3/AdministrativeGender\"/><code value=\"M\"/><display value=\"Male\"/></coding><text value=\"Male\"/></gender><birthDate value=\"1997-01-01\"/><address><use value=\"home\"/><text value=\"99 Houston Road, BENTLEIGH, 3204\"/><line value=\"99 Houston Road\"/><city value=\"BENTLEIGH\"/><state value=\"Victoria\"/><zip value=\"3204\"/><period><start value=\"2006-06-16\"/></period></address><active value=\"true\"/></Patient>";
+
-		Patient pt = ourCtx.newXmlParser().parseResource(Patient.class, input);
+		Binary patient = new Binary();
+		patient.setContentType("foo");
+		patient.setContent(new byte[] {1,2,3,4});
+		
+		String val = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertEquals("<Binary xmlns=\"http://hl7.org/fhir\" contentType=\"foo\">AQIDBA==</Binary>", val);
 		
-		assertEquals("zh-CN", pt.getLanguage().getValue());
 	}
 	
 	@Test
@@ -88,283 +91,10 @@ public class XmlParserTest {
 
 	}
 
-	@Test
-	public void testNestedContainedResources() {
-
-		Observation A = new Observation();
-		A.getName().setText("A");
-		
-		Observation B = new Observation();
-		B.getName().setText("B");
-		A.addRelated().setTarget(new ResourceReferenceDt(B));
-		
-		Observation C = new Observation();
-		C.getName().setText("C");
-		B.addRelated().setTarget(new ResourceReferenceDt(C));
-
-		String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(A);
-		ourLog.info(str);
-		
-		assertThat(str, stringContainsInOrder(Arrays.asList("<text value=\"B\"/>", "<text value=\"C\"/>", "<text value=\"A\"/>")));
-		assertThat(str, stringContainsInOrder(Arrays.asList("<contained>", "</contained>")));
-		
-		// Only one (outer) contained block
-		int idx0 = str.indexOf("<contained>");
-		int idx1 = str.indexOf("<contained>",idx0+1);
-		assertNotEquals(-1, idx0);
-		assertEquals(-1, idx1);
-		
-		Observation obs = ourCtx.newXmlParser().parseResource(Observation.class, str);
-		assertEquals("A",obs.getName().getText().getValue());
-		
-		Observation obsB = (Observation) obs.getRelatedFirstRep().getTarget().getResource();
-		assertEquals("B",obsB.getName().getText().getValue());
-
-		Observation obsC = (Observation) obsB.getRelatedFirstRep().getTarget().getResource();
-		assertEquals("C",obsC.getName().getText().getValue());
-
-		
-	}
-
-	
-
-	@Test
-	public void testParseQuery() {
-		String msg = "<Query xmlns=\"http://hl7.org/fhir\">\n" + 
-				"  <text>\n" + 
-				"    <status value=\"generated\"/>\n" + 
-				"    <div xmlns=\"http://www.w3.org/1999/xhtml\">[Put rendering here]</div>\n" + 
-				"  </text>\n" + 
-				"\n" + 
-				"  <!--   this is an extermely simple query - a request to execute the query 'example' on the\n" + 
-				"   responder   -->\n" + 
-				"  <identifier value=\"urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376\"/>\n" + 
-				"  <parameter url=\"http://hl7.org/fhir/query#_query\">\n" + 
-				"    <valueString value=\"example\"/>\n" + 
-				"  </parameter>\n" + 
-				"</Query>";
-		Query query = ourCtx.newXmlParser().parseResource(Query.class, msg);
-		
-		assertEquals("urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376", query.getIdentifier().getValueAsString());
-		assertEquals("http://hl7.org/fhir/query#_query", query.getParameterFirstRep().getUrlAsString());
-		assertEquals("example", query.getParameterFirstRep().getValueAsPrimitive().getValueAsString());
-		
-	}
-	
-	@Test
-	public void testEncodeQuery() {
-		Query q = new Query();
-		ExtensionDt parameter = q.addParameter();
-		parameter.setUrl("http://foo").setValue(new StringDt("bar"));
-		
-		
-		String val = ourCtx.newXmlParser().encodeResourceToString(q);
-		ourLog.info(val);
-
-		assertEquals("<Query xmlns=\"http://hl7.org/fhir\"><parameter url=\"http://foo\"><valueString value=\"bar\"/></parameter></Query>", val);
-		
-	}
-
-	
-	@Test
-	public void testEncodeBinaryResource() {
-
-		Binary patient = new Binary();
-		patient.setContentType("foo");
-		patient.setContent(new byte[] {1,2,3,4});
-		
-		String val = ourCtx.newXmlParser().encodeResourceToString(patient);
-		assertEquals("<Binary xmlns=\"http://hl7.org/fhir\" contentType=\"foo\">AQIDBA==</Binary>", val);
-		
-	}
-
-	
-	@Test
-	public void testParseBinaryResource() {
-
-		Binary val = ourCtx.newXmlParser().parseResource(Binary.class, "<Binary xmlns=\"http://hl7.org/fhir\" contentType=\"foo\">AQIDBA==</Binary>");
-		assertEquals("foo", val.getContentType());
-		assertArrayEquals(new byte[] {1,2,3,4}, val.getContent());
-
-	}
-
-	@Test
-	public void testTagList() {
-		
-		//@formatter:off
-		String tagListStr = "<taglist xmlns=\"http://hl7.org/fhir\"> \n" + 
-				"    <category term=\"term0\" label=\"label0\" scheme=\"scheme0\" /> \n" + 
-				"    <category term=\"term1\" label=\"label1\" scheme=\"\" /> \n" + 
-				"    <category term=\"term2\" label=\"label2\" /> \n" + 
-				"</taglist>";
-		//@formatter:on
-		
-		TagList tagList = ourCtx.newXmlParser().parseTagList(tagListStr);
-		assertEquals(3, tagList.size());
-		assertEquals("term0", tagList.get(0).getTerm());
-		assertEquals("label0", tagList.get(0).getLabel());
-		assertEquals("scheme0", tagList.get(0).getScheme());
-		assertEquals("term1", tagList.get(1).getTerm());
-		assertEquals("label1", tagList.get(1).getLabel());
-		assertEquals(null, tagList.get(1).getScheme());
-		assertEquals("term2", tagList.get(2).getTerm());
-		assertEquals("label2", tagList.get(2).getLabel());
-		assertEquals(null, tagList.get(2).getScheme());
-		
-		/*
-		 * Encode
-		 */
-
-		//@formatter:off
-		String expected = "<taglist xmlns=\"http://hl7.org/fhir\">" + 
