Merge branch 'master' of ssh://nacharya@git.code.sf.net/p/hl7api/fhircode

.gitignore

@@ -2,3 +2,4 @@
 /target
 *.log
 *.log*
+nohup.out

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

@@ -30,6 +30,12 @@
 			<action type="fix">
 				Support for Query resources fixed (in parser)
 			</action>
+			<action type="fix">
+				Nested contained resources (e.g. encoding a resource with a contained resource that itself contains a resource)
+				now parse and encode correctly, meaning that all contained resources are placed in the "contained" element
+				of the root resource, and the parser looks in the root resource for all container levels when stitching
+				contained resources back together.
+			</action>
         </release>			
 	</body>
 </document>

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

@@ -46,6 +46,8 @@ public abstract class BaseRuntimeChildDefinition {
 		List<? extends IElement> getValues(Object theTarget);
 	}
 
+	public abstract String getElementName();
+	
 	public abstract int getMax();
 	
 	public abstract int getMin();

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

@@ -147,4 +147,9 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		return 0;
 	}
 
+	@Override
+	public String getElementName() {
+		return "extension";
+	}
+
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/CodeableConceptDt.java

@@ -71,6 +71,13 @@ public class CodeableConceptDt
 		// nothing
 	}
 
+	/**
+	 * Constructor which creates a CodeableConceptDt with one coding repetition, containing
+	 * the given system and code
+	 */
+	public CodeableConceptDt(String theSystem, String theCode) {
+		addCoding().setSystem(theSystem).setCode(theCode);
+	}
 
 	@Child(name="coding", type=CodingDt.class, order=0, min=0, max=Child.MAX_UNLIMITED)	
 	@Description(

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/ResourceReferenceDt.java

@@ -201,6 +201,9 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
 
 	@Override
 	public IdDt getResourceId() {
+		if (myReference == null) {
+			return new IdDt();
+		}
 		return new IdDt(myReference.getValue());
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/UriDt.java

@@ -121,4 +121,18 @@ public class UriDt extends BasePrimitive<URI> {
 		return true;
 	}
 
+	/**
+	 * Creates a new UriDt instance which uses the given OID as the content (and prepends "urn:oid:" to the 
+	 * OID string in the value of the newly created UriDt, per the FHIR specification).
+	 *  
+	 * @param theOid The OID to use (<code>null</code> is acceptable and will result in a UriDt instance with a <code>null</code> value)
+	 * @return A new UriDt instance
+	 */
+	public static UriDt fromOid(String theOid) {
+		if (theOid == null) {
+			return new UriDt();
+		}
+		return new UriDt("urn:oid:" + theOid);
+	}
+
 }

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

@@ -33,6 +33,7 @@ import java.util.UUID;
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
 import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IElement;
@@ -44,6 +45,11 @@ import ca.uhn.fhir.model.primitive.IdDt;
 public abstract class BaseParser implements IParser {
 
 	private boolean mySuppressNarratives;
+	private FhirContext myContext;
+	
+	public BaseParser(FhirContext theContext) {
+		myContext = theContext;
+	}
 
 	@Override
 	public TagList parseTagList(String theString) {
@@ -116,7 +122,13 @@ public abstract class BaseParser implements IParser {
 	}
 
 	public void containResourcesForEncoding(IResource theResource) {
-		List<ResourceReferenceDt> allElements = theResource.getAllPopulatedChildElementsOfType(ResourceReferenceDt.class);
+		containResourcesForEncoding(theResource, theResource);
+	}
+
+	private long myNextContainedId = 1;
+	
+	private void containResourcesForEncoding(IResource theResource, IResource theTarget) {
+		List<ResourceReferenceDt> allElements = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, ResourceReferenceDt.class);
 
 		Set<String> allIds = new HashSet<String>();
 
