Start JSON parser

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

@@ -26,6 +26,10 @@ public abstract class BaseRuntimeChildDefinition {
 		List<? extends IElement> getValues(Object theTarget);
 	}
 
+	public abstract int getMax();
+	
+	public abstract int getMin();
+	
 	public interface IMutator {
 		void addValue(Object theTarget, IElement theValue);
 	}

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

@@ -9,6 +9,7 @@ import java.util.Map;
 import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.parser.JsonParser;
 import ca.uhn.fhir.parser.XmlParser;
 import ca.uhn.fhir.rest.client.IRestfulClientFactory;
 import ca.uhn.fhir.rest.client.RestfulClientFactory;
@@ -92,4 +93,8 @@ public class FhirContext {
 		return myIdToResourceDefinition.values();
 	}
 
+	public IParser newJsonParser() {
+		return new JsonParser(this);
+	}
+
 }

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

@@ -13,6 +13,7 @@ import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.BaseResourceReference;
 import ca.uhn.fhir.model.api.UndeclaredExtension;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 
 public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildDefinition {
 
@@ -77,6 +78,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		def.sealAndInitialize(theClassToElementDefinitions);
 		myAttributeNameToDefinition.put("valueResource", def);
 		myDatatypeToDefinition.put(BaseResourceReference.class, def);
+		myDatatypeToDefinition.put(ResourceReferenceDt.class, def);
 	}
 
 
@@ -109,4 +111,16 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 	}
 
 
+	@Override
+	public int getMax() {
+		return 1;
+	}
+
+
+	@Override
+	public int getMin() {
+		return 0;
+	}
+
+
 }

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

@@ -2,7 +2,7 @@ package ca.uhn.fhir.model.api;
 
 import java.util.List;
 
-public interface ISupportsUndeclaredExtensions {
+public interface ISupportsUndeclaredExtensions extends IElement {
 	
 	/**
 	 * Returns a list containing all undeclared non-modifier extensions

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

@@ -13,7 +13,7 @@ public @interface ResourceDef {
 
 	String name();
 
-	String id();
+	String id() default "";
 	
 	String profile() default "";
 	