-				"<category term=\"term0\" label=\"label0\" scheme=\"scheme0\"/>" + 
-				"<category term=\"term1\" label=\"label1\"/>" + 
-				"<category term=\"term2\" label=\"label2\"/>" + 
-				"</taglist>";
-		//@formatter:on
-		
-		String encoded = ourCtx.newXmlParser().encodeTagListToString(tagList);
-		assertEquals(expected,encoded);
-		
-	}
-	
-	
-	@Test
-	public void testTotalResultsUsingOldNamespace() {
-
-		//@formatter:off
-		String bundle = "<feed xmlns=\"http://www.w3.org/2005/Atom\">\n" + 
-				"  <title>Search results for Patient</title>\n" + 
-				"  <id>urn:uuid:374f2876-0da7-4441-87da-526e2fc624f8</id>\n" + 
-				"  <totalResults xmlns=\"http://purl.org/atompub/tombstones/1.0\">15</totalResults>\n" + 
-				"  <updated>2014-05-04T13:19:47.027-04:00</updated>\n" + 
-				"  <author>\n" + 
-				"    <name>AEGIS Wildfhir Server</name>\n" + 
-				"  </author>" +
-				"</feed>";
-		//@formatter:off
-
-		Bundle bundleR = ourCtx.newXmlParser().parseBundle(bundle);
-		assertEquals(15, bundleR.getTotalResults().getValue().intValue());
-	}
-
-	@Test
-	public void testEncodeExtensionWithResourceContent() {
-		IParser parser = ourCtx.newXmlParser();
-
-		Patient patient = new Patient();
-		patient.addAddress().setUse(AddressUseEnum.HOME);
-		patient.addUndeclaredExtension(false, "urn:foo", new ResourceReferenceDt("Organization/123"));
-
-		String val = parser.encodeResourceToString(patient);
-		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
-
-		Patient actual = parser.parseResource(Patient.class, val);
-		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
-		List<ExtensionDt> ext = actual.getUndeclaredExtensionsByUrl("urn:foo");
-		assertEquals(1, ext.size());
-		ResourceReferenceDt ref = (ResourceReferenceDt) ext.get(0).getValue();
-		assertEquals("Organization/123", ref.getReference().getValue());
-
-	}
-
-	@Test
-	public void testEncodeDeclaredExtensionWithResourceContent() {
-		IParser parser = ourCtx.newXmlParser();
-
-		MyPatientWithOneDeclaredExtension patient = new MyPatientWithOneDeclaredExtension();
-		patient.addAddress().setUse(AddressUseEnum.HOME);
-		patient.setFoo(new ResourceReferenceDt("Organization/123"));
-
-		String val = parser.encodeResourceToString(patient);
-		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
-
-		MyPatientWithOneDeclaredExtension actual = parser.parseResource(MyPatientWithOneDeclaredExtension.class, val);
-		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
-		ResourceReferenceDt ref = actual.getFoo();
-		assertEquals("Organization/123", ref.getReference().getValue());
-
-	}
-
-	@Test
-	public void testEncodeDeclaredExtensionWithAddressContent() {
-		IParser parser = ourCtx.newXmlParser();
-
-		MyPatientWithOneDeclaredAddressExtension patient = new MyPatientWithOneDeclaredAddressExtension();
-		patient.addAddress().setUse(AddressUseEnum.HOME);
-		patient.setFoo(new AddressDt().addLine("line1"));
-
-		String val = parser.encodeResourceToString(patient);
-		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueAddress><line value=\"line1\"/></valueAddress></extension>"));
-
-		MyPatientWithOneDeclaredAddressExtension actual = parser.parseResource(MyPatientWithOneDeclaredAddressExtension.class, val);
-		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
-		AddressDt ref = actual.getFoo();
-		assertEquals("line1", ref.getLineFirstRep().getValue());
-
-	}
-
-	@Test
-	public void testEncodeUndeclaredExtensionWithAddressContent() {
-		IParser parser = ourCtx.newXmlParser();
-
-		Patient patient = new Patient();
-		patient.addAddress().setUse(AddressUseEnum.HOME);
-		patient.addUndeclaredExtension(false, "urn:foo", new AddressDt().addLine("line1"));
-
-		String val = parser.encodeResourceToString(patient);
-		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueAddress><line value=\"line1\"/></valueAddress></extension>"));
-
-		MyPatientWithOneDeclaredAddressExtension actual = parser.parseResource(MyPatientWithOneDeclaredAddressExtension.class, val);
-		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
-		AddressDt ref = actual.getFoo();
-		assertEquals("line1", ref.getLineFirstRep().getValue());
-
-	}
-
-	@Test
-	public void testEncodeBundleResultCount() {
-
-		Bundle b = new Bundle();
-		b.getTotalResults().setValue(123);
-
-		String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
-		ourLog.info(val);
-
-		assertThat(val, StringContains.containsString("<os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">123</os:totalResults>"));
-
-	}
-
-	@Test
-	public void testEncodeBundleCategory() {
-
-		Bundle b = new Bundle();
-		BundleEntry e = b.addEntry();
-		e.setResource(new Patient());
-		e.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
-
-		String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
-		ourLog.info(val);
-
-		assertThat(val, StringContains.containsString("<category term=\"term\" label=\"label\" scheme=\"scheme\"/>"));
-
-		b = ourCtx.newXmlParser().parseBundle(val);
-		assertEquals(1, b.getEntries().size());
-		assertEquals(1, b.getEntries().get(0).getCategories().size());
-		assertEquals("term", b.getEntries().get(0).getCategories().get(0).getTerm());
-		assertEquals("label", b.getEntries().get(0).getCategories().get(0).getLabel());
-		assertEquals("scheme", b.getEntries().get(0).getCategories().get(0).getScheme());
-		assertNull(b.getEntries().get(0).getResource());
-
-	}
-
 	@Test
 	public void testEncodeBundle() throws InterruptedException {
 		Bundle b= new Bundle();
+		b.getCategories().addTag("http://hl7.org/fhir/tag", "http://hl7.org/fhir/tag/message", "Message"); 
 