@@ -124,15 +136,18 @@ public abstract class BaseParser implements IParser {
 			IResource resource = next.getResource();
 			if (resource != null) {
 				if (resource.getId().isEmpty()) {
-					resource.setId(new IdDt(UUID.randomUUID().toString()));
+					resource.setId(new IdDt(myNextContainedId++));
+//					resource.setId(new IdDt(UUID.randomUUID().toString()));
 				}
 
 				if (!allIds.contains(resource.getId().getValue())) {
-					theResource.getContained().getContainedResources().add(resource);
+					theTarget.getContained().getContainedResources().add(resource);
 					allIds.add(resource.getId().getValue());
 				}
 
 				next.setReference("#" + resource.getId().getValue());
+				
+				containResourcesForEncoding(resource, theTarget);
 			}
 		}
 

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

@@ -104,6 +104,7 @@ public class JsonParser extends BaseParser implements IParser {
 	private boolean myPrettyPrint;
 
 	public JsonParser(FhirContext theContext) {
+		super(theContext);
 		myContext = theContext;
 	}
 
@@ -211,7 +212,7 @@ public class JsonParser extends BaseParser implements IParser {
 			IResource resource = nextEntry.getResource();
 			if (resource != null && !resource.isEmpty()) {
 				RuntimeResourceDefinition resDef = myContext.getResourceDefinition(resource);
-				encodeResourceToJsonStreamWriter(resDef, resource, eventWriter, "content");
+				encodeResourceToJsonStreamWriter(resDef, resource, eventWriter, "content", false);
 			}
 
 			eventWriter.writeEnd(); // entry object
@@ -299,7 +300,7 @@ public class JsonParser extends BaseParser implements IParser {
 			theWriter.writeStartArray(theChildName);
 			ContainedDt value = (ContainedDt) theValue;
 			for (IResource next : value.getContainedResources()) {
-				encodeResourceToJsonStreamWriter(theResDef, next, theWriter, null);
+				encodeResourceToJsonStreamWriter(theResDef, next, theWriter, null, true);
 			}
 			theWriter.writeEnd();
 			break;
@@ -465,8 +466,10 @@ public class JsonParser extends BaseParser implements IParser {
 		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theElement, theEventWriter, resDef.getChildren());
 	}
 
-	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull) throws IOException {
+	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull, boolean theIncludedResource) throws IOException {
-		super.containResourcesForEncoding(theResource);
+		if (!theIncludedResource) {
+			super.containResourcesForEncoding(theResource);
+		}
 
 		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
 
@@ -499,7 +502,7 @@ public class JsonParser extends BaseParser implements IParser {
 		JsonGenerator eventWriter = createJsonGenerator(theWriter);
 
 		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
-		encodeResourceToJsonStreamWriter(resDef, theResource, eventWriter, null);
+		encodeResourceToJsonStreamWriter(resDef, theResource, eventWriter, null,false);
 		eventWriter.flush();
 	}
 

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

@@ -109,6 +109,37 @@ class ParserState<T> {
 		return myState.isPreResource();
 	}
 
+	private void pop() {
+		myState = myState.myStack;
+		myState.wereBack();
+	}
+
+	private void push(BaseState theState) {
+		theState.setStack(myState);
+		myState = theState;
+	}
+
+	private void putPlacerResourceInDeletedEntry(BundleEntry entry) {
+		IdDt id = null;
+		if (entry.getLinkSelf() != null && entry.getLinkSelf().isEmpty() == false) {
+			id = new IdDt(entry.getLinkSelf().getValue());
+		} else {
+			id = entry.getId();
+		}
+
+		IResource resource = entry.getResource();
+		if (resource == null && id != null && isNotBlank(id.getResourceType())) {
+			resource = myContext.getResourceDefinition(id.getResourceType()).newInstance();
+			resource.setId(id);
+			entry.setResource(resource);
+		}
+
+		if (resource != null) {
+			resource.getResourceMetadata().put(ResourceMetadataKeyEnum.DELETED_AT, entry.getDeletedAt());
+			resource.getResourceMetadata().put(ResourceMetadataKeyEnum.VERSION_ID, id);
+		}
+	}
+
 	public void string(String theData) {
 		myState.string(theData);
 	}
@@ -128,16 +159,6 @@ class ParserState<T> {
 		myState.xmlEvent(theNextEvent);
 	}
 
