Clean up encoding of contained resources so that resources are not

modified as a part of the encoding

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

@@ -96,6 +96,14 @@
 				have also caused resource validation to fail occasionally on these platforms as well.
 				Thanks to Bill de Beaubien for reporting!
 			</action>			
+			<action type="fix">
+				toString() method on TokenParam was incorrectly showing the system as the value.
+				Thanks to Bill de Beaubien for reporting!
+			</action>			
+			<action type="update">
+				Documentation on contained resources contained a typo and did not actually produce contained resources. Thanks
+				to David Hay of Orion Health for reporting!
+			</action>			
 		</release>
 		<release version="0.6" date="2014-Sep-08" description="This release brings a number of new features and bug fixes!">
 			<!-- 

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

@@ -201,6 +201,9 @@ public class FhirContext {
 	 * Create and return a new JSON parser.
 	 * 
 	 * <p>
+	 * Thread safety: <b>Parsers are not guaranteed to be thread safe</b>. Create a new parser instance for every thread or every message being parsed/encoded.
+	 * </p>
+	 * <p>
 	 * Performance Note: <b>This method is cheap</b> to call, and may be called once for every message being processed without incurring any performance penalty
 	 * </p>
 	 */
@@ -261,6 +264,9 @@ public class FhirContext {
 	 * Create and return a new XML parser.
 	 * 
 	 * <p>
+	 * Thread safety: <b>Parsers are not guaranteed to be thread safe</b>. Create a new parser instance for every thread or every message being parsed/encoded.
+	 * </p>
+	 * <p>
 	 * Performance Note: <b>This method is cheap</b> to call, and may be called once for every message being processed without incurring any performance penalty
 	 * </p>
 	 */

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

@@ -25,7 +25,9 @@ import java.io.Reader;
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.io.Writer;
+import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.IdentityHashMap;
 import java.util.List;
 import java.util.Set;
 
@@ -45,29 +47,60 @@ import ca.uhn.fhir.model.primitive.IdDt;
 
 public abstract class BaseParser implements IParser {
 
-	private boolean mySuppressNarratives;
+	private ContainedResources myContainedResources;
 	private FhirContext myContext;
-	
+	private boolean mySuppressNarratives;
+
 	public BaseParser(FhirContext theContext) {
 		myContext = theContext;
 	}
 
-	@Override
+	private void containResourcesForEncoding(ContainedResources theContained, IResource theResource, IResource theTarget) {
-	public TagList parseTagList(String theString) {
+		List<ResourceReferenceDt> allElements = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, ResourceReferenceDt.class);
-		return parseTagList(new StringReader(theString));
+
+		Set<String> allIds = new HashSet<String>();
+
+		for (IResource next : theTarget.getContained().getContainedResources()) {
+			String nextId = next.getId().getValue();
+			if (StringUtils.isNotBlank(nextId)) {
+				allIds.add(nextId);
+			}
+		}
+
+		for (ResourceReferenceDt next : allElements) {
+			IResource resource = next.getResource();
+			if (resource != null) {
+				if (resource.getId().isEmpty()) {
+					theContained.addContained(resource);
+				} else {
+					continue;
+				}
+
+				containResourcesForEncoding(theContained, resource, theTarget);
+			}
+		}
+
 	}
 
-	@SuppressWarnings("cast")
+	public void containResourcesForEncoding(IResource theResource) {
-	@Override
+		ContainedResources contained = new ContainedResources();
-	public <T extends IResource> T parseResource(Class<T> theResourceType, String theMessageString) {
+		containResourcesForEncoding(contained, theResource, theResource);
-		StringReader reader = new StringReader(theMessageString);
+		myContainedResources = contained;
-		return (T) parseResource(theResourceType, reader);
 	}
 
 	@Override
-	public Bundle parseBundle(String theXml) throws ConfigurationException, DataFormatException {
+	public String encodeBundleToString(Bundle theBundle) throws DataFormatException {
-		StringReader reader = new StringReader(theXml);
+		if (theBundle == null) {
-		return parseBundle(reader);
+			throw new NullPointerException("Bundle can not be null");
+		}
+		StringWriter stringWriter = new StringWriter();
+		try {
+			encodeBundleToWriter(theBundle, stringWriter);
+		} catch (IOException e) {
+			throw new Error("Encountered IOException during write to string - This should not happen!");
+		}
+
+		return stringWriter.toString();
 	}
 
 	@Override
@@ -92,24 +125,15 @@ public abstract class BaseParser implements IParser {
 		return stringWriter.toString();
 	}
 