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

@@ -0,0 +1,391 @@
+package ca.uhn.fhir.parser;
+
+
+public class CopyOfJsonParser  {
+
+//	private FhirContext myContext;
+//
+//	public CopyOfJsonParser(FhirContext theContext) {
+//		myContext = theContext;
+//	}
+//
+//	@Override
+//	public String encodeBundleToString(Bundle theBundle) throws DataFormatException {
+//		StringWriter stringWriter = new StringWriter();
+//		encodeBundleToWriter(theBundle, stringWriter);
+//
+//		return stringWriter.toString();
+//	}
+//
+//	@Override
+//	public void encodeBundleToWriter(Bundle theBundle, Writer theWriter) {
+//		try {
+//			XMLStreamWriter eventWriter;
+//			eventWriter = myXmlOutputFactory.createXMLStreamWriter(theWriter);
+//			eventWriter = decorateStreamWriter(eventWriter);
+//
+//			eventWriter.writeStartElement("feed");
+//			eventWriter.writeDefaultNamespace(ATOM_NS);
+//
+//			writeTagWithTextNode(eventWriter, "title", theBundle.getTitle());
+//			writeTagWithTextNode(eventWriter, "id", theBundle.getId());
+//
+//			writeAtomLink(eventWriter, "self", theBundle.getLinkSelf());
+//			writeAtomLink(eventWriter, "first", theBundle.getLinkFirst());
+//			writeAtomLink(eventWriter, "previous", theBundle.getLinkPrevious());
+//			writeAtomLink(eventWriter, "next", theBundle.getLinkNext());
+//			writeAtomLink(eventWriter, "last", theBundle.getLinkLast());
+//			writeAtomLink(eventWriter, "fhir-base", theBundle.getLinkBase());
+//
+//			if (theBundle.getTotalResults().getValue() != null) {
+//				eventWriter.writeStartElement("os", OPENSEARCH_NS, "totalResults");
+//				eventWriter.writeNamespace("os", OPENSEARCH_NS);
+//				eventWriter.writeCharacters(theBundle.getTotalResults().getValue().toString());
+//				eventWriter.writeEndElement();
+//			}
+//
+//			writeOptionalTagWithTextNode(eventWriter, "updated", theBundle.getUpdated());
+//			writeOptionalTagWithTextNode(eventWriter, "published", theBundle.getPublished());
+//
+//			if (StringUtils.isNotBlank(theBundle.getAuthorName().getValue())) {
+//				eventWriter.writeStartElement("author");
+//				writeTagWithTextNode(eventWriter, "name", theBundle.getAuthorName());
+//				writeOptionalTagWithTextNode(eventWriter, "uri", theBundle.getAuthorUri());
+//				eventWriter.writeEndElement();
+//			}
+//
+//			for (BundleEntry nextEntry : theBundle.getEntries()) {
+//				eventWriter.writeStartElement("entry");
+//
+//				eventWriter.writeStartElement("content");
+//				eventWriter.writeAttribute("type", "text/xml");
+//
+//				IResource resource = nextEntry.getResource();
+//				encodeResourceToXmlStreamWriter(resource, eventWriter);
+//
+//				eventWriter.writeEndElement(); // content
+//				eventWriter.writeEndElement(); // entry
+//			}
+//
+//			eventWriter.writeEndElement();
+//			eventWriter.close();
+//		} catch (XMLStreamException e) {
+//			throw new ConfigurationException("Failed to initialize STaX event factory", e);
+//		}
+//	}
+//
+//	private void encodeChildElementToStreamWriter(JsonWriter theEventWriter, IElement nextValue, String childName, BaseRuntimeElementDefinition<?> childDef, String theExtensionUrl) {
+//		if (nextValue.isEmpty()) {
+//			return;
+//		}
+//
+//		switch (childDef.getChildType()) {
+//		case PRIMITIVE_DATATYPE: {
+//			IPrimitiveDatatype<?> pd = (IPrimitiveDatatype<?>) nextValue;
+//			if (pd.getValue() != null) {
+//				theEventWriter.name(childName);
+//				if (pd instanceof IntegerDt) {
+//					theEventWriter.value(((IntegerDt)pd).getValue());
+//				} else if (pd instanceof DecimalDt) {
+//					theEventWriter.value(((DecimalDt)pd).getValue());
+//				} else if (pd instanceof BooleanDt) {
+//					theEventWriter.value(((BooleanDt)pd).getValue());
+//				} else {
+//					String value = pd.getValueAsString();
+//					theEventWriter.value(value);
+//				}
+//				theEventWriter.writeAttribute("value", value);
+//				encodeExtensionsIfPresent(theEventWriter, nextValue);
+//				theEventWriter.writeEndElement();
+//			}
+//			break;
+//		}
+//		case RESOURCE_BLOCK:
+//		case COMPOSITE_DATATYPE: {
+//			theEventWriter.writeStartElement(childName);
+//			if (isNotBlank(theExtensionUrl)) {
+//				theEventWriter.writeAttribute("url", theExtensionUrl);
+//			}
+//			BaseRuntimeElementCompositeDefinition<?> childCompositeDef = (BaseRuntimeElementCompositeDefinition<?>) childDef;
+//			encodeCompositeElementToStreamWriter(nextValue, theEventWriter, childCompositeDef);
+//			encodeExtensionsIfPresent(theEventWriter, nextValue);
+//			theEventWriter.writeEndElement();
+//			break;
+//		}
+//		case RESOURCE_REF: {
+//			ResourceReferenceDt ref = (ResourceReferenceDt) nextValue;
+//			if (!ref.isEmpty()) {
+//				theEventWriter.writeStartElement(childName);
+//				encodeResourceReferenceToStreamWriter(theEventWriter, ref);
+//				theEventWriter.writeEndElement();
+//			}
+//			break;
+//		}
+//		case RESOURCE: {
+//			throw new IllegalStateException(); // should not happen
+//		}
+//		case PRIMITIVE_XHTML: {
+//			XhtmlDt dt = (XhtmlDt) nextValue;
+//			if (dt.hasContent()) {
+//				encodeXhtml(dt, theEventWriter);
+//			}
+//			break;
+//		}
+//		case UNDECL_EXT: {
+//			throw new IllegalStateException("should not happen");
+//		}
+//		}
+//
+//	}
+//
+//	private void encodeCompositeElementChildrenToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> children) throws XMLStreamException,
+//			DataFormatException {
+//		for (BaseRuntimeChildDefinition nextChild : children) {
+//			List<? extends IElement> values = nextChild.getAccessor().getValues(theElement);
+//			if (values == null || values.isEmpty()) {
+//				continue;
+//			}
+//
+//			for (IElement nextValue : values) {
+//				if (nextValue == null) {
+//					continue;
+//				}
+//				Class<? extends IElement> type = nextValue.getClass();
+//				String childName = nextChild.getChildNameByDatatype(type);
+//				String extensionUrl = nextChild.getExtensionUrl();
+//				BaseRuntimeElementDefinition<?> childDef = nextChild.getChildElementDefinitionByDatatype(type);
+//				if (childDef == null) {
+//					throw new IllegalStateException(nextChild + " has no child of type " + type);
+//				}
+//
+//				if (extensionUrl != null && childName.equals("extension") == false) {
+//					RuntimeChildDeclaredExtensionDefinition extDef = (RuntimeChildDeclaredExtensionDefinition) nextChild;
+//					if (extDef.isModifier()) {
+//						theEventWriter.writeStartElement("modifierExtension");
+//					}else {
+//						theEventWriter.writeStartElement("extension");
+//					}
+//					
+//					theEventWriter.writeAttribute("url", extensionUrl);
+//					encodeChildElementToStreamWriter(theEventWriter, nextValue, childName, childDef, null);
+//					theEventWriter.writeEndElement();
+//				} else {
+//					encodeChildElementToStreamWriter(theEventWriter, nextValue, childName, childDef, extensionUrl);
+//				}
+//			}
+//		}
+//	}
+//
+//	private void encodeCompositeElementToStreamWriter(IElement theElement, JsonWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> resDef) throws XMLStreamException,
+//			DataFormatException {
+//		encodeExtensionsIfPresent(theEventWriter, theElement);
+//		encodeCompositeElementChildrenToStreamWriter(theElement, theEventWriter, resDef.getExtensions());
+//		encodeCompositeElementChildrenToStreamWriter(theElement, theEventWriter, resDef.getChildren());
+//	}
+//
+//	private void encodeExtensionsIfPresent(JsonWriter theWriter, IElement theResource)  {
+//		if (theResource instanceof ISupportsUndeclaredExtensions) {
+//			ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theResource;
+//			encodeUndeclaredExtensions(theWriter, res.getUndeclaredExtensions(), "extension");
+//			encodeUndeclaredExtensions(theWriter, res.getUndeclaredModifierExtensions(), "modifierExtension");
+//		}
+//	}
+//
+//	private void encodeUndeclaredExtensions(JsonWriter theWriter, List<UndeclaredExtension> extensions, String theTagName) throws XMLStreamException {
+//		if (extensions.isEmpty()) {
+//			return;
+//		}
+//		
+//		theWriter.name(theTagName);
+//		theWriter.beginArray();
+//		
+//		for (UndeclaredExtension next : extensions) {
+//			theWriter.name("url");
+//			theWriter.value(next.getUrl());
+//
+//			if (next.getValue() != null) {
+//				IElement nextValue = next.getValue();
+//				RuntimeChildUndeclaredExtensionDefinition extDef = myContext.getRuntimeChildUndeclaredExtensionDefinition();
+//				String childName = extDef.getChildNameByDatatype(nextValue.getClass());
+//				BaseRuntimeElementDefinition<?> childDef = extDef.getChildElementDefinitionByDatatype(nextValue.getClass());
+//				encodeChildElementToStreamWriter(theWriter, nextValue, childName, childDef, null);
+//			}
+//
+//			// child extensions
+//			encodeExtensionsIfPresent(theWriter, next);
+//
+//		}
+//		
+//		theWriter.endArray();
+//	}
+//
+//	private void encodeResourceReferenceToStreamWriter(XMLStreamWriter theEventWriter, ResourceReferenceDt theRef) throws XMLStreamException {
+//		if (!(theRef.getDisplay().isEmpty())) {
+//			theEventWriter.writeStartElement("display");
+//			theEventWriter.writeAttribute("value", theRef.getDisplay().getValue());
+//			theEventWriter.writeEndElement();
+//		}
+//		if (!(theRef.getReference().isEmpty())) {
+//			theEventWriter.writeStartElement("reference");
+//			theEventWriter.writeAttribute("value", theRef.getReference().getValue());
+//			theEventWriter.writeEndElement();
+//		}
+//	}
+//
+//
+//	@Override
+//	public String encodeResourceToString(IResource theResource) throws DataFormatException {
+//		Writer stringWriter = new StringWriter();
+//		encodeResourceToWriter(theResource, stringWriter);
+//		return stringWriter.toString();
+//	}
+//
+//	@Override
+//	public void encodeResourceToWriter(IResource theResource, Writer theWriter) {
+//		JsonWriter eventWriter = new JsonWriter(theWriter);
+////		try {
+//			encodeResourceToXmlStreamWriter(theResource, eventWriter);
+//			eventWriter.flush();
+////		} catch (XMLStreamException e) {
+////			throw new ConfigurationException("Failed to initialize STaX event factory", e);
+////		}
+//	}
+//
+//
+//	private void encodeResourceToXmlStreamWriter(IResource theResource, JsonWriter theEventWriter) throws XMLStreamException, DataFormatException {
+//		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
+//		
+//		theEventWriter.beginObject();
+//		
+//		theEventWriter.name("resourceType");
+//		theEventWriter.value(resDef.getName());
+//		
+//		encodeCompositeElementToStreamWriter(theResource, theEventWriter, resDef);
+//
+//		theEventWriter.writeEndElement();
+//	}
+//
+//	private void encodeXhtml(XhtmlDt theDt, XMLStreamWriter theEventWriter) throws XMLStreamException {
+//		if (theDt == null || theDt.getValue() == null) {
+//			return;
+//		}
+//
+//		boolean firstEvent = true;
+//		for (XMLEvent event : theDt.getValue()) {
+//			switch (event.getEventType()) {
+//			case XMLStreamConstants.ATTRIBUTE:
+//				Attribute attr = (Attribute) event;
+//				if (isBlank(attr.getName().getPrefix())) {
+//					if (isBlank(attr.getName().getNamespaceURI())) {
+//						theEventWriter.writeAttribute(attr.getName().getLocalPart(), attr.getValue());
+//					} else {
+//						theEventWriter.writeAttribute(attr.getName().getNamespaceURI(), attr.getName().getLocalPart(), attr.getValue());
+//					}
+//				} else {
+//					theEventWriter.writeAttribute(attr.getName().getPrefix(), attr.getName().getNamespaceURI(), attr.getName().getLocalPart(), attr.getValue());
+//				}
+//
+//				break;
+//			case XMLStreamConstants.CDATA:
+//				theEventWriter.writeCData(((Characters) event).getData());
+//				break;
+//			case XMLStreamConstants.CHARACTERS:
+//			case XMLStreamConstants.SPACE:
+//				theEventWriter.writeCharacters(((Characters) event).getData());
+//				break;
+//			case XMLStreamConstants.COMMENT:
+//				theEventWriter.writeComment(((Comment) event).getText());
+//				break;
+//			case XMLStreamConstants.END_ELEMENT:
+//				theEventWriter.writeEndElement();
+//				break;
+//			case XMLStreamConstants.ENTITY_REFERENCE:
+//				EntityReference er = (EntityReference) event;
+//				theEventWriter.writeEntityRef(er.getName());
+//				break;
+//			case XMLStreamConstants.NAMESPACE:
+//				Namespace ns = (Namespace) event;
+//				theEventWriter.writeNamespace(ns.getPrefix(), ns.getNamespaceURI());
+//				break;
+//			case XMLStreamConstants.START_ELEMENT:
+//				StartElement se = event.asStartElement();
+//				if (firstEvent) {
+//					theEventWriter.writeStartElement(se.getName().getLocalPart());
+//					if (StringUtils.isBlank(se.getName().getPrefix())) {
+//						theEventWriter.writeDefaultNamespace(se.getName().getNamespaceURI());
+//					} else {
+//						theEventWriter.writeNamespace(se.getName().getPrefix(), se.getName().getNamespaceURI());
+//					}
+//				} else {
+//					if (isBlank(se.getName().getPrefix())) {
+//						if (isBlank(se.getName().getNamespaceURI())) {
+//							theEventWriter.writeStartElement(se.getName().getLocalPart());
+//						} else {
+//							if (StringUtils.isBlank(se.getName().getPrefix())) {
+//								theEventWriter.writeStartElement(se.getName().getLocalPart());
+//								theEventWriter.writeDefaultNamespace(se.getName().getNamespaceURI());
+//							} else {
+//								theEventWriter.writeStartElement(se.getName().getNamespaceURI(), se.getName().getLocalPart());
+//							}
+//						}
+//					} else {
+//						theEventWriter.writeStartElement(se.getName().getPrefix(), se.getName().getLocalPart(), se.getName().getNamespaceURI());
+//					}
+//				}
+//				break;
+//			case XMLStreamConstants.DTD:
+//			case XMLStreamConstants.END_DOCUMENT:
+//			case XMLStreamConstants.ENTITY_DECLARATION:
+//			case XMLStreamConstants.NOTATION_DECLARATION:
+//			case XMLStreamConstants.PROCESSING_INSTRUCTION:
+//			case XMLStreamConstants.START_DOCUMENT:
+//				break;
+//			}
+//
+//			firstEvent = false;
+//		}
+//	}
+//	
+//	@Override
+//	public Bundle parseBundle(Reader theReader) {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//	public Bundle parseBundle(String theMessageString) throws ConfigurationException, DataFormatException {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//	public IResource parseResource(String theMessageString) throws ConfigurationException, DataFormatException {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//	public IResource parseResource(Reader theReader) throws ConfigurationException, DataFormatException {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//	public IResource parseResource(XMLEventReader theStreamReader) {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//	public <T extends IResource> T parseResource(Class<T> theResourceType, String theMessageString) {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+//
+//	@Override
+//	public IResource parseResource(Class<? extends IResource> theResourceType, Reader theReader) {
+//		// TODO Auto-generated method stub
+//		return null;
+//	}
+
+}