-	private void pop() {
-		myState = myState.myStack;
-		myState.wereBack();
-	}
-
-	private void push(BaseState theState) {
-		theState.setStack(myState);
-		myState = theState;
-	}
-
 	public static ParserState<Bundle> getPreAtomInstance(FhirContext theContext, Class<? extends IResource> theResourceType, boolean theJsonMode) throws DataFormatException {
 		ParserState<Bundle> retVal = new ParserState<Bundle>(theContext, theJsonMode);
 		retVal.push(retVal.new PreAtomState(theResourceType));
@@ -191,13 +212,10 @@ class ParserState<T> {
 
 		private static final int STATE_LABEL = 2;
 		private static final int STATE_NONE = 0;
-
 		private static final int STATE_SCHEME = 3;
-
 		private static final int STATE_TERM = 1;
-
+		
 		private int myCatState = STATE_NONE;
-
 		private Tag myInstance;
 
 		public AtomCategoryState(Tag theEntry) {
@@ -261,32 +279,68 @@ class ParserState<T> {
 
 	}
 
-	private void putPlacerResourceInDeletedEntry(BundleEntry entry) {
+	public class AtomDeletedEntryState extends AtomEntryState {
-		IdDt id = null;
+
-		if (entry.getLinkSelf() != null && entry.getLinkSelf().isEmpty() == false) {
+		public AtomDeletedEntryState(Bundle theInstance, Class<? extends IResource> theResourceType) {
-			id = new IdDt(entry.getLinkSelf().getValue());
+			super(theInstance, theResourceType);
-		} else {
-			id = entry.getId();
 		}
 
-		IResource resource = entry.getResource();
+		@Override
-		if (resource == null && id != null && isNotBlank(id.getResourceType())) {
+		public void attributeValue(String theName, String theValue) throws DataFormatException {
-			resource = myContext.getResourceDefinition(id.getResourceType()).newInstance();
+			if ("ref".equals(theName)) {
-			resource.setId(id);
+				getEntry().setId(new IdDt(theValue));
-			entry.setResource(resource);
+			} else if ("when".equals(theName)) {
+				getEntry().setDeleted(new InstantDt(theValue));
+			}
 		}
 
-		if (resource != null) {
+		@Override
-			resource.getResourceMetadata().put(ResourceMetadataKeyEnum.DELETED_AT, entry.getDeletedAt());
+		public void endingElement() throws DataFormatException {
-			resource.getResourceMetadata().put(ResourceMetadataKeyEnum.VERSION_ID, id);
+			putPlacerResourceInDeletedEntry(getEntry());
+			super.endingElement();
 		}
+
+	}
+
+	private class AtomDeletedJsonWhenState extends BaseState {
+
+		private String myData;
+		private IPrimitiveDatatype<?> myPrimitive;
+
+		public AtomDeletedJsonWhenState(IPrimitiveDatatype<?> thePrimitive) {
+			super(null);
+			Validate.notNull(thePrimitive, "thePrimitive");
+			myPrimitive = thePrimitive;
+		}
+
+		@Override
+		public void attributeValue(String theName, String theValue) throws DataFormatException {
+			myData = theValue;
+		}
+
+		@Override
+		public void endingElement() throws DataFormatException {
+			myPrimitive.setValueAsString(myData);
+			pop();
+		}
+
+		@Override
+		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
+			throw new DataFormatException("Unexpected nested element in atom tag: " + theLocalPart);
+		}
+
+		@Override
+		protected IElement getCurrentElement() {
+			return null;
+		}
+
 	}
 
 	public class AtomEntryState extends BaseState {
 
+		private boolean myDeleted;
 		private BundleEntry myEntry;
 		private Class<? extends IResource> myResourceType;
-		private boolean myDeleted;
 
 		public AtomEntryState(Bundle theInstance, Class<? extends IResource> theResourceType) {
 			super(null);
@@ -295,10 +349,6 @@ class ParserState<T> {
 			theInstance.getEntries().add(myEntry);
 		}
 