-	@Override
+	ContainedResources getContainedResources() {
-	public String encodeBundleToString(Bundle theBundle) throws DataFormatException {
+		return myContainedResources;
-		if (theBundle == null) {
-			throw new NullPointerException("Bundle can not be null");
-		}
-		StringWriter stringWriter = new StringWriter();
-		try {
-			encodeBundleToWriter(theBundle, stringWriter);
-		} catch (IOException e) {
-			throw new Error("Encountered IOException during write to string - This should not happen!");
-		}
-
-		return stringWriter.toString();
 	}
 
-	@Override
+	/**
-	public IResource parseResource(String theMessageString) throws ConfigurationException, DataFormatException {
+	 * If set to <code>true</code> (default is <code>false</code>), narratives will not be included in the encoded values.
-		return parseResource(null, theMessageString);
+	 */
+	public boolean getSuppressNarratives() {
+		return mySuppressNarratives;
 	}
 
 	@Override
@@ -117,49 +141,38 @@ public abstract class BaseParser implements IParser {
 		return parseBundle(null, theReader);
 	}
 
+	@Override
+	public Bundle parseBundle(String theXml) throws ConfigurationException, DataFormatException {
+		StringReader reader = new StringReader(theXml);
+		return parseBundle(reader);
+	}
+
+	@SuppressWarnings("cast")
+	@Override
+	public <T extends IResource> T parseResource(Class<T> theResourceType, String theMessageString) {
+		StringReader reader = new StringReader(theMessageString);
+		return (T) parseResource(theResourceType, reader);
+	}
+
 	@Override
 	public IResource parseResource(Reader theReader) throws ConfigurationException, DataFormatException {
 		return parseResource(null, theReader);
 	}
 
-	public void containResourcesForEncoding(IResource theResource) {
+	@Override
-		containResourcesForEncoding(theResource, theResource);
+	public IResource parseResource(String theMessageString) throws ConfigurationException, DataFormatException {
+		return parseResource(null, theMessageString);
 	}
 
-	private long myNextContainedId = 1;
+	@Override
-	
+	public TagList parseTagList(String theString) {
-	private void containResourcesForEncoding(IResource theResource, IResource theTarget) {
+		return parseTagList(new StringReader(theString));
-		List<ResourceReferenceDt> allElements = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, ResourceReferenceDt.class);
+	}
-
-		Set<String> allIds = new HashSet<String>();
-		
-		for (IResource next : theTarget.getContained().getContainedResources()) {
-			String nextId = next.getId().getValue();
-			if (StringUtils.isNotBlank(nextId)) {
-				allIds.add(nextId);
-			}
-		}
-		
-		for (ResourceReferenceDt next : allElements) {
-			IResource resource = next.getResource();
-			if (resource != null) {
-				if (resource.getId().isEmpty()) { // TODO: make this configurable between the two below (and something else?)
-					resource.setId(new IdDt(myNextContainedId++));
-//					resource.setId(new IdDt(UUID.randomUUID().toString()));
-				}
-
-				String nextResourceId = resource.getId().getValue();
-				if (!allIds.contains(nextResourceId)) {
-					theTarget.getContained().getContainedResources().add(resource);
-					allIds.add(resource.getId().getValue());
-				}
-
-				next.setReference("#" + resource.getId().getValue());
-				
-				containResourcesForEncoding(resource, theTarget);
-			}
-		}
 
+	@Override
+	public IParser setSuppressNarratives(boolean theSuppressNarratives) {
+		mySuppressNarratives = theSuppressNarratives;
+		return this;
 	}
 
 	protected void throwExceptionForUnknownChildType(BaseRuntimeChildDefinition nextChild, Class<? extends IElement> type) {
@@ -178,18 +191,37 @@ public abstract class BaseParser implements IParser {
 		throw new DataFormatException(nextChild + " has no child of type " + type);
 	}
 
-	@Override
+	static class ContainedResources {
-	public IParser setSuppressNarratives(boolean theSuppressNarratives) {
+		private long myNextContainedId = 1;
-		mySuppressNarratives = theSuppressNarratives;
+
-		return this;
+		private IdentityHashMap<IResource, IdDt> myResourceToId = new IdentityHashMap<IResource, IdDt>();
-	}
+		private List<IResource> myResources = new ArrayList<IResource>();
+
+		public void addContained(IResource theResource) {
+			if (myResourceToId.containsKey(theResource)) {
+				return;
+			}
+
+			// TODO: make this configurable between the two below (and something else?)
+			IdDt newId = new IdDt(myNextContainedId++);
+			// newId = new IdDt(UUID.randomUUID().toString());
+
+			myResourceToId.put(theResource, newId);
+			myResources.add(theResource);
+		}
+
+		public List<IResource> getContainedResources() {
+			return myResources;
+		}
+		
+		public IdDt getResourceId(IResource theResource) {
+			return myResourceToId.get(theResource);
+		}
+
+		public boolean isEmpty() {
+			return myResourceToId.isEmpty();
+		}
 