 		InstantDt pub = InstantDt.withCurrentTime();
 		b.setPublished(pub);
@@ -393,6 +123,7 @@ public class XmlParserTest {
 
 		List<String> strings = new ArrayList<String>();
 		strings.addAll(Arrays.asList("<published>", pub.getValueAsString(), "</published>"));
+		strings.add("<category term=\"http://hl7.org/fhir/tag/message\" label=\"Message\" scheme=\"http://hl7.org/fhir/tag\"/>");
 		strings.addAll(Arrays.asList("<entry>", "<id>1</id>", "</entry>"));
 		strings.addAll(Arrays.asList("<entry>", "<id>2</id>", "<link rel=\"alternate\" href=\"http://foo/bar\"/>", "<link rel=\"search\" href=\"http://foo/bar/search\"/>","</entry>"));
 		strings.addAll(Arrays.asList("<at:deleted-entry", "ref=\"Patient/3", "/>"));
@@ -402,6 +133,44 @@ public class XmlParserTest {
 	}
 
 	
+
+	@Test
+	public void testEncodeBundleCategory() {
+
+		Bundle b = new Bundle();
+		BundleEntry e = b.addEntry();
+		e.setResource(new Patient());
+		e.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
+
+		String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(val);
+
+		assertThat(val, StringContains.containsString("<category term=\"term\" label=\"label\" scheme=\"scheme\"/>"));
+
+		b = ourCtx.newXmlParser().parseBundle(val);
+		assertEquals(1, b.getEntries().size());
+		assertEquals(1, b.getEntries().get(0).getCategories().size());
+		assertEquals("term", b.getEntries().get(0).getCategories().get(0).getTerm());
+		assertEquals("label", b.getEntries().get(0).getCategories().get(0).getLabel());
+		assertEquals("scheme", b.getEntries().get(0).getCategories().get(0).getScheme());
+		assertNull(b.getEntries().get(0).getResource());
+
+	}
+	
+	@Test
+	public void testEncodeBundleResultCount() {
+
+		Bundle b = new Bundle();
+		b.getTotalResults().setValue(123);
+
+		String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(val);
+
+		assertThat(val, StringContains.containsString("<os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">123</os:totalResults>"));
+
+	}
+
+	
 	@Test
 	public void testEncodeContainedAndIncludedResources() {
 