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

@@ -1,12 +1,9 @@
 package ca.uhn.fhir.parser;
 
+import java.io.IOException;
 import java.io.Reader;
 import java.io.Writer;
 
-import javax.xml.stream.XMLEventReader;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamWriter;
-
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
@@ -17,11 +14,9 @@ public interface IParser {
 
 	void encodeBundleToWriter(Bundle theBundle, Writer theWriter);
 
-	String encodeResourceToString(IResource theResource) throws DataFormatException;
+	String encodeResourceToString(IResource theResource) throws DataFormatException, IOException;
 
-	void encodeResourceToWriter(IResource theResource, Writer stringWriter);
+	void encodeResourceToWriter(IResource theResource, Writer stringWriter) throws IOException;
-
-	void encodeResourceToXmlStreamWriter(IResource theResource, XMLStreamWriter eventWriter) throws XMLStreamException, DataFormatException;
 
 	Bundle parseBundle(Reader theReader);
 
@@ -31,8 +26,6 @@ public interface IParser {
 
 	IResource parseResource(Reader theReader) throws ConfigurationException, DataFormatException;
 
-	IResource parseResource(XMLEventReader theStreamReader);
-
 	<T extends IResource> T parseResource(Class<T> theResourceType, String theMessageString);
 
 	IResource parseResource(Class<? extends IResource> theResourceType, Reader theReader);