-	/**
-	 * If set to <code>true</code> (default is <code>false</code>), narratives
-	 * will not be included in the encoded values.
-	 */
-	public boolean getSuppressNarratives() {
-		return mySuppressNarratives;
 	}
 
 }

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

@@ -29,6 +29,12 @@ import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.TagList;
 
+/**
+ * 
+ * <p>
+ * Thread safety: <b>Parsers are not guaranteed to be thread safe</b>. Create a new parser instance for every thread or every message being parsed/encoded.
+ * </p>
+ */
 public interface IParser {
 
 	String encodeBundleToString(Bundle theBundle) throws DataFormatException;
@@ -40,26 +46,24 @@ public interface IParser {
 	void encodeResourceToWriter(IResource theResource, Writer theWriter) throws IOException, DataFormatException;
 
 	/**
-	 * Encodes a tag list, as defined in the <a
+	 * Encodes a tag list, as defined in the <a href="http://hl7.org/implement/standards/fhir/http.html#tags">FHIR Specification</a>.
-	 * href="http://hl7.org/implement/standards/fhir/http.html#tags">FHIR
-	 * Specification</a>.
 	 * 
-	 * @param theTagList The tag list to encode. Must not be null.
+	 * @param theTagList
+	 *            The tag list to encode. Must not be null.
 	 * @return An encoded tag list
 	 */
 	String encodeTagListToString(TagList theTagList);
 
 	/**
-	 * Encodes a tag list, as defined in the <a
+	 * Encodes a tag list, as defined in the <a href="http://hl7.org/implement/standards/fhir/http.html#tags">FHIR Specification</a>.
-	 * href="http://hl7.org/implement/standards/fhir/http.html#tags">FHIR
-	 * Specification</a>.
 	 * 
-	 * @param theTagList The tag list to encode. Must not be null.
+	 * @param theTagList
-	 * @param theWriter The writer to encode to
+	 *            The tag list to encode. Must not be null.
+	 * @param theWriter
+	 *            The writer to encode to
 	 */
 	void encodeTagListToWriter(TagList theTagList, Writer theWriter) throws IOException;
 
-	
 	<T extends IResource> Bundle parseBundle(Class<T> theResourceType, Reader theReader);
 
 	Bundle parseBundle(Reader theReader);
@@ -70,15 +74,12 @@ public interface IParser {
 	 * Parses a resource
 	 * 
 	 * @param theResourceType
-	 *            The resource type to use. This can be used to explicitly
+	 *            The resource type to use. This can be used to explicitly specify a class which extends a built-in type (e.g. a custom type extending the default Patient class)
-	 *            specify a class which extends a built-in type (e.g. a custom
-	 *            type extending the default Patient class)
 	 * @param theReader
 	 *            The reader to parse input from. Note that the Reader will not be closed by the parser upon completion.
 	 * @return A parsed resource
 	 * @throws DataFormatException
-	 *             If the resource can not be parsed because the data is not
+	 *             If the resource can not be parsed because the data is not recognized or invalid for any reason
-	 *             recognized or invalid for any reason
 	 */
 	<T extends IResource> T parseResource(Class<T> theResourceType, Reader theReader) throws DataFormatException;
 
@@ -86,15 +87,12 @@ public interface IParser {
 	 * Parses a resource
 	 * 
 	 * @param theResourceType
-	 *            The resource type to use. This can be used to explicitly
+	 *            The resource type to use. This can be used to explicitly specify a class which extends a built-in type (e.g. a custom type extending the default Patient class)
-	 *            specify a class which extends a built-in type (e.g. a custom
-	 *            type extending the default Patient class)
 	 * @param theString
 	 *            The string to parse
 	 * @return A parsed resource
 	 * @throws DataFormatException
-	 *             If the resource can not be parsed because the data is not
+	 *             If the resource can not be parsed because the data is not recognized or invalid for any reason
-	 *             recognized or invalid for any reason
 	 */
 	<T extends IResource> T parseResource(Class<T> theResourceType, String theString) throws DataFormatException;
 
@@ -105,8 +103,7 @@ public interface IParser {
 	 *            The reader to parse input from. Note that the Reader will not be closed by the parser upon completion.
 	 * @return A parsed resource
 	 * @throws DataFormatException
-	 *             If the resource can not be parsed because the data is not
+	 *             If the resource can not be parsed because the data is not recognized or invalid for any reason
-	 *             recognized or invalid for any reason
 	 */
 	IResource parseResource(Reader theReader) throws ConfigurationException, DataFormatException;
 
@@ -117,15 +114,12 @@ public interface IParser {
 	 *            The string to parse
 	 * @return A parsed resource
 	 * @throws DataFormatException
-	 *             If the resource can not be parsed because the data is not
+	 *             If the resource can not be parsed because the data is not recognized or invalid for any reason
-	 *             recognized or invalid for any reason
 	 */
 	IResource parseResource(String theMessageString) throws ConfigurationException, DataFormatException;
 