@@ -421,8 +190,6 @@ public class XmlParserTest {
 	}
 
 	
-	
-	
 	@Test
 	public void testEncodeContainedResources() {
 
@@ -446,6 +213,66 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testEncodeDeclaredExtensionWithAddressContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		MyPatientWithOneDeclaredAddressExtension patient = new MyPatientWithOneDeclaredAddressExtension();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		patient.setFoo(new AddressDt().addLine("line1"));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueAddress><line value=\"line1\"/></valueAddress></extension>"));
+
+		MyPatientWithOneDeclaredAddressExtension actual = parser.parseResource(MyPatientWithOneDeclaredAddressExtension.class, val);
+		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
+		AddressDt ref = actual.getFoo();
+		assertEquals("line1", ref.getLineFirstRep().getValue());
+
+	}
+	
+	
+	@Test
+	public void testEncodeDeclaredExtensionWithResourceContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		MyPatientWithOneDeclaredExtension patient = new MyPatientWithOneDeclaredExtension();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		patient.setFoo(new ResourceReferenceDt("Organization/123"));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
+
+		MyPatientWithOneDeclaredExtension actual = parser.parseResource(MyPatientWithOneDeclaredExtension.class, val);
+		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
+		ResourceReferenceDt ref = actual.getFoo();
+		assertEquals("Organization/123", ref.getReference().getValue());
+
+	}
+
+	@Test
+	public void testEncodeExtensionWithResourceContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		Patient patient = new Patient();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		patient.addUndeclaredExtension(false, "urn:foo", new ResourceReferenceDt("Organization/123"));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
+
+		Patient actual = parser.parseResource(Patient.class, val);
+		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
+		List<ExtensionDt> ext = actual.getUndeclaredExtensionsByUrl("urn:foo");
+		assertEquals(1, ext.size());
+		ResourceReferenceDt ref = (ResourceReferenceDt) ext.get(0).getValue();
+		assertEquals("Organization/123", ref.getReference().getValue());
+
+	}
+
 	@Test
 	public void testEncodeInvalidChildGoodException() {
 		Observation obs = new Observation();
@@ -502,6 +329,19 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testEncodeQuery() {
+		Query q = new Query();
+		ExtensionDt parameter = q.addParameter();
+		parameter.setUrl("http://foo").setValue(new StringDt("bar"));
+		
+		
+		String val = ourCtx.newXmlParser().encodeResourceToString(q);
+		ourLog.info(val);
+
+		assertEquals("<Query xmlns=\"http://hl7.org/fhir\"><parameter url=\"http://foo\"><valueString value=\"bar\"/></parameter></Query>", val);
+		
+	}
 
 	@Test
 	public void testEncodeResourceRef() throws DataFormatException {
@@ -525,6 +365,76 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testEncodeUndeclaredExtensionWithAddressContent() {
+		IParser parser = ourCtx.newXmlParser();
+
+		Patient patient = new Patient();
+		patient.addAddress().setUse(AddressUseEnum.HOME);
+		patient.addUndeclaredExtension(false, "urn:foo", new AddressDt().addLine("line1"));
+
+		String val = parser.encodeResourceToString(patient);
+		ourLog.info(val);
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueAddress><line value=\"line1\"/></valueAddress></extension>"));
+
+		MyPatientWithOneDeclaredAddressExtension actual = parser.parseResource(MyPatientWithOneDeclaredAddressExtension.class, val);
+		assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
+		AddressDt ref = actual.getFoo();
+		assertEquals("line1", ref.getLineFirstRep().getValue());
+
+	}
+
+	@Test
+	public void testExtensionOnComposite() throws Exception {
+
+		Patient patient = new Patient();
+
+		HumanNameDt name = patient.addName();
+		name.addFamily().setValue("Shmoe");
+		HumanNameDt given = name.addGiven("Joe");
+		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("Hello"));
+		given.addUndeclaredExtension(ext2);
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(output);
+
+		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertThat(enc, containsString("<name><extension url=\"http://examples.com#givenext\"><valueString value=\"Hello\"/></extension><family value=\"Shmoe\"/><given value=\"Joe\"/></name>"));
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, new StringReader(enc));
+		assertEquals(1, parsed.getNameFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").size());
+		ExtensionDt ext = parsed.getNameFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").get(0);
+		assertEquals("Hello", ext.getValueAsPrimitive().getValue());
+
+	}
+
+	
+	@Test
+	public void testExtensionOnPrimitive() throws Exception {
+
+		Patient patient = new Patient();
+
+		HumanNameDt name = patient.addName();
+		StringDt family = name.addFamily();
+		family.setValue("Shmoe");
+
+		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("Hello"));
+		family.addUndeclaredExtension(ext2);
+		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(output);
+
+		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
+		assertThat(enc, containsString("<name><family value=\"Shmoe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"Hello\"/></extension></family></name>"));
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, new StringReader(enc));
+		assertEquals(1, parsed.getNameFirstRep().getFamilyFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").size());
+		ExtensionDt ext = parsed.getNameFirstRep().getFamilyFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").get(0);
+		assertEquals("Hello", ext.getValueAsPrimitive().getValue());
+
+	}
+
+	
+	
+	
 	@Test
 	public void testExtensions() throws DataFormatException {
 