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

@@ -0,0 +1,355 @@
+package ca.uhn.fhir.parser;
+
+import static org.apache.commons.lang3.StringUtils.*;
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.StringWriter;
+import java.io.Writer;
+import java.util.List;
+
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLOutputFactory;
+
+import org.apache.commons.lang3.StringUtils;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import com.google.gson.stream.JsonWriter;
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeChildDeclaredExtensionDefinition;
+import ca.uhn.fhir.context.RuntimeChildUndeclaredExtensionDefinition;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.api.BundleEntry;
+import ca.uhn.fhir.model.api.ICompositeDatatype;
+import ca.uhn.fhir.model.api.IElement;
+import ca.uhn.fhir.model.api.IPrimitiveDatatype;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
+import ca.uhn.fhir.model.api.UndeclaredExtension;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.primitive.BooleanDt;
+import ca.uhn.fhir.model.primitive.DecimalDt;
+import ca.uhn.fhir.model.primitive.IntegerDt;
+import ca.uhn.fhir.model.primitive.XhtmlDt;
+
+public class JsonParser implements IParser {
+
+	private FhirContext myContext;
+
+	public JsonParser(FhirContext theContext) {
+		myContext = theContext;
+	}
+
+	@Override
+	public String encodeBundleToString(Bundle theBundle) throws DataFormatException {
+		StringWriter stringWriter = new StringWriter();
+		encodeBundleToWriter(theBundle, stringWriter);
+
+		return stringWriter.toString();
+	}
+
+	@Override
+	public void encodeBundleToWriter(Bundle theBundle, Writer theWriter) {
+		// try {
+		// XMLStreamWriter eventWriter;
+		// eventWriter = myXmlOutputFactory.createXMLStreamWriter(theWriter);
+		// eventWriter = decorateStreamWriter(eventWriter);
+		//
+		// eventWriter.writeStartElement("feed");
+		// eventWriter.writeDefaultNamespace(ATOM_NS);
+		//
+		// writeTagWithTextNode(eventWriter, "title", theBundle.getTitle());
+		// writeTagWithTextNode(eventWriter, "id", theBundle.getId());
+		//
+		// writeAtomLink(eventWriter, "self", theBundle.getLinkSelf());
+		// writeAtomLink(eventWriter, "first", theBundle.getLinkFirst());
+		// writeAtomLink(eventWriter, "previous", theBundle.getLinkPrevious());
+		// writeAtomLink(eventWriter, "next", theBundle.getLinkNext());
+		// writeAtomLink(eventWriter, "last", theBundle.getLinkLast());
+		// writeAtomLink(eventWriter, "fhir-base", theBundle.getLinkBase());
+		//
+		// if (theBundle.getTotalResults().getValue() != null) {
+		// eventWriter.writeStartElement("os", OPENSEARCH_NS, "totalResults");
+		// eventWriter.writeNamespace("os", OPENSEARCH_NS);
+		// eventWriter.writeCharacters(theBundle.getTotalResults().getValue().toString());
+		// eventWriter.writeEndElement();
+		// }
+		//
+		// writeOptionalTagWithTextNode(eventWriter, "updated",
+		// theBundle.getUpdated());
+		// writeOptionalTagWithTextNode(eventWriter, "published",
+		// theBundle.getPublished());
+		//
+		// if (StringUtils.isNotBlank(theBundle.getAuthorName().getValue())) {
+		// eventWriter.writeStartElement("author");
+		// writeTagWithTextNode(eventWriter, "name", theBundle.getAuthorName());
+		// writeOptionalTagWithTextNode(eventWriter, "uri",
+		// theBundle.getAuthorUri());
+		// eventWriter.writeEndElement();
+		// }
+		//
+		// for (BundleEntry nextEntry : theBundle.getEntries()) {
+		// eventWriter.writeStartElement("entry");
+		//
+		// eventWriter.writeStartElement("content");
+		// eventWriter.writeAttribute("type", "text/xml");
+		//
+		// IResource resource = nextEntry.getResource();
+		// encodeResourceToJsonStreamWriter(resource, eventWriter);
+		//
+		// eventWriter.writeEndElement(); // content
+		// eventWriter.writeEndElement(); // entry
+		// }
+		//
+		// eventWriter.writeEndElement();
+		// eventWriter.close();
+		// } catch (XMLStreamException e) {
+		// throw new
+		// ConfigurationException("Failed to initialize STaX event factory", e);
+		// }
+	}
+
+	private void encodeCompositeElementToStreamWriter(IElement theElement, JsonWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> resDef) throws IOException, DataFormatException {
+		encodeExtensionsIfPresent(theEventWriter, theElement);
+		encodeCompositeElementChildrenToStreamWriter(theElement, theEventWriter, resDef.getExtensions());
+		encodeCompositeElementChildrenToStreamWriter(theElement, theEventWriter, resDef.getChildren());
+	}
+
+	private void encodeCompositeElementChildrenToStreamWriter(IElement theElement, JsonWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> theChildren) throws IOException {
+		for (BaseRuntimeChildDefinition nextChild : theChildren) {
+			List<? extends IElement> values = nextChild.getAccessor().getValues(theElement);
+			if (values == null || values.isEmpty()) {
+				continue;
+			}
+
+			String currentChildName = null;
+			boolean inArray = false;
+			
+			IElement[] extensions = new IElement[values.size()];
+			IElement[] modifierExtensions = new IElement[values.size()];
+			boolean haveExtensions = false;
+			boolean haveModifierExtensions = false;
+			
+			for (IElement nextValue : values) {
+				if (nextValue == null || nextValue.isEmpty()) {
+					continue;
+				}
+				
+				Class<? extends IElement> type = nextValue.getClass();
+				String childName = nextChild.getChildNameByDatatype(type);
+				String extensionUrl = nextChild.getExtensionUrl();
+				BaseRuntimeElementDefinition<?> childDef = nextChild.getChildElementDefinitionByDatatype(type);
+				if (childDef == null) {
+					throw new IllegalStateException(nextChild + " has no child of type " + type);
+				}
+
+				if (extensionUrl != null && childName.equals("extension") == false) {
+					
+					RuntimeChildDeclaredExtensionDefinition extDef = (RuntimeChildDeclaredExtensionDefinition) nextChild;
+					if (extDef.isModifier()) {
+						theEventWriter.name("modifierExtension");
+					} else {
+						theEventWriter.name("extension");
+					}
+
+					theEventWriter.beginObject();
+					theEventWriter.name("url");
+					theEventWriter.value(extensionUrl);
+					theEventWriter.name(childName);
+					encodeChildElementToStreamWriter(theEventWriter, nextValue, childName, childDef);
+					theEventWriter.endObject();
+					
+				} else {
+					
+					if (currentChildName == null || !currentChildName.equals(childName)) {
+						if (inArray) {
+							theEventWriter.endArray();
+						}
+						theEventWriter.name(childName);
+						if (nextChild.getMax() > 1 || nextChild.getMax() == Child.MAX_UNLIMITED){
+							theEventWriter.beginArray();
+							inArray = true;
+						}
+						currentChildName = childName;
+					}
+					
+					encodeChildElementToStreamWriter(theEventWriter, nextValue, childName, childDef);
+				}
+			}
+			
+			
+			
+			if (inArray) {
+				theEventWriter.endArray();
+			}
+		}
+	}
+
+	private void encodeExtensionsIfPresent(JsonWriter theWriter, IElement theResource) throws IOException {
+		if (theResource instanceof ISupportsUndeclaredExtensions) {
+			ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theResource;
+			encodeUndeclaredExtensions(theWriter, res.getUndeclaredExtensions(), "extension");
+			encodeUndeclaredExtensions(theWriter, res.getUndeclaredModifierExtensions(), "modifierExtension");
+		}
+	}
+
+	private void encodeUndeclaredExtensions(JsonWriter theWriter, List<UndeclaredExtension> extensions, String theTagName) throws IOException {
+		if (extensions.isEmpty()) {
+			return;
+		}
+
+		theWriter.name(theTagName);
+		theWriter.beginArray();
+
+		for (UndeclaredExtension next : extensions) {
+
+			theWriter.beginObject();
+			theWriter.name("url");
+			theWriter.value(next.getUrl());
+
+			if (next.getValue() != null) {
+				IElement nextValue = next.getValue();
+				RuntimeChildUndeclaredExtensionDefinition extDef = myContext.getRuntimeChildUndeclaredExtensionDefinition();
+				String childName = extDef.getChildNameByDatatype(nextValue.getClass());
+				BaseRuntimeElementDefinition<?> childDef = extDef.getChildElementDefinitionByDatatype(nextValue.getClass());
+				encodeChildElementToStreamWriter(theWriter, nextValue, childName, childDef);
+			}
+
+			encodeUndeclaredExtensions(theWriter, next.getUndeclaredExtensions(), "extension");
+			encodeUndeclaredExtensions(theWriter, next.getUndeclaredModifierExtensions(), "modifierExtension");
+
+			theWriter.endObject();
+		}
+
+		theWriter.endArray();
+	}
+
+	private void encodeChildElementToStreamWriter(JsonWriter theWriter, IElement theValue, String theChildName, BaseRuntimeElementDefinition<?> theChildDef) throws IOException {
+
+		switch (theChildDef.getChildType()) {
+		case PRIMITIVE_DATATYPE: {
+			IPrimitiveDatatype<?> value = (IPrimitiveDatatype<?>) theValue;
+			if (value instanceof IntegerDt) {
+				theWriter.value(((IntegerDt) value).getValue());
+			} else if (value instanceof DecimalDt) {
+				theWriter.value(((DecimalDt) value).getValue());
+			} else if (value instanceof BooleanDt) {
+				theWriter.value(((BooleanDt) value).getValue());
+			} else {
+				String valueStr = value.getValueAsString();
+				theWriter.value(valueStr);
+			}
+			break;
+		}
+		case RESOURCE_BLOCK:
+		case COMPOSITE_DATATYPE: {
+			BaseRuntimeElementCompositeDefinition<?> childCompositeDef = (BaseRuntimeElementCompositeDefinition<?>) theChildDef;
+			theWriter.beginObject();
+			encodeCompositeElementToStreamWriter(theValue, theWriter, childCompositeDef);
+			theWriter.endObject();
+			break;
+		}
+		case RESOURCE_REF: {
+			ResourceReferenceDt value = (ResourceReferenceDt) theValue;
+			theWriter.beginObject();
+			if (value.getReference().isEmpty()==false) {
+				theWriter.name("resource");
+				theWriter.value(value.getReference().getValueAsString());
+			}
+			if (value.getDisplay().isEmpty() == false) {
+				theWriter.name("display");
+				theWriter.value(value.getDisplay().getValueAsString());
+			}
+			theWriter.endObject();
+			break;
+		}
+		case PRIMITIVE_XHTML: {
+			XhtmlDt dt = (XhtmlDt) theValue;
+			theWriter.value(dt.getValueAsString());
+			break;
+		}
+		case UNDECL_EXT:
+		default:
+			throw new IllegalStateException("Should not have this state here: "+theChildDef.getChildType().name());
+		}
+		
+	}
+
+	@Override
+	public String encodeResourceToString(IResource theResource) throws DataFormatException, IOException {
+		Writer stringWriter = new StringWriter();
+		encodeResourceToWriter(theResource, stringWriter);
+		return stringWriter.toString();
+	}
+
+	@Override
+	public void encodeResourceToWriter(IResource theResource, Writer theWriter) throws IOException {
+		JsonWriter eventWriter = new JsonWriter(theWriter);
+		eventWriter.setIndent("  ");
+		// try {
+		encodeResourceToJsonStreamWriter(theResource, eventWriter);
+		eventWriter.flush();
+		// } catch (XMLStreamException e) {
+		// throw new
+		// ConfigurationException("Failed to initialize STaX event factory", e);
+		// }
+	}
+
+	private void encodeResourceToJsonStreamWriter(IResource theResource, JsonWriter theEventWriter) throws IOException {
+		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
+
+		theEventWriter.beginObject();
+
+		theEventWriter.name("resourceType");
+		theEventWriter.value(resDef.getName());
+
+		encodeCompositeElementToStreamWriter(theResource, theEventWriter, resDef);
+
+		theEventWriter.endObject();
+	}
+
+	@Override
+	public Bundle parseBundle(Reader theReader) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public Bundle parseBundle(String theMessageString) throws ConfigurationException, DataFormatException {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public IResource parseResource(String theMessageString) throws ConfigurationException, DataFormatException {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public IResource parseResource(Reader theReader) throws ConfigurationException, DataFormatException {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public <T extends IResource> T parseResource(Class<T> theResourceType, String theMessageString) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public IResource parseResource(Class<? extends IResource> theResourceType, Reader theReader) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+}