 	/**
-	 * Parses a tag list, as defined in the <a
+	 * Parses a tag list, as defined in the <a href="http://hl7.org/implement/standards/fhir/http.html#tags">FHIR Specification</a>.
-	 * href="http://hl7.org/implement/standards/fhir/http.html#tags">FHIR
-	 * Specification</a>.
 	 * 
 	 * @param theReader
 	 *            A reader which will supply a tag list
@@ -134,9 +128,7 @@ public interface IParser {
 	TagList parseTagList(Reader theReader);
 
 	/**
-	 * Parses a tag list, as defined in the <a
+	 * Parses a tag list, as defined in the <a href="http://hl7.org/implement/standards/fhir/http.html#tags">FHIR Specification</a>.
-	 * href="http://hl7.org/implement/standards/fhir/http.html#tags">FHIR
-	 * Specification</a>.
 	 * 
 	 * @param theString
 	 *            A string containing a tag list
@@ -145,20 +137,16 @@ public interface IParser {
 	TagList parseTagList(String theString);
 
 	/**
-	 * Sets the "pretty print" flag, meaning that the parser will encode
+	 * Sets the "pretty print" flag, meaning that the parser will encode resources with human-readable spacing and newlines between elements instead of condensing output as much as possible.
-	 * resources with human-readable spacing and newlines between elements
-	 * instead of condensing output as much as possible.
 	 * 
 	 * @param thePrettyPrint
 	 *            The flag
-	 * @return Returns an instance of <code>this</code> parser so that method
+	 * @return Returns an instance of <code>this</code> parser so that method calls can be conveniently chained
-	 *         calls can be conveniently chained
 	 */
 	IParser setPrettyPrint(boolean thePrettyPrint);
 
 	/**
-	 * If set to <code>true</code> (default is <code>false</code>), narratives
+	 * If set to <code>true</code> (default is <code>false</code>), narratives will not be included in the encoded values.
-	 * will not be included in the encoded values.
 	 */
 	IParser setSuppressNarratives(boolean theSuppressNarratives);
 

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

@@ -230,7 +230,7 @@ public class JsonParser extends BaseParser implements IParser {
 	}
 
 	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, JsonGenerator theWriter, IElement theValue, BaseRuntimeElementDefinition<?> theChildDef,
-			String theChildName) throws IOException {
+			String theChildName, boolean theIsSubElementWithinResource) throws IOException {
 
 		switch (theChildDef.getChildType()) {
 		case PRIMITIVE_DATATYPE: {
@@ -278,7 +278,7 @@ public class JsonParser extends BaseParser implements IParser {
 			if (theValue instanceof ExtensionDt) {
 				theWriter.write("url", ((ExtensionDt) theValue).getUrlAsString());
 			}
-			encodeCompositeElementToStreamWriter(theResDef, theResource, theValue, theWriter, childCompositeDef);
+			encodeCompositeElementToStreamWriter(theResDef, theResource, theValue, theWriter, childCompositeDef, theIsSubElementWithinResource);
 			theWriter.writeEnd();
 			break;
 		}
@@ -297,6 +297,16 @@ public class JsonParser extends BaseParser implements IParser {
 					reference = myContext.getResourceDefinition(value.getResourceType()).getName() + '/' + value.getIdPart();
 				}
 			}
+			if (StringUtils.isBlank(reference)) {
+				if (referenceDt.getResource() != null) {
+					IdDt containedId = getContainedResources().getResourceId(referenceDt.getResource());
+					if (containedId != null) {
+						reference = "#" + containedId.getValue();
+					} else if (referenceDt.getResource().getId() != null && referenceDt.getResource().getId().hasIdPart()) {
+						reference = referenceDt.getResource().getId().getValue();
+					}
+				}
+			}
 
 			if (StringUtils.isNotBlank(reference)) {
 				theWriter.write(XmlParser.RESREF_REFERENCE, reference);
@@ -313,6 +323,10 @@ public class JsonParser extends BaseParser implements IParser {
 			for (IResource next : value.getContainedResources()) {
 				encodeResourceToJsonStreamWriter(theResDef, next, theWriter, null, true);
 			}
+			for (IResource next : getContainedResources().getContainedResources()) {
+				IdDt resourceId = getContainedResources().getResourceId(next);
+				encodeResourceToJsonStreamWriter(theResDef, next, theWriter, null, true, resourceId.getValue());
+			}
 			theWriter.writeEnd();
 			break;
 		}
@@ -341,7 +355,7 @@ public class JsonParser extends BaseParser implements IParser {
 	}
 