@@ -630,6 +540,7 @@ public class XmlParserTest {
 		assertTrue(d.toString(), d.identical());
 	}
 
+	
 	@Test
 	public void testLoadAndEncodeUndeclaredExtensions() throws ConfigurationException, DataFormatException, SAXException, IOException {
 		IParser p = ourCtx.newXmlParser();
@@ -683,25 +594,6 @@ public class XmlParserTest {
 		assertTrue(d.toString(), d.identical());
 	}
 
-	
-	@Test
-	public void testParseWithXmlHeader() throws ConfigurationException, DataFormatException {
-		IParser p = ourCtx.newXmlParser();
-
-		//@formatter:off
-		String msg = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" +
-				"<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-				"	<identifier>\n" + 
-				"		<label value=\"IdentifierLabel\"/>\n" + 
-				"	</identifier>\n" + 
-				"</Patient>";
-		//@formatter:on
-
-		Patient resource = (Patient) p.parseResource(msg);
-		assertEquals("IdentifierLabel", resource.getIdentifier().get(0).getLabel().getValue());
-	}
-	
-	
 	@Test
 	public void testLoadObservation() throws ConfigurationException, DataFormatException, IOException {
 
@@ -767,6 +659,52 @@ public class XmlParserTest {
 
 	}
 
+	
+	@Test
+	public void testMoreExtensions() throws Exception {
+
+		Patient patient = new Patient();
+		patient.addIdentifier(IdentifierUseEnum.OFFICIAL, "urn:example", "7000135", null);
+
+		ExtensionDt ext = new ExtensionDt();
+		ext.setModifier(false);
+		ext.setUrl("http://example.com/extensions#someext");
+		ext.setValue(new DateTimeDt("2011-01-02T11:13:15"));
+
+		// Add the extension to the resource
+		patient.addUndeclaredExtension(ext);
+		// END SNIPPET: resourceExtension
+
+		// START SNIPPET: resourceStringExtension
+		HumanNameDt name = patient.addName();
+		name.addFamily().setValue("Shmoe");
+		StringDt given = name.addGiven();
+		given.setValue("Joe");
+		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("given"));
+		given.addUndeclaredExtension(ext2);
+		// END SNIPPET: resourceStringExtension
+
+		// START SNIPPET: subExtension
+		ExtensionDt parent = new ExtensionDt(false, "http://example.com#parent");
+		patient.addUndeclaredExtension(parent);
+
+		ExtensionDt child1 = new ExtensionDt(false, "http://example.com#child", new StringDt("value1"));
+		parent.addUndeclaredExtension(child1);
+
+		ExtensionDt child2 = new ExtensionDt(false, "http://example.com#child", new StringDt("value1"));
+		parent.addUndeclaredExtension(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>"));
+	}
+	
+	
 	@Test
 	public void testNarrativeGeneration() throws DataFormatException {
 
@@ -791,12 +729,50 @@ public class XmlParserTest {
 	}
 
 	@Test
-	public void testParseBundleWithMixedReturnTypes() {
+	public void testNestedContainedResources() {
-		InputStreamReader str = new InputStreamReader(getClass().getResourceAsStream("/mixed-return-bundle.xml"));
+
-		Bundle b = ourCtx.newXmlParser().parseBundle(Patient.class, str);
+		Observation A = new Observation();
-		assertEquals(Patient.class, b.getEntries().get(0).getResource().getClass());
+		A.getName().setText("A");
-		assertEquals(Patient.class, b.getEntries().get(1).getResource().getClass());
+		
-		assertEquals(Organization.class, b.getEntries().get(2).getResource().getClass());
+		Observation B = new Observation();
+		B.getName().setText("B");
+		A.addRelated().setTarget(new ResourceReferenceDt(B));
+		
+		Observation C = new Observation();
+		C.getName().setText("C");
+		B.addRelated().setTarget(new ResourceReferenceDt(C));
+
+		String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(A);
+		ourLog.info(str);
+		
+		assertThat(str, stringContainsInOrder(Arrays.asList("<text value=\"B\"/>", "<text value=\"C\"/>", "<text value=\"A\"/>")));
+		assertThat(str, stringContainsInOrder(Arrays.asList("<contained>", "</contained>")));
+		
+		// Only one (outer) contained block
+		int idx0 = str.indexOf("<contained>");
+		int idx1 = str.indexOf("<contained>",idx0+1);
+		assertNotEquals(-1, idx0);
+		assertEquals(-1, idx1);
+		
+		Observation obs = ourCtx.newXmlParser().parseResource(Observation.class, str);
+		assertEquals("A",obs.getName().getText().getValue());
+		
+		Observation obsB = (Observation) obs.getRelatedFirstRep().getTarget().getResource();
+		assertEquals("B",obsB.getName().getText().getValue());
+
+		Observation obsC = (Observation) obsB.getRelatedFirstRep().getTarget().getResource();
+		assertEquals("C",obsC.getName().getText().getValue());
+
+		
+	}
+
+	@Test
+	public void testParseBinaryResource() {
+
+		Binary val = ourCtx.newXmlParser().parseResource(Binary.class, "<Binary xmlns=\"http://hl7.org/fhir\" contentType=\"foo\">AQIDBA==</Binary>");
+		assertEquals("foo", val.getContentType());
+		assertArrayEquals(new byte[] {1,2,3,4}, val.getContent());
+
 	}
 