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

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.parser;
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.*;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.Reader;
 import java.io.StringReader;
@@ -43,7 +42,6 @@ import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
-import ca.uhn.fhir.model.api.BaseResourceReference;
 import ca.uhn.fhir.model.api.UndeclaredExtension;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
@@ -149,11 +147,6 @@ public class XmlParser implements IParser {
 		}
 	}
 
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ca.uhn.fhir.parser.IParser#encodeBundleToString(ca.uhn.fhir.model.api.Bundle)
-	 */
 	@Override
 	public String encodeBundleToString(Bundle theBundle) throws DataFormatException {
 		StringWriter stringWriter = new StringWriter();
@@ -162,11 +155,6 @@ public class XmlParser implements IParser {
 		return stringWriter.toString();
 	}
 
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ca.uhn.fhir.parser.IParser#encodeBundleToWriter(ca.uhn.fhir.model.api.Bundle, java.io.Writer)
-	 */
 	@Override
 	public void encodeBundleToWriter(Bundle theBundle, Writer theWriter) {
 		try {
@@ -366,11 +354,7 @@ public class XmlParser implements IParser {
 		}
 	}
 
-	/*
+
-	 * (non-Javadoc)
-	 * 
-	 * @see ca.uhn.fhir.parser.IParser#encodeResourceToString(ca.uhn.fhir.model.api.IResource)
-	 */
 	@Override
 	public String encodeResourceToString(IResource theResource) throws DataFormatException {
 		Writer stringWriter = new StringWriter();
@@ -378,11 +362,6 @@ public class XmlParser implements IParser {
 		return stringWriter.toString();
 	}
 
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ca.uhn.fhir.parser.IParser#encodeResourceToWriter(ca.uhn.fhir.model.api.IResource, java.io.Writer)
-	 */
 	@Override
 	public void encodeResourceToWriter(IResource theResource, Writer stringWriter) {
 		XMLStreamWriter eventWriter;
@@ -397,13 +376,8 @@ public class XmlParser implements IParser {
 		}
 	}
 
-	/*
+
-	 * (non-Javadoc)
+	private void encodeResourceToXmlStreamWriter(IResource theResource, XMLStreamWriter eventWriter) throws XMLStreamException, DataFormatException {
-	 * 
-	 * @see ca.uhn.fhir.parser.IParser#encodeResourceToXmlStreamWriter(ca.uhn.fhir.model.api.IResource, javax.xml.stream.XMLStreamWriter)
-	 */
-	@Override
-	public void encodeResourceToXmlStreamWriter(IResource theResource, XMLStreamWriter eventWriter) throws XMLStreamException, DataFormatException {
 		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
 		eventWriter.writeStartElement(resDef.getName());
 		eventWriter.writeDefaultNamespace(FHIR_NS);
@@ -520,13 +494,7 @@ public class XmlParser implements IParser {
 		return parseResource(null, theMessageString);
 	}
 
-	/*
+	private IResource parseResource(XMLEventReader theStreamReader) {
-	 * (non-Javadoc)
-	 * 
-	 * @see ca.uhn.fhir.parser.IParser#parseResource(javax.xml.stream.XMLEventReader)
-	 */
-	@Override
-	public IResource parseResource(XMLEventReader theStreamReader) {
 		return parseResource(null, theStreamReader);
 	}
 

hapi-fhir-base/src/site/example/java/example/FhirContextIntro.java

@@ -1,5 +1,7 @@
 package example;
 
+import java.io.IOException;
+
 import ca.uhn.fhir.model.dstu.composite.HumanNameDt;
 import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu.resource.Observation;
@@ -7,6 +9,7 @@ import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.dstu.valueset.NameUseEnum;
 import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.context.FhirContext;
 