 	private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, IElement theElement, JsonGenerator theEventWriter,
-			List<? extends BaseRuntimeChildDefinition> theChildren) throws IOException {
+			List<? extends BaseRuntimeChildDefinition> theChildren, boolean theIsSubElementWithinResource) throws IOException {
 		for (BaseRuntimeChildDefinition nextChild : theChildren) {
 			if (nextChild instanceof RuntimeChildNarrativeDefinition) {
 				INarrativeGenerator gen = myContext.getNarrativeGenerator();
@@ -351,7 +365,7 @@ public class JsonParser extends BaseParser implements IParser {
 						RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
 						String childName = nextChild.getChildNameByDatatype(child.getDatatype());
 						BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, narr, type, childName);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, narr, type, childName, theIsSubElementWithinResource);
 						continue;
 					}
 				}
@@ -371,7 +385,13 @@ public class JsonParser extends BaseParser implements IParser {
 			int valueIdx = 0;
 			for (IElement nextValue : values) {
 				if (nextValue == null || nextValue.isEmpty()) {
-					continue;
+					if (nextValue instanceof ContainedDt) {
+						if (theIsSubElementWithinResource || getContainedResources().isEmpty()) {
+							continue;
+						}
+					} else {
+						continue;
+					}
 				}
 
 				Class<? extends IElement> type = nextValue.getClass();
@@ -382,6 +402,10 @@ public class JsonParser extends BaseParser implements IParser {
 				}
 				boolean primitive = childDef.getChildType() == ChildTypeEnum.PRIMITIVE_DATATYPE;
 				
+				if (childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES && theIsSubElementWithinResource) {
+					continue;
+				}
+				
 				if (nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
 					// Don't encode extensions
 //					RuntimeChildDeclaredExtensionDefinition extDef = (RuntimeChildDeclaredExtensionDefinition) nextChild;
@@ -399,13 +423,13 @@ public class JsonParser extends BaseParser implements IParser {
 						if (nextChild.getMax() > 1 || nextChild.getMax() == Child.MAX_UNLIMITED) {
 							theEventWriter.writeStartArray(childName);
 							inArray = true;
-							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null);
+							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theIsSubElementWithinResource);
 						} else {
-							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName);
+							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theIsSubElementWithinResource);
 						}
 						currentChildName = childName;
 					} else {
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theIsSubElementWithinResource);
 					}
 
 					if (nextValue instanceof ISupportsUndeclaredExtensions && primitive) {
@@ -453,14 +477,24 @@ public class JsonParser extends BaseParser implements IParser {
 	}
 
 	private void encodeCompositeElementToStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, IElement theElement, JsonGenerator theEventWriter,
-			BaseRuntimeElementCompositeDefinition<?> resDef) throws IOException, DataFormatException {
+			BaseRuntimeElementCompositeDefinition<?> resDef, boolean theIsSubElementWithinResource) throws IOException, DataFormatException {
 		extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, resDef, theResDef, theResource);
-		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theElement, theEventWriter, resDef.getExtensions());
+		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theElement, theEventWriter, resDef.getExtensions(), theIsSubElementWithinResource);
-		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theElement, theEventWriter, resDef.getChildren());
+		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theElement, theEventWriter, resDef.getChildren(),theIsSubElementWithinResource);
 	}
 
 	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull,
 			boolean theIsSubElementWithinResource) throws IOException {
+		String resourceId = null;
+		if (theIsSubElementWithinResource && StringUtils.isNotBlank(theResource.getId().getValue())) {
+			resourceId = theResource.getId().getValue();
+		}
+
+		encodeResourceToJsonStreamWriter(theResDef, theResource, theEventWriter, theObjectNameOrNull, theIsSubElementWithinResource, resourceId);
+	}
+
+	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull, boolean theIsSubElementWithinResource,
+			String theResourceId) throws IOException {
 		if (!theIsSubElementWithinResource) {
 			super.containResourcesForEncoding(theResource);
 		}
@@ -474,8 +508,8 @@ public class JsonParser extends BaseParser implements IParser {
 		}
 
 		theEventWriter.write("resourceType", resDef.getName());
-		if (theIsSubElementWithinResource && theResource.getId() != null && isNotBlank(theResource.getId().getValue())) {
+		if (theResourceId != null) {
-			theEventWriter.write("id", theResource.getId().getValue());
+			theEventWriter.write("id", theResourceId);
 		}
 
 		if (theResource instanceof Binary) {
@@ -483,7 +517,7 @@ public class JsonParser extends BaseParser implements IParser {
 			theEventWriter.write("contentType", bin.getContentType());
 			theEventWriter.write("content", bin.getContentAsBase64());
 		} else {
-			encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, resDef);
+			encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, resDef, theIsSubElementWithinResource);
 		}
 		theEventWriter.writeEnd();
 	}
@@ -972,7 +1006,7 @@ public class JsonParser extends BaseParser implements IParser {
 					// theEventWriter, myValue, def, "value" +
 					// WordUtils.capitalize(def.getName()));
 					String childName = myDef.getChildNameByDatatype(myValue.getClass());
-					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName);
+					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName,false);
 				}
 