-		protected BundleEntry getEntry() {
-			return myEntry;
-		}
-
 		@Override
 		public void endingElement() throws DataFormatException {
 			populateResourceMetadata();
@@ -340,6 +390,10 @@ class ParserState<T> {
 			// TODO: handle category
 		}
 
+		protected BundleEntry getEntry() {
+			return myEntry;
+		}
+
 		@SuppressWarnings("deprecation")
 		private void populateResourceMetadata() {
 			if (myEntry.getResource() == null) {
@@ -378,29 +432,6 @@ class ParserState<T> {
 
 	}
 
-	public class AtomDeletedEntryState extends AtomEntryState {
-
-		public AtomDeletedEntryState(Bundle theInstance, Class<? extends IResource> theResourceType) {
-			super(theInstance, theResourceType);
-		}
-
-		@Override
-		public void attributeValue(String theName, String theValue) throws DataFormatException {
-			if ("ref".equals(theName)) {
-				getEntry().setId(new IdDt(theValue));
-			} else if ("when".equals(theName)) {
-				getEntry().setDeleted(new InstantDt(theValue));
-			}
-		}
-
-		@Override
-		public void endingElement() throws DataFormatException {
-			putPlacerResourceInDeletedEntry(getEntry());
-			super.endingElement();
-		}
-
-	}
-
 	private class AtomLinkState extends BaseState {
 
 		private BundleEntry myEntry;
@@ -460,77 +491,6 @@ class ParserState<T> {
 
 	}
 
-	private class BinaryResourceState extends BaseState {
-
-		private static final int SUBSTATE_CT = 1;
-		private static final int SUBSTATE_CONTENT = 2;
-		private Binary myInstance;
-		private String myData;
-		private int mySubState = 0;
-
-		public BinaryResourceState(PreResourceState thePreResourceState, Binary theInstance) {
-			super(thePreResourceState);
-			myInstance = theInstance;
-		}
-
-		@Override
-		public void attributeValue(String theName, String theValue) throws DataFormatException {
-			if ("contentType".equals(theName)) {
-				myInstance.setContentType(theValue);
-			} else if (myJsonMode && "value".equals(theName)) {
-				string(theValue);
-			}
-		}
-
-		@Override
-		public void endingElement() throws DataFormatException {
-			if (mySubState == SUBSTATE_CT) {
-				myInstance.setContentType(myData);
-				mySubState = 0;
-				myData=null;
-				return;
-			} else if (mySubState == SUBSTATE_CONTENT) {
-				myInstance.setContentAsBase64(myData);
-				mySubState = 0;
-				myData=null;
-				return;
-			} else {
-				if (!myJsonMode) {
-				myInstance.setContentAsBase64(myData);
-				}
-				pop();
-			}
-		}
-
-		@Override
-		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
-			if (myJsonMode && "contentType".equals(theLocalPart) && mySubState == 0) {
-				mySubState = SUBSTATE_CT;
-			} else if (myJsonMode && "content".equals(theLocalPart) && mySubState == 0) {
-				mySubState = SUBSTATE_CONTENT;
-			} else {
-				throw new DataFormatException("Unexpected nested element in atom tag: " + theLocalPart);
-			}
-		}
-
-		@Override
-		public void string(String theData) {
-			if (myData == null) {
-				myData = theData;
-			} else {
-				// this shouldn't generally happen so it's ok that it's
-				// inefficient
-				myData = myData + theData;
-			}
-		}
-
-		@Override
-		protected IElement getCurrentElement() {
-			return null;
-		}
-
-	}
-
 	private class AtomPrimitiveState extends BaseState {
 
 		private String myData;
@@ -561,6 +521,11 @@ class ParserState<T> {
 			throw new DataFormatException("Unexpected nested element in atom tag: " + theLocalPart);
 		}
 