 	@SuppressWarnings("deprecation")
@@ -814,6 +790,7 @@ public class XmlParserTest {
 				"  <title>FHIR Core Valuesets</title>\n" + 
 				"  <id>http://hl7.org/fhir/profile/valuesets</id>\n" + 
 				"  <link href=\"http://hl7.org/implement/standards/fhir/valuesets.xml\" rel=\"self\"/>\n" +
+				"  <category term=\"http://hl7.org/fhir/tag/message\" label=\"Message\" scheme=\"http://hl7.org/fhir/tag\"/>\n" + 
 				"  <updated>2014-02-10T04:11:24.435-00:00</updated>\n" + 
 				"  <entry>\n" + 
 				"    <title>Valueset &quot;256a5231-a2bb-49bd-9fea-f349d428b70d&quot; to support automated processing</title>\n" + 
@@ -867,6 +844,9 @@ public class XmlParserTest {
 		IParser p = new FhirContext(ValueSet.class).newXmlParser();
 		Bundle bundle = p.parseBundle(msg);
 
+		assertEquals(1, bundle.getCategories().size());
+		assertEquals("http://hl7.org/fhir/tag", bundle.getCategories().get(0).getScheme());
+		
 		assertEquals("FHIR Core Valuesets", bundle.getTitle().getValue());
 		assertEquals("http://hl7.org/implement/standards/fhir/valuesets.xml", bundle.getLinkSelf().getValue());
 		assertEquals("2014-02-10T04:11:24.435+00:00", bundle.getUpdated().getValueAsString());
@@ -946,7 +926,6 @@ public class XmlParserTest {
 		
 	}
 
-	
 	@Test
 	public void testParseBundleLarge() throws IOException {
 
@@ -961,6 +940,15 @@ public class XmlParserTest {
 
 	}
 	
+	@Test
+	public void testParseBundleWithMixedReturnTypes() {
+		InputStreamReader str = new InputStreamReader(getClass().getResourceAsStream("/mixed-return-bundle.xml"));
+		Bundle b = ourCtx.newXmlParser().parseBundle(Patient.class, str);
+		assertEquals(Patient.class, b.getEntries().get(0).getResource().getClass());
+		assertEquals(Patient.class, b.getEntries().get(1).getResource().getClass());
+		assertEquals(Organization.class, b.getEntries().get(2).getResource().getClass());
+	}
+
 	@Test
 	public void testParseContainedResources() throws IOException {
 
@@ -976,19 +964,6 @@ public class XmlParserTest {
 
 	}
 
-	/**
-	 * This sample has extra elements in <searchParam> that are not actually a
-	 * part of the spec any more..
-	 */
-	@Test
-	public void testParseFuroreMetadataWithExtraElements() throws IOException {
-		String msg = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/furore-conformance.xml"));
-
-		IParser p = new FhirContext(ValueSet.class).newXmlParser();
-		Conformance conf = p.parseResource(Conformance.class, msg);
-		RestResource res = conf.getRestFirstRep().getResourceFirstRep();
-		assertEquals("_id", res.getSearchParam().get(1).getName().getValue());
-	}
 	
 	@Test
 	public void testParseEncodeNarrative() {
@@ -1010,103 +985,66 @@ public class XmlParserTest {
 
 	}
 
-	@BeforeClass
+	/**
-	public static void beforeClass() {
+	 * This sample has extra elements in <searchParam> that are not actually a
-		XMLUnit.setIgnoreAttributeOrder(true);
+	 * part of the spec any more..
-		XMLUnit.setIgnoreComments(true);
+	 */
-		XMLUnit.setIgnoreWhitespace(true);
+	@Test
-		ourCtx = new FhirContext();
+	public void testParseFuroreMetadataWithExtraElements() throws IOException {
+		String msg = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/furore-conformance.xml"));
+
+		IParser p = new FhirContext(ValueSet.class).newXmlParser();
+		Conformance conf = p.parseResource(Conformance.class, msg);
+		RestResource res = conf.getRestFirstRep().getResourceFirstRep();
+		assertEquals("_id", res.getSearchParam().get(1).getName().getValue());
 	}
 