 				// theEventWriter.name(myUndeclaredExtension.get);
@@ -1003,7 +1037,7 @@ public class JsonParser extends BaseParser implements IParser {
 					throw new ConfigurationException("Unable to encode extension, unregognized child element type: " + value.getClass().getCanonicalName());
 				}
 				BaseRuntimeElementDefinition<?> childDef = extDef.getChildElementDefinitionByDatatype(value.getClass());
-				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName);
+				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName,true);
 			}
 
 			// theEventWriter.name(myUndeclaredExtension.get);

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

@@ -34,8 +34,6 @@ import java.util.List;
 import javax.xml.namespace.QName;
 import javax.xml.stream.FactoryConfigurationError;
 import javax.xml.stream.XMLEventReader;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLOutputFactory;
 import javax.xml.stream.XMLStreamConstants;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamWriter;
@@ -52,6 +50,7 @@ import org.apache.commons.lang3.StringUtils;
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeChildDeclaredExtensionDefinition;
@@ -153,9 +152,9 @@ public class XmlParser extends BaseParser implements IParser {
 					eventWriter.writeNamespace("at", TOMBSTONES_NS);
 					eventWriter.writeAttribute("ref", nextEntry.getId().getValueAsString());
 					eventWriter.writeAttribute("when", nextEntry.getDeletedAt().getValueAsString());
-					if (nextEntry.getDeletedByEmail().isEmpty() == false || nextEntry.getDeletedByName().isEmpty()==false) {
+					if (nextEntry.getDeletedByEmail().isEmpty() == false || nextEntry.getDeletedByName().isEmpty() == false) {
 						eventWriter.writeStartElement(TOMBSTONES_NS, "by");
-						if (nextEntry.getDeletedByName().isEmpty()==false) {
+						if (nextEntry.getDeletedByName().isEmpty() == false) {
 							eventWriter.writeStartElement(TOMBSTONES_NS, "name");
 							eventWriter.writeCharacters(nextEntry.getDeletedByName().getValue());
 							eventWriter.writeEndElement();
@@ -167,7 +166,7 @@ public class XmlParser extends BaseParser implements IParser {
 						}
 						eventWriter.writeEndElement();
 					}
-					if (nextEntry.getDeletedComment().isEmpty()==false) {
+					if (nextEntry.getDeletedComment().isEmpty() == false) {
 						eventWriter.writeStartElement(TOMBSTONES_NS, "comment");
 						eventWriter.writeCharacters(nextEntry.getDeletedComment().getValue());
 						eventWriter.writeEndElement();
@@ -206,14 +205,13 @@ public class XmlParser extends BaseParser implements IParser {
 				} else {
 					ourLog.debug("Bundle entry contains null resource");
 				}
-				
+
 				if (!nextEntry.getSummary().isEmpty()) {
 					eventWriter.writeStartElement("summary");
 					eventWriter.writeAttribute("type", "xhtml");
 					encodeXhtml(nextEntry.getSummary(), eventWriter);
 					eventWriter.writeEndElement();
 				}
-				
 
 				eventWriter.writeEndElement(); // entry
 			}
@@ -225,7 +223,7 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 	}
 
-	private void writeCategories(XMLStreamWriter eventWriter,  TagList categories) throws XMLStreamException {
+	private void writeCategories(XMLStreamWriter eventWriter, TagList categories) throws XMLStreamException {
 		if (categories != null) {
 			for (Tag next : categories) {
 				eventWriter.writeStartElement("category");
@@ -335,16 +333,16 @@ public class XmlParser extends BaseParser implements IParser {
 		} catch (XMLStreamException e1) {
 			throw new DataFormatException(e1);
 		}
-		
+
-//		XMLEventReader streamReader;
+		// XMLEventReader streamReader;
-//		try {
+		// try {
-//			streamReader = myXmlInputFactory.createXMLEventReader(theReader);
+		// streamReader = myXmlInputFactory.createXMLEventReader(theReader);
-//		} catch (XMLStreamException e) {
+		// } catch (XMLStreamException e) {
-//			throw new DataFormatException(e);
+		// throw new DataFormatException(e);
-//		} catch (FactoryConfigurationError e) {
+		// } catch (FactoryConfigurationError e) {
-//			throw new ConfigurationException("Failed to initialize STaX event factory", e);
+		// throw new ConfigurationException("Failed to initialize STaX event factory", e);
-//		}
+		// }
-//		return streamReader;
+		// return streamReader;
 	}
 