@@ -33,7 +36,7 @@ Patient patient = new Patient();
 		
 	}
 		
-	public void encodeMsg() {
+	public void encodeMsg() throws DataFormatException, IOException {
 FhirContext ctx = new FhirContext(Patient.class, Observation.class);
 //START SNIPPET: encodeMsg
 

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

@@ -2,6 +2,8 @@ package ca.uhn.fhir.context;
 
 import static org.junit.Assert.*;
 
+import java.io.IOException;
+
 import org.junit.Test;
 
 import ca.uhn.fhir.model.dstu.resource.Patient;
@@ -9,12 +11,13 @@ import ca.uhn.fhir.model.dstu.resource.Profile;
 import ca.uhn.fhir.model.dstu.resource.Profile.ExtensionDefn;
 import ca.uhn.fhir.model.dstu.resource.Profile.Structure;
 import ca.uhn.fhir.model.dstu.valueset.DataTypeEnum;
+import ca.uhn.fhir.parser.DataFormatException;
 
 public class RuntimeResourceDefinitionTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RuntimeResourceDefinitionTest.class);
 
 	@Test
-	public void testToProfileStandard() {
+	public void testToProfileStandard() throws Exception {
 		FhirContext ctx = new FhirContext(Patient.class, Profile.class);
 		RuntimeResourceDefinition def = ctx.getResourceDefinition(Patient.class);
 
@@ -33,7 +36,7 @@ public class RuntimeResourceDefinitionTest {
 	}
 	
 	@Test
-	public void testToProfileExtensions() {
+	public void testToProfileExtensions() throws Exception {
 		FhirContext ctx = new FhirContext(ResourceWithExtensionsA.class, Profile.class);
 		RuntimeResourceDefinition def = ctx.getResourceDefinition(ResourceWithExtensionsA.class);
 

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

@@ -0,0 +1,27 @@
+package ca.uhn.fhir.parser;
+
+import java.io.IOException;
+
+import org.apache.commons.io.IOUtils;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu.resource.Observation;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+
+public class JsonParserTest {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserTest.class);
+
+	@Test
+	public void testSimpleEncode() throws IOException {
+
+		FhirContext ctx = new FhirContext(Observation.class);
+//		String name = "/observation-example-eeg.xml";
+		String name = "/example-patient-general.xml";
+		Patient obs = ctx.newXmlParser().parseResource(Patient.class, IOUtils.toString(JsonParser.class.getResourceAsStream(name)));
+		String encoded = ctx.newJsonParser().encodeResourceToString(obs);
+
+		ourLog.info(encoded);
+	}
+
+}

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

@@ -145,6 +145,29 @@ public class XmlParserTest {
 
 	}
 	
+
+	@Test
+	public void testMessageWithMultipleTypes() throws SAXException, IOException {
+
+		//@formatter:off
+		String msg = "<Patient xmlns=\"http://hl7.org/fhir\">" 
+				+ "<identifier><label value=\"SSN\" /><system value=\"http://orionhealth.com/mrn\" /><value value=\"PRP1660\" /></identifier>"
+				+ "</Patient>";
+		//@formatter:on
+		
+		FhirContext ctx = new FhirContext(Patient.class, ca.uhn.fhir.testmodel.Patient.class);
+		Patient patient1 = ctx.newXmlParser().parseResource(Patient.class, msg);
+		String encoded1 = ctx.newXmlParser().encodeResourceToString(patient1);
+
+		ca.uhn.fhir.testmodel.Patient patient2 = ctx.newXmlParser().parseResource(ca.uhn.fhir.testmodel.Patient.class, msg);
+		String encoded2 = ctx.newXmlParser().encodeResourceToString(patient2);
+
+		Diff d = new Diff(new StringReader(encoded1), new StringReader(encoded2));
+		assertTrue(d.toString(), d.identical());
+
+	}
+
+	
 	@Test
 	public void testLoadAndEncodeDeclaredExtensions() throws ConfigurationException, DataFormatException, SAXException, IOException {
 		FhirContext ctx = new FhirContext(ResourceWithExtensionsA.class);

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/client/Tester.java

@@ -1,15 +1,18 @@
 package ca.uhn.fhir.rest.client;
 
+import java.io.IOException;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.client.exceptions.NonFhirResponseException;
 
 public class Tester {
 
-	public static final void main(String[] args) {
+	public static final void main(String[] args) throws DataFormatException, IOException {
 		try {
 
 			FhirContext ctx = new FhirContext(Patient.class);