+		@Override
+		protected IElement getCurrentElement() {
+			return null;
+		}
+
 		@Override
 		public void string(String theData) {
 			if (myData == null) {
@@ -572,45 +537,6 @@ class ParserState<T> {
 			}
 		}
 
-		@Override
-		protected IElement getCurrentElement() {
-			return null;
-		}
-
-	}
-
-	private class AtomDeletedJsonWhenState extends BaseState {
-
-		private String myData;
-		private IPrimitiveDatatype<?> myPrimitive;
-
-		public AtomDeletedJsonWhenState(IPrimitiveDatatype<?> thePrimitive) {
-			super(null);
-			Validate.notNull(thePrimitive, "thePrimitive");
-			myPrimitive = thePrimitive;
-		}
-
-		@Override
-		public void endingElement() throws DataFormatException {
-			myPrimitive.setValueAsString(myData);
-			pop();
-		}
-
-		@Override
-		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
-			throw new DataFormatException("Unexpected nested element in atom tag: " + theLocalPart);
-		}
-
-		@Override
-		public void attributeValue(String theName, String theValue) throws DataFormatException {
-			myData = theValue;
-		}
-
-		@Override
-		protected IElement getCurrentElement() {
-			return null;
-		}
-
 	}
 
 	private class AtomState extends BaseState {
@@ -710,6 +636,10 @@ class ParserState<T> {
 			}
 		}
 
+		protected Object getCurrentElement() {
+			return null;
+		}
+
 		public PreResourceState getPreResourceState() {
 			return myPreResourceState;
 		}
@@ -734,10 +664,77 @@ class ParserState<T> {
 			// ignore
 		}
 
-		protected Object getCurrentElement() {
+	}
+
+	private class BinaryResourceState extends BaseState {
+
+		private static final int SUBSTATE_CONTENT = 2;
+		private static final int SUBSTATE_CT = 1;
+		private String myData;
+		private Binary myInstance;
+		private int mySubState = 0;
+
+		public BinaryResourceState(PreResourceState thePreResourceState, Binary theInstance) {
+			super(thePreResourceState);
+			myInstance = theInstance;
+		}
+
+		@Override
+		public void attributeValue(String theName, String theValue) throws DataFormatException {
+			if ("contentType".equals(theName)) {
+				myInstance.setContentType(theValue);
+			} else if (myJsonMode && "value".equals(theName)) {
+				string(theValue);
+			}
+		}
+
+		@Override
+		public void endingElement() throws DataFormatException {
+			if (mySubState == SUBSTATE_CT) {
+				myInstance.setContentType(myData);
+				mySubState = 0;
+				myData=null;
+				return;
+			} else if (mySubState == SUBSTATE_CONTENT) {
+				myInstance.setContentAsBase64(myData);
+				mySubState = 0;
+				myData=null;
+				return;
+			} else {
+				if (!myJsonMode) {
+				myInstance.setContentAsBase64(myData);
+				}
+				pop();
+			}
+		}
+
+		@Override
+		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
+			if (myJsonMode && "contentType".equals(theLocalPart) && mySubState == 0) {
+				mySubState = SUBSTATE_CT;
+			} else if (myJsonMode && "content".equals(theLocalPart) && mySubState == 0) {
+				mySubState = SUBSTATE_CONTENT;
+			} else {
+				throw new DataFormatException("Unexpected nested element in atom tag: " + theLocalPart);
+			}
+		}
+
+		@Override
+		protected IElement getCurrentElement() {
 			return null;
 		}
 