 	@Test
-	public void testMoreExtensions() throws Exception {
+	public void testParseLanguage() {
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\"><language value=\"zh-CN\"/><text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> 海生 <b>王 </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>URNo</td></tr><tr><td>Address</td><td><span>99 Houston Road </span><br/><span>BENTLEIGH </span><span>Victoria </span></td></tr><tr><td>Date of birth</td><td><span>01 January 1997</span></td></tr></tbody></table></div></text><identifier><use value=\"usual\"/><label value=\"URNo\"/><value value=\"89532\"/></identifier><name><text value=\"王海生\"/><family value=\"王\"/><given value=\"海生\"/></name><telecom><system value=\"phone\"/><value value=\"9899 9878\"/><use value=\"home\"/></telecom><telecom><system value=\"email\"/><value value=\"zimmerman@datacorp.com.au\"/><use value=\"home\"/></telecom><gender><coding><system value=\"http://hl7.org/fhir/v3/AdministrativeGender\"/><code value=\"M\"/><display value=\"Male\"/></coding><text value=\"Male\"/></gender><birthDate value=\"1997-01-01\"/><address><use value=\"home\"/><text value=\"99 Houston Road, BENTLEIGH, 3204\"/><line value=\"99 Houston Road\"/><city value=\"BENTLEIGH\"/><state value=\"Victoria\"/><zip value=\"3204\"/><period><start value=\"2006-06-16\"/></period></address><active value=\"true\"/></Patient>";
+		Patient pt = ourCtx.newXmlParser().parseResource(Patient.class, input);
 		
-		Patient patient = new Patient();
+		assertEquals("zh-CN", pt.getLanguage().getValue());
-		patient.addIdentifier(IdentifierUseEnum.OFFICIAL, "urn:example", "7000135", null);
-
-		ExtensionDt ext = new ExtensionDt();
-		ext.setModifier(false);
-		ext.setUrl("http://example.com/extensions#someext");
-		ext.setValue(new DateTimeDt("2011-01-02T11:13:15"));
-
-		// Add the extension to the resource
-		patient.addUndeclaredExtension(ext);
-		// END SNIPPET: resourceExtension
-
-		// START SNIPPET: resourceStringExtension
-		HumanNameDt name = patient.addName();
-		name.addFamily().setValue("Shmoe");
-		StringDt given = name.addGiven();
-		given.setValue("Joe");
-		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("given"));
-		given.addUndeclaredExtension(ext2);
-		// END SNIPPET: resourceStringExtension
-
-		// START SNIPPET: subExtension
-		ExtensionDt parent = new ExtensionDt(false, "http://example.com#parent");
-		patient.addUndeclaredExtension(parent);
-
-		ExtensionDt child1 = new ExtensionDt(false, "http://example.com#child", new StringDt("value1"));
-		parent.addUndeclaredExtension(child1);
-
-		ExtensionDt child2 = new ExtensionDt(false, "http://example.com#child", new StringDt("value1"));
-		parent.addUndeclaredExtension(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>"));
 	}
 
 	@Test
-	public void testExtensionOnComposite() throws Exception {
+	public void testParseQuery() {
+		String msg = "<Query xmlns=\"http://hl7.org/fhir\">\n" + 
+				"  <text>\n" + 
+				"    <status value=\"generated\"/>\n" + 
+				"    <div xmlns=\"http://www.w3.org/1999/xhtml\">[Put rendering here]</div>\n" + 
+				"  </text>\n" + 
+				"\n" + 
+				"  <!--   this is an extermely simple query - a request to execute the query 'example' on the\n" + 
+				"   responder   -->\n" + 
+				"  <identifier value=\"urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376\"/>\n" + 
+				"  <parameter url=\"http://hl7.org/fhir/query#_query\">\n" + 
+				"    <valueString value=\"example\"/>\n" + 
+				"  </parameter>\n" + 
+				"</Query>";
+		Query query = ourCtx.newXmlParser().parseResource(Query.class, msg);
 		
-		Patient patient = new Patient();
+		assertEquals("urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376", query.getIdentifier().getValueAsString());
-
+		assertEquals("http://hl7.org/fhir/query#_query", query.getParameterFirstRep().getUrlAsString());
-		HumanNameDt name = patient.addName();
+		assertEquals("example", query.getParameterFirstRep().getValueAsPrimitive().getValueAsString());
-		name.addFamily().setValue("Shmoe");
-		HumanNameDt given = name.addGiven("Joe");
-		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("Hello"));
-		given.addUndeclaredExtension(ext2);
-		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-		ourLog.info(output);
-
-		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
-		assertThat(enc, containsString("<name><extension url=\"http://examples.com#givenext\"><valueString value=\"Hello\"/></extension><family value=\"Shmoe\"/><given value=\"Joe\"/></name>"));
-
-		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, new StringReader(enc));
-		assertEquals(1, parsed.getNameFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").size());
-		ExtensionDt ext = parsed.getNameFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").get(0);
-		assertEquals("Hello", ext.getValueAsPrimitive().getValue());
 		