hapi-fhir-base/src/test/java/ca/uhn/fhir/testmodel/IdentifierDt.java

@@ -0,0 +1,391 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+package ca.uhn.fhir.testmodel;
+
+import ca.uhn.fhir.model.api.BaseElement;
+import ca.uhn.fhir.model.api.ICompositeDatatype;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.DatatypeDef;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.dstu.composite.PeriodDt;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu.resource.Organization;
+import ca.uhn.fhir.model.dstu.valueset.IdentifierUseEnum;
+import ca.uhn.fhir.model.primitive.BoundCodeDt;
+import ca.uhn.fhir.model.primitive.CodeDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.primitive.UriDt;
+
+/**
+ * HAPI/FHIR <b>Identifier</b> Datatype
+ * (An identifier intended for computation)
+ *
+ * <p>
+ * <b>Definition:</b>
+ * A technical identifier - identifies some entity uniquely and unambiguously
+ * </p> 
+ *
+ * <p>
+ * <b>Requirements:</b>
+ * Need to be able to identify things with confidence and be sure that the identification is not subject to misinterpretation
+ * </p> 
+ */
+@DatatypeDef(name="Identifier") 
+public class IdentifierDt 
+        extends  BaseElement         implements ICompositeDatatype  , IQueryParameterType {
+
+	/**
+	 * Creates a new identifier
+	 */
+	public IdentifierDt() {
+		// nothing
+	}
+
+	/**
+	 * Creates a new identifier with the given system and value
+	 */
+	public IdentifierDt(String theSystem, String theValue) {
+		setSystem(theSystem);
+		setValue(theValue);
+	}
+
+	@Child(name="use", type=CodeDt.class, order=0, min=0, max=1)	
+	@Description(
+		shortDefinition="usual | official | temp | secondary (If known)",
+		formalDefinition="The purpose of this identifier"
+	)
+	private BoundCodeDt<IdentifierUseEnum> myUse;
+	
+	@Child(name="label", type=StringDt.class, order=1, min=0, max=1)	
+	@Description(
+		shortDefinition="Description of identifier",
+		formalDefinition="A text string for the identifier that can be displayed to a human so they can recognize the identifier"
+	)
+	private StringDt myLabel;
+	
+	@Child(name="system", type=UriDt.class, order=2, min=0, max=1)	
+	@Description(
+		shortDefinition="The namespace for the identifier",
+		formalDefinition="Establishes the namespace in which set of possible id values is unique."
+	)
+	private UriDt mySystem;
+	
+	@Child(name="value", type=StringDt.class, order=3, min=0, max=1)	
+	@Description(
+		shortDefinition="The value that is unique",
+		formalDefinition="The portion of the identifier typically displayed to the user and which is unique within the context of the system."
+	)
+	private StringDt myValue;
+	
+	@Child(name="period", type=PeriodDt.class, order=4, min=0, max=1)	
+	@Description(
+		shortDefinition="Time period when id is/was valid for use",
+		formalDefinition="Time period during which identifier is/was valid for use"
+	)
+	private PeriodDt myPeriod;
+	
+	@Child(name="assigner", order=5, min=0, max=1, type={
+		Organization.class,
+	})
+	@Description(
+		shortDefinition="Organization that issued id (may be just text)",
+		formalDefinition="Organization that issued/manages the identifier"
+	)
+	private ResourceReferenceDt myAssigner;
+	
+
+	@Override
+	public boolean isEmpty() {
+		return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(  myUse,  myLabel,  mySystem,  myValue,  myPeriod,  myAssigner);
+	}
+
+	/**
+	 * Gets the value(s) for <b>use</b> (usual | official | temp | secondary (If known)).
+	 * creating it if it does
+	 * not exist. Will not return <code>null</code>.
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The purpose of this identifier
+     * </p> 
+	 */
+	public BoundCodeDt<IdentifierUseEnum> getUse() {  
+		if (myUse == null) {
+			myUse = new BoundCodeDt<IdentifierUseEnum>(IdentifierUseEnum.VALUESET_BINDER);
+		}
+		return myUse;
+	}
+
+	/**
+	 * Sets the value(s) for <b>use</b> (usual | official | temp | secondary (If known))
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The purpose of this identifier
+     * </p> 
+	 */
+	public void setUse(BoundCodeDt<IdentifierUseEnum> theValue) {
+		myUse = theValue;
+	}
+
+
+	/**
+	 * Sets the value(s) for <b>use</b> (usual | official | temp | secondary (If known))
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The purpose of this identifier
+     * </p> 
+	 */
+	public void setUse(IdentifierUseEnum theValue) {
+		getUse().setValueAsEnum(theValue);
+	}
+
+  
+	/**
+	 * Gets the value(s) for <b>label</b> (Description of identifier).
+	 * creating it if it does
+	 * not exist. Will not return <code>null</code>.
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * A text string for the identifier that can be displayed to a human so they can recognize the identifier
+     * </p> 
+	 */
+	public StringDt getLabel() {  
+		if (myLabel == null) {
+			myLabel = new StringDt();
+		}
+		return myLabel;
+	}
+
+	/**
+	 * Sets the value(s) for <b>label</b> (Description of identifier)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * A text string for the identifier that can be displayed to a human so they can recognize the identifier
+     * </p> 
+	 */
+	public void setLabel(StringDt theValue) {
+		myLabel = theValue;
+	}
+
+
+ 	/**
+	 * Sets the value for <b>label</b> (Description of identifier)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * A text string for the identifier that can be displayed to a human so they can recognize the identifier
+     * </p> 
+	 */
+	public void setLabel( String theString) {
+		myLabel = new StringDt(theString); 
+	}
+
+ 
+	/**
+	 * Gets the value(s) for <b>system</b> (The namespace for the identifier).
+	 * creating it if it does
+	 * not exist. Will not return <code>null</code>.
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Establishes the namespace in which set of possible id values is unique.
+     * </p> 
+	 */
+	public UriDt getSystem() {  
+		if (mySystem == null) {
+			mySystem = new UriDt();
+		}
+		return mySystem;
+	}
+
+	/**
+	 * Sets the value(s) for <b>system</b> (The namespace for the identifier)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Establishes the namespace in which set of possible id values is unique.
+     * </p> 
+	 */
+	public void setSystem(UriDt theValue) {
+		mySystem = theValue;
+	}
+
+
+ 	/**
+	 * Sets the value for <b>system</b> (The namespace for the identifier)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Establishes the namespace in which set of possible id values is unique.
+     * </p> 
+	 */
+	public void setSystem( String theUri) {
+		mySystem = new UriDt(theUri); 
+	}
+
+ 
+	/**
+	 * Gets the value(s) for <b>value</b> (The value that is unique).
+	 * creating it if it does
+	 * not exist. Will not return <code>null</code>.
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The portion of the identifier typically displayed to the user and which is unique within the context of the system.
+     * </p> 
+	 */
+	public StringDt getValue() {  
+		if (myValue == null) {
+			myValue = new StringDt();
+		}
+		return myValue;
+	}
+
+	/**
+	 * Sets the value(s) for <b>value</b> (The value that is unique)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The portion of the identifier typically displayed to the user and which is unique within the context of the system.
+     * </p> 
+	 */
+	public void setValue(StringDt theValue) {
+		myValue = theValue;
+	}
+
+
+ 	/**
+	 * Sets the value for <b>value</b> (The value that is unique)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * The portion of the identifier typically displayed to the user and which is unique within the context of the system.
+     * </p> 
+	 */
+	public void setValue( String theString) {
+		myValue = new StringDt(theString); 
+	}
+
+ 
+	/**
+	 * Gets the value(s) for <b>period</b> (Time period when id is/was valid for use).
+	 * creating it if it does
+	 * not exist. Will not return <code>null</code>.
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Time period during which identifier is/was valid for use
+     * </p> 
+	 */
+	public PeriodDt getPeriod() {  
+		if (myPeriod == null) {
+			myPeriod = new PeriodDt();
+		}
+		return myPeriod;
+	}
+
+	/**
+	 * Sets the value(s) for <b>period</b> (Time period when id is/was valid for use)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Time period during which identifier is/was valid for use
+     * </p> 
+	 */
+	public void setPeriod(PeriodDt theValue) {
+		myPeriod = theValue;
+	}
+
+
+  
+	/**
+	 * Gets the value(s) for <b>assigner</b> (Organization that issued id (may be just text)).
+	 * creating it if it does
+	 * not exist. Will not return <code>null</code>.
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Organization that issued/manages the identifier
+     * </p> 
+	 */
+	public ResourceReferenceDt getAssigner() {  
+		if (myAssigner == null) {
+			myAssigner = new ResourceReferenceDt();
+		}
+		return myAssigner;
+	}
+
+	/**
+	 * Sets the value(s) for <b>assigner</b> (Organization that issued id (may be just text))
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * Organization that issued/manages the identifier
+     * </p> 
+	 */
+	public void setAssigner(ResourceReferenceDt theValue) {
+		myAssigner = theValue;
+	}
+
+
+  
+
+	/**
+	 * Returns true if <code>this</code> identifier has the same {@link IdentifierDt#getValue() value}
+	 * and {@link IdentifierDt#getSystem() system} (as compared by simple equals comparison).
+	 * Does not compare other values (e.g. {@link IdentifierDt#getUse() use}) or any extensions. 
+	 */
+	public boolean matchesSystemAndValue(IdentifierDt theIdentifier) {
+		if (theIdentifier == null) {
+			return false;
+		}
+		return getValue().equals(theIdentifier.getValue()) && getSystem().equals(theIdentifier.getSystem());
+	}
+
+	/**
+	 * {@inheritDoc}
+	 */
+	@Override
+	public String getValueAsQueryToken() {
+		if (org.apache.commons.lang3.StringUtils.isNotBlank(getSystem().getValueAsString())) {
+			return getSystem().getValueAsString() + '|' + getValue().getValueAsString(); 
+		} else {
+			return getValue().getValueAsString();
+		}
+	}
+
+	/**
+	 * {@inheritDoc}
+	 */
+	@Override
+	public void setValueAsQueryToken(String theParameter) {
+		int barIndex = theParameter.indexOf('|');
+		if (barIndex != -1) {
+			setSystem(new UriDt(theParameter.substring(0, barIndex)));
+			setValue(theParameter.substring(barIndex + 1));
+		} else {
+			setValue(theParameter);
+		}
+	}	
+
+
+}