 	private XMLStreamWriter decorateStreamWriter(XMLStreamWriter eventWriter) {
@@ -426,7 +424,11 @@ public class XmlParser extends BaseParser implements IParser {
 	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IResource theResource, XMLStreamWriter theEventWriter, IElement nextValue, String childName,
 			BaseRuntimeElementDefinition<?> childDef, String theExtensionUrl, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
 		if (nextValue.isEmpty()) {
-			return;
+			if (childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES && getContainedResources().isEmpty()==false && theIncludedResource == false) {
+				// We still want to go in..
+			} else {
+				return;
+			}
 		}
 
 		switch (childDef.getChildType()) {
@@ -467,6 +469,10 @@ public class XmlParser extends BaseParser implements IParser {
 			for (IResource next : value.getContainedResources()) {
 				encodeResourceToXmlStreamWriter(next, theEventWriter, true);
 			}
+			for (IResource next : getContainedResources().getContainedResources()) {
+				IdDt resourceId = getContainedResources().getResourceId(next);
+				encodeResourceToXmlStreamWriter(next, theEventWriter, true, resourceId.getValue());
+			}
 			theEventWriter.writeEndElement();
 			break;
 		}
@@ -512,7 +518,7 @@ public class XmlParser extends BaseParser implements IParser {
 			}
 
 			for (IElement nextValue : values) {
-				if (nextValue == null || nextValue.isEmpty()) {
+				if ((nextValue == null || nextValue.isEmpty()) && !(nextValue instanceof ContainedDt)) {
 					continue;
 				}
 				Class<? extends IElement> type = nextValue.getClass();
@@ -570,6 +576,17 @@ public class XmlParser extends BaseParser implements IParser {
 		// }
 		// }
 
+		if (isBlank(reference)) {
+			if (theRef.getResource() != null) {
+				IdDt containedId = getContainedResources().getResourceId(theRef.getResource());
+				if (containedId != null) {
+					reference = "#" + containedId.getValue();
+				} else if (theRef.getResource().getId() != null && theRef.getResource().getId().hasIdPart()) {
+					reference = theRef.getResource().getId().getValue();
+				}
+			}
+		}
+		
 		if (StringUtils.isNotBlank(reference)) {
 			theEventWriter.writeStartElement(RESREF_REFERENCE);
 			theEventWriter.writeAttribute("value", reference);
@@ -582,12 +599,16 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 	}
 
-	/**
-	 * @param theIncludedResource
-	 *            Set to true only if this resource is an "included" resource, as opposed to a "root level" resource by itself or in a bundle entry
-	 * 
-	 */
 	private void encodeResourceToXmlStreamWriter(IResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
+		String resourceId = null;
+		if (theIncludedResource && StringUtils.isNotBlank(theResource.getId().getValue())) {
+			resourceId = theResource.getId().getValue();
+		}
+		
+		encodeResourceToXmlStreamWriter(theResource, theEventWriter, theIncludedResource, resourceId);
+	}
+
+	private void encodeResourceToXmlStreamWriter(IResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource, String theResourceId) throws XMLStreamException {
 		if (!theIncludedResource) {
 			super.containResourcesForEncoding(theResource);
 		}
@@ -600,8 +621,8 @@ public class XmlParser extends BaseParser implements IParser {
 		theEventWriter.writeStartElement(resDef.getName());
 		theEventWriter.writeDefaultNamespace(FHIR_NS);
 
-		if (theIncludedResource && StringUtils.isNotBlank(theResource.getId().getValue())) {
+		if (theResourceId != null) {
-			theEventWriter.writeAttribute("id", theResource.getId().getValue());
+			theEventWriter.writeAttribute("id", theResourceId);
 		}
 
 		if (theResource instanceof Binary) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/TokenParam.java

@@ -159,13 +159,13 @@ public class TokenParam extends BaseParam implements IQueryParameterType {
 	@Override
 	public String toString() {
 		ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
-		builder.append("system", defaultString(getValue()));
+		builder.append("system", defaultString(getSystem()));
 		builder.append("value", getValue());
 		if (myText) {
-			builder.append("text", myText);
+			builder.append(":text", myText);
 		}
 		if (getMissing() != null) {
-			builder.append("missing", getMissing());
+			builder.append(":missing", getMissing());
 		}
 		return builder.toString();
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/exceptions/UnprocessableEntityException.java

@@ -72,13 +72,15 @@ public class UnprocessableEntityException extends BaseServerResponseException {
 	}
 
 	private static OperationOutcome toOperationOutcome(String... theMessage) {
-		OperationOutcome operationOutcome = new OperationOutcome();
+		OperationOutcome OperationOutcome = new OperationOutcome();
 		if (theMessage != null) {
 			for (String next : theMessage) {
-				operationOutcome.addIssue().setDetails(next);
+				OperationOutcome.addIssue().setDetails(next);
 			}
 		}
-		return operationOutcome;
+		return OperationOutcome;
 	}
 