 	}
 	
 	@Test
-	public void testExtensionOnPrimitive() throws Exception {
+	public void testParseWithXmlHeader() throws ConfigurationException, DataFormatException {
+		IParser p = ourCtx.newXmlParser();
 
-		Patient patient = new Patient();
+		//@formatter:off
-
+		String msg = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" +
-		HumanNameDt name = patient.addName();
+				"<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-		StringDt family = name.addFamily();
+				"	<identifier>\n" + 
-		family.setValue("Shmoe");
+				"		<label value=\"IdentifierLabel\"/>\n" + 
-
+				"	</identifier>\n" + 
-		ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#givenext", new StringDt("Hello"));
+				"</Patient>";
-		family.addUndeclaredExtension(ext2);
+		//@formatter:on
-		String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
-		ourLog.info(output);
-
-		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
-		assertThat(enc, containsString("<name><family value=\"Shmoe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"Hello\"/></extension></family></name>"));
-
-		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, new StringReader(enc));
-		assertEquals(1, parsed.getNameFirstRep().getFamilyFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").size());
-		ExtensionDt ext = parsed.getNameFirstRep().getFamilyFirstRep().getUndeclaredExtensionsByUrl("http://examples.com#givenext").get(0);
-		assertEquals("Hello", ext.getValueAsPrimitive().getValue());
 
+		Patient resource = (Patient) p.parseResource(msg);
+		assertEquals("IdentifierLabel", resource.getIdentifier().get(0).getLabel().getValue());
 	}
 
 	@Test
@@ -1167,4 +1105,71 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testTagList() {
+		
+		//@formatter:off
+		String tagListStr = "<taglist xmlns=\"http://hl7.org/fhir\"> \n" + 
+				"    <category term=\"term0\" label=\"label0\" scheme=\"scheme0\" /> \n" + 
+				"    <category term=\"term1\" label=\"label1\" scheme=\"\" /> \n" + 
+				"    <category term=\"term2\" label=\"label2\" /> \n" + 
+				"</taglist>";
+		//@formatter:on
+		
+		TagList tagList = ourCtx.newXmlParser().parseTagList(tagListStr);
+		assertEquals(3, tagList.size());
+		assertEquals("term0", tagList.get(0).getTerm());
+		assertEquals("label0", tagList.get(0).getLabel());
+		assertEquals("scheme0", tagList.get(0).getScheme());
+		assertEquals("term1", tagList.get(1).getTerm());
+		assertEquals("label1", tagList.get(1).getLabel());
+		assertEquals(null, tagList.get(1).getScheme());
+		assertEquals("term2", tagList.get(2).getTerm());
+		assertEquals("label2", tagList.get(2).getLabel());
+		assertEquals(null, tagList.get(2).getScheme());
+		
+		/*
+		 * Encode
+		 */
+
+		//@formatter:off
+		String expected = "<taglist xmlns=\"http://hl7.org/fhir\">" + 
+				"<category term=\"term0\" label=\"label0\" scheme=\"scheme0\"/>" + 
+				"<category term=\"term1\" label=\"label1\"/>" + 
+				"<category term=\"term2\" label=\"label2\"/>" + 
+				"</taglist>";
+		//@formatter:on
+		
+		String encoded = ourCtx.newXmlParser().encodeTagListToString(tagList);
+		assertEquals(expected,encoded);
+		
+	}
+
+	@Test
+	public void testTotalResultsUsingOldNamespace() {
+
+		//@formatter:off
+		String bundle = "<feed xmlns=\"http://www.w3.org/2005/Atom\">\n" + 
+				"  <title>Search results for Patient</title>\n" + 
+				"  <id>urn:uuid:374f2876-0da7-4441-87da-526e2fc624f8</id>\n" + 
+				"  <totalResults xmlns=\"http://purl.org/atompub/tombstones/1.0\">15</totalResults>\n" + 
+				"  <updated>2014-05-04T13:19:47.027-04:00</updated>\n" + 
+				"  <author>\n" + 
+				"    <name>AEGIS Wildfhir Server</name>\n" + 
+				"  </author>" +
+				"</feed>";
+		//@formatter:off
+
+		Bundle bundleR = ourCtx.newXmlParser().parseBundle(bundle);
+		assertEquals(15, bundleR.getTotalResults().getValue().intValue());
+	}
+
+	@BeforeClass
+	public static void beforeClass() {
+		XMLUnit.setIgnoreAttributeOrder(true);
+		XMLUnit.setIgnoreComments(true);
+		XMLUnit.setIgnoreWhitespace(true);
+		ourCtx = new FhirContext();
+	}
+
 }

hapi-fhir-base/src/test/resources/atom-document-large.json

@@ -25,6 +25,11 @@
     }
   ],
   "updated" : "2014-03-22T15:37:12Z",
+  "category" : [{
+    "term" : "http://term",
+    "label" : "label",
+    "scheme" : "http://scheme"
+  }],
   "totalResults" : "356",
   "entry" : [
     {