hapi-fhir-base/src/test/java/ca/uhn/fhir/testmodel/Patient.java

@@ -0,0 +1,101 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+package ca.uhn.fhir.testmodel;
+
+import java.util.*;
+import ca.uhn.fhir.model.api.*;
+import ca.uhn.fhir.model.api.annotation.*;
+
+/**
+ * HAPI/FHIR <b>Patient</b> Resource
+ * (Information about a person or animal receiving health care services)
+ *
+ * <p>
+ * <b>Definition:</b>
+ * Demographics and other administrative information about a person or animal receiving care or other health-related services
+ * </p> 
+ *
+ * <p>
+ * <b>Requirements:</b>
+ * Tracking patient is the center of the healthcare process
+ * </p> 
+ */
+@ResourceDef(name="Patient", profile="http://hl7.org/fhir/profiles/Patient")
+public class Patient extends BaseResource implements IResource {
+
+
+	@Child(name="identifier", type=IdentifierDt.class, order=0, min=0, max=Child.MAX_UNLIMITED)	
+	@Description(
+		shortDefinition="An identifier for the person as this patient",
+		formalDefinition="An identifier that applies to this person as a patient"
+	)
+	private List<IdentifierDt> myIdentifier;
+	
+
+	@Override
+	public boolean isEmpty() {
+		return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(  myIdentifier);
+	}
+
+	/**
+	 * Gets the value(s) for <b>identifier</b> (An identifier for the person as this patient).
+	 * creating it if it does
+	 * not exist. Will not return <code>null</code>.
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * An identifier that applies to this person as a patient
+     * </p> 
+	 */
+	public List<IdentifierDt> getIdentifier() {  
+		if (myIdentifier == null) {
+			myIdentifier = new ArrayList<IdentifierDt>();
+		}
+		return myIdentifier;
+	}
+
+	/**
+	 * Sets the value(s) for <b>identifier</b> (An identifier for the person as this patient)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * An identifier that applies to this person as a patient
+     * </p> 
+	 */
+	public void setIdentifier(List<IdentifierDt> theValue) {
+		myIdentifier = theValue;
+	}
+
+	/**
+	 * Adds and returns a new value for <b>identifier</b> (An identifier for the person as this patient)
+	 *
+     * <p>
+     * <b>Definition:</b>
+     * An identifier that applies to this person as a patient
+     * </p> 
+	 */
+	public IdentifierDt addIdentifier() {
+		IdentifierDt newType = new IdentifierDt();
+		getIdentifier().add(newType);
+		return newType; 
+	}
+
+  
+
+
+
+}

hapi-fhir-base/src/test/resources/example-patient-general.xml

@@ -0,0 +1,114 @@
+<Patient xmlns="http://hl7.org/fhir">
+  <text>
+    <status value="generated"/>
+    <div xmlns="http://www.w3.org/1999/xhtml">
+      <table>
+        <tbody>
+          <tr>
+            <td>Name</td>
+            <td>Peter James <b>Chalmers</b> (&quot;Jim&quot;)</td>
+          </tr>
+          <tr>
+            <td>Address</td>
+            <td>534 Erewhon, Pleasantville, Vic, 3999</td>
+          </tr>
+          <tr>
+            <td>Contacts</td>
+            <td>Home: unknown. Work: (03) 5555 6473</td>
+          </tr>
+          <tr>
+            <td>Id</td>
+            <td>MRN: 12345 (Acme Healthcare)</td>
+          </tr>
+        </tbody>
+      </table>
+    </div>
+  </text>
+
+  <!--   MRN assigned by ACME healthcare on 6-May 2001   -->
+  <identifier>
+    <use value="usual"/>
+    <label value="MRN"/>
+    <system value="urn:oid:1.2.36.146.595.217.0.1"/>
+    <value value="12345"/>
+    <period>
+      <start value="2001-05-06"/>
+    </period>
+    <assigner>
+      <display value="Acme Healthcare"/>
+    </assigner>
+  </identifier>
+
+  <!--   Peter James Chalmers, but called &quot;Jim&quot;   -->
+  <name>
+    <use value="official"/>
+    <family value="Chalmers"/>
+    <given value="Peter"/>
+    <given value="James"/>
+  </name>
+  <name>
+    <use value="usual"/>
+    <given value="Jim"/>
+  </name>
+
+  <telecom>
+    <use value="home"/>
+    <!--   home communication details aren't known   -->
+  </telecom>
+  <telecom>
+    <system value="phone"/>
+    <value value="(03) 5555 6473"/>
+    <use value="work"/>
+  </telecom>
+
+  <!--   use FHIR code system for male / female   -->
+  <gender>
+    <coding>
+      <system value="http://hl7.org/fhir/v3/AdministrativeGender"/>
+      <code value="M"/>
+      <display value="Male"/>
+    </coding>
+  </gender>
+  <birthDate value="1974-12-25"/>
+  <deceasedBoolean value="false"/>
+
+  <address>
+    <use value="home"/>
+    <line value="534 Erewhon St"/>
+    <city value="PleasantVille"/>
+    <state value="Vic"/>
+    <zip value="3999"/>
+  </address>
+
+  <contact>
+    <relationship>
+      <coding>
+        <system value="http://hl7.org/fhir/patient-contact-relationship"/>
+        <code value="partner"/>
+      </coding>
+    </relationship>
+
+    <name>
+      <family value="du">
+        <!--   the &quot;du&quot; part is a family name prefix (VV in iso 21090)   -->
+        <extension url="http://hl7.org/fhir/Profile/iso-21090#qualifier">
+          <valueCode value="VV"/>
+        </extension>
+      </family>
+      <family value="Marché"/>
+      <given value="Bénédicte"/>
+    </name>
+
+    <telecom>
+      <system value="phone"/>
+      <value value="+33 (237) 998327"/>
+    </telecom>
+  </contact>
+
+  <managingOrganization>
+    <reference value="Organization/1"/>
+  </managingOrganization>
+
+  <active value="true"/>
+
+</Patient>

hapi-fhir-base/src/test/resources/observation-example-eeg.xml

@@ -2,7 +2,6 @@
 <!-- This example is taken from the v3 data types (SLIST) -->
 
 <Observation xmlns="http://hl7.org/fhir" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hl7.org/fhir ..\..\schema\observation.xsd">
-	<!--
 	<extension url="http://acme.org/fhir/Profile/main#trial-status">
 		<extension url="http://acme.org/fhir/Profile/main#trial-status-code">
 			<valueCode value="unsure" />
@@ -16,13 +15,13 @@
 			</valueResource>
 		</extension>
 	</extension>
-	 -->
+	<extension url="http://acme.org/fhir/Profile/main#foobar">
-	 <!-- 
+		<valueCode value="unsure" />
+	</extension>
 	<text>
 		<status value="generated" />
 		<div xmlns="http://www.w3.org/1999/xhtml">Sept 17, 2012: Systolic Blood pressure 107 mmHg (normal)</div>
 	</text>
-	 -->
 	<name>
 		<!-- Actually, this is not a vull EEG. A todo is to turn it into one -->
 		<coding>