+		@Override
+		public void string(String theData) {
+			if (myData == null) {
+				myData = theData;
+			} else {
+				// this shouldn't generally happen so it's ok that it's
+				// inefficient
+				myData = myData + theData;
+			}
+		}
+
 	}
 
 	private class ContainedResourcesState extends PreResourceState {
@@ -952,7 +949,8 @@ class ParserState<T> {
 				return;
 			}
 			case UNDECL_EXT:
-			case RESOURCE: {
+			case RESOURCE: 
+			case EXTENSION_DECLARED:{
 				// Throw an exception because this shouldn't happen here
 				break;
 			}
@@ -1031,6 +1029,8 @@ class ParserState<T> {
 			case RESOURCE:
 			case RESOURCE_BLOCK:
 			case UNDECL_EXT:
+			case EXTENSION_DECLARED:
+			case CONTAINED_RESOURCES:
 				break;
 			}
 		}
@@ -1068,17 +1068,17 @@ class ParserState<T> {
 
 		}
 
+		@Override
+		protected IElement getCurrentElement() {
+			return myInstance;
+		}
+
 		@SuppressWarnings("unchecked")
 		@Override
 		public void wereBack() {
 			myObject = (T) myInstance;
 		}
 
-		@Override
-		protected IElement getCurrentElement() {
-			return myInstance;
-		}
-
 	}
 
 	private class PreResourceState extends BaseState {
@@ -1087,7 +1087,6 @@ class ParserState<T> {
 		private BundleEntry myEntry;
 		private IResource myInstance;
 		private List<ResourceReferenceDt> myResourceReferences = new ArrayList<ResourceReferenceDt>();
-
 		private Class<? extends IResource> myResourceType;
 
 		public PreResourceState(BundleEntry theEntry, Class<? extends IResource> theResourceType) {
@@ -1113,7 +1112,7 @@ class ParserState<T> {
 		public void endingElement() throws DataFormatException {
 			pop();
 		}
-
+		
 		@Override
 		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
 			BaseRuntimeElementDefinition<?> definition;
@@ -1136,9 +1135,9 @@ class ParserState<T> {
 			}
 
 			if ("Binary".equals(def.getName())) {
-				push(new BinaryResourceState(this, (Binary) myInstance));
+				push(new BinaryResourceState(getRootPreResourceState(), (Binary) myInstance));
 			} else {
-				push(new ElementCompositeState(this, def, myInstance));
+				push(new ElementCompositeState(getRootPreResourceState(), def, myInstance));
 			}
 		}
 
@@ -1146,10 +1145,23 @@ class ParserState<T> {
 			return myContainedResources;
 		}
 
+		@Override
+		protected IResource getCurrentElement() {
+			return myInstance;
+		}
+
 		public List<ResourceReferenceDt> getResourceReferences() {
 			return myResourceReferences;
 		}
 
+		private PreResourceState getRootPreResourceState() {
+			if (getPreResourceState() != null) {
+				return getPreResourceState();
+			}else {
+				return this;
+			}
+		}
+
 		@Override
 		public boolean isPreResource() {
 			return true;
@@ -1178,11 +1190,6 @@ class ParserState<T> {
 
 		}
 
-		@Override
-		protected IResource getCurrentElement() {
-			return myInstance;
-		}
-
 	}
 
 	private class PreTagListState extends BaseState {
@@ -1208,6 +1215,11 @@ class ParserState<T> {
 			push(new TagListState(myTagList));
 		}
 
+		@Override
+		protected TagList getCurrentElement() {
+			return myTagList;
+		}
+
 		@Override
 		public boolean isPreResource() {
 			return true;
@@ -1219,11 +1231,6 @@ class ParserState<T> {
 			myObject = (T) myTagList;
 		}
 
-		@Override
-		protected TagList getCurrentElement() {
-			return myTagList;
-		}
-
 	}
 
 	private class PrimitiveState extends BaseState {
@@ -1507,6 +1514,11 @@ class ParserState<T> {
 			super.endingElement();
 		}
 
+		@Override
+		protected IElement getCurrentElement() {
+			return myDt;
+		}
+
 		@Override
 		public void xmlEvent(XMLEvent theEvent) {
 			if (theEvent.isEndElement()) {
@@ -1529,11 +1541,6 @@ class ParserState<T> {
 			}
 		}
 
-		@Override
-		protected IElement getCurrentElement() {
-			return myDt;
-		}
-
 	}
 
 }

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

@@ -95,6 +95,7 @@ public class XmlParser extends BaseParser implements IParser {
 	private XMLOutputFactory myXmlOutputFactory;
 
 	public XmlParser(FhirContext theContext) {
+		super(theContext);
 		myContext = theContext;
 		myXmlInputFactory = XMLInputFactory.newInstance();
 		myXmlOutputFactory = XMLOutputFactory.newInstance();
@@ -543,7 +544,9 @@ public class XmlParser extends BaseParser implements IParser {
 	 * 
 	 */
 	private void encodeResourceToXmlStreamWriter(IResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
-		super.containResourcesForEncoding(theResource);
+		if (!theIncludedResource) {
+			super.containResourcesForEncoding(theResource);
+		}
 
 		RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
 		if (resDef == null) {

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

@@ -36,6 +36,7 @@ import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
 import ca.uhn.fhir.model.dstu.composite.ContainedDt;
 import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.parser.DataFormatException;
 
 public class FhirTerser {
 
@@ -147,7 +148,13 @@ public class FhirTerser {
 						if (nextValue == null) {
 							continue;
 						}
+						if (nextValue.isEmpty()) {
+							continue;
+						}
 						BaseRuntimeElementDefinition<?> childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());
+						if (childElementDef == null) {
+							throw new DataFormatException("Found value of type[" + nextValue.getClass().getSimpleName() + "] which is not valid for field[" + nextChild.getElementName() + "] in " + childDef.getName());
+						}
 						getAllChildElementsOfType(nextValue, childElementDef, theType, theList);
 					}
 				}

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.parser;
 
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.stringContainsInOrder;
 import static org.junit.Assert.*;
 import static org.mockito.Matchers.eq;
 import static org.mockito.Mockito.mock;
@@ -83,6 +84,44 @@ public class JsonParserTest {
 		
 	}
 
+	@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.newJsonParser().setPrettyPrint(true).encodeResourceToString(A);
+		ourLog.info(str);
+		
+		assertThat(str, stringContainsInOrder(Arrays.asList("\"text\":\"B\"", "\"text\":\"C\"", "\"text\":\"A\"")));
+		
+		// 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.newJsonParser().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 = "{\n" + 

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

@@ -17,6 +17,7 @@ import java.util.List;
 import org.apache.commons.io.IOUtils;
 import org.custommonkey.xmlunit.Diff;
 import org.custommonkey.xmlunit.XMLUnit;
+import org.hamcrest.Matchers;
 import org.hamcrest.core.IsNot;
 import org.hamcrest.core.StringContains;
 import org.hamcrest.text.StringContainsInOrder;
@@ -80,6 +81,46 @@ 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" + 

hapi-fhir-structures-dstu/.classpath

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry including="**/*.java" kind="src" path="target/generated-sources/tinder"/>
+	<classpathentry kind="src" path="target/generated-sources/tinder"/>
 	<classpathentry kind="var" path="M2_REPO/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2.jar" sourcepath="M2_REPO/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2-sources.jar"/>
 	<classpathentry kind="var" path="M2_REPO/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar" sourcepath="M2_REPO/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0-sources.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>

hapi-tinder-plugin/src/main/resources/vm/dt_composite.vm

@@ -43,6 +43,15 @@ public class ${className}
 #########################
 ### Type-specific constructors
 #########################
+#if ( ${className} == "CodeableConceptDt" )
+	/**
+	 * Constructor which creates a CodeableConceptDt with one coding repetition, containing
+	 * the given system and code
+	 */
+	public CodeableConceptDt(String theSystem, String theCode) {
+		addCoding().setSystem(theSystem).setCode(theCode);
+	}
+#end
 #if ( ${className} == "CodingDt" )
 	/**
 	 * Creates a new Coding with the given system and code