+	
+	
 }

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

@@ -103,31 +103,109 @@ patient.getManagingOrganization().setReference("Organization/124362");]]></sourc
 				<p>
 					In the following example, the Organization resource has an ID set, so it will not
 					be contained but will rather appear as a distinct entry in any returned
-					bundles.
+					bundles. Both resources are added to a bundle, which will then have
+					two entries:
 				</p>
-				<source><![CDATA[Organization org = new Organization();
+				<source><![CDATA[// Create an organization
+Organization org = new Organization();
 org.setId("Organization/65546");
 org.getName().setValue("Contained Test Organization");
 
+// Create a patient
 Patient patient = new Patient();
 patient.setId("Patient/1333");
 patient.addIdentifier("urn:mrns", "253345");
-patient.getManagingOrganization().setResource(patient);]]></source>
+patient.getManagingOrganization().setResource(org);
 
+// Create a list containing both resources. In a server method, you might just
+// return this list, but here we will create a bundle to encode.
+List<IResource> resources = new ArrayList<IResource>();
+resources.add(org);
+resources.add(patient);		
+
+// Create a bundle with both
+Bundle b = Bundle.withResources(resources, ourCtx, "http://example.com/base");
+
+// Encode the buntdle
+String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
+System.out.println(encoded);]]></source>
+
+				<p>
+					This will give the following output:
+				</p>
+				<source><![CDATA[<feed xmlns="http://www.w3.org/2005/Atom">
+   <entry>
+      <title>Organization Organization/65546</title>
+      <id>http://example.com/base/Organization/65546</id>
+      <published>2014-10-14T09:22:54-04:00</published>
+      <link rel="self" href="http://example.com/base/Organization/65546"/>
+      <content type="text/xml">
+         <Organization xmlns="http://hl7.org/fhir">
+            <name value="Contained Test Organization"/>
+         </Organization>
+      </content>
+   </entry>
+   <entry>
+      <title>Patient Patient/1333</title>
+      <id>http://example.com/base/Patient/1333</id>
+      <published>2014-10-14T09:22:54-04:00</published>
+      <link rel="self" href="http://example.com/base/Patient/1333"/>
+      <content type="text/xml">
+         <Patient xmlns="http://hl7.org/fhir">
+            <identifier>
+               <system value="urn:mrns"/>
+               <value value="253345"/>
+            </identifier>
+            <managingOrganization>
+               <reference value="Organization/65546"/>
+            </managingOrganization>
+         </Patient>
+      </content>
+   </entry>
+</feed>]]></source>
+		
+			</subsection>
+			
+			<subsection name="Contained Resources">
+				
 				<p>
 					On the other hand, if the linked resource
 					does not have an ID set, the linked resource will
 					be included in the returned bundle as a "contained" resource. In this
-					case, HAPI itself will define a local reference ID (e.g. "#001").
+					case, HAPI itself will define a local reference ID (e.g. "#1").
 				</p>
-				<source><![CDATA[Organization org = new Organization();
+				<source><![CDATA[// Create an organization, note that the organization does not have an ID
-// org.setId("Organization/65546");
+Organization org = new Organization();
-org.getName().setValue("Normal (not contained) Test Organization");
+org.getName().setValue("Contained Test Organization");
 
+// Create a patient
 Patient patient = new Patient();
 patient.setId("Patient/1333");
 patient.addIdentifier("urn:mrns", "253345");
-patient.getManagingOrganization().setResource(patient);]]></source>
+
+// Put the organization as a reference in the patient resource
+patient.getManagingOrganization().setResource(org);
+
+String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+System.out.println(encoded);]]></source>
+				
+				<p>
+					This will give the following output:
+				</p>
+				<source><![CDATA[<Patient xmlns="http://hl7.org/fhir">
+   <contained>
+      <Organization xmlns="http://hl7.org/fhir" id="1">
+         <name value="Contained Test Organization"/>
+      </Organization>
+   </contained>
+   <identifier>
+      <system value="urn:mrns"/>
+      <value value="253345"/>
+   </identifier>
+   <managingOrganization>
+      <reference value="#1"/>
+   </managingOrganization>
+</Patient>]]></source>
 				
 			</subsection>
 			

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

@@ -133,11 +133,11 @@ public class ContainedResourceEncodingTest {
 		final String expectedCompXml = parser.encodeResourceToString(this.comp);
 		logger.debug("[xmlEncoding] first encoding: {}", expectedCompXml);
 
-		assertEquals(3, this.comp.getContained().getContainedResources().size());
+		assertEquals(0, this.comp.getContained().getContainedResources().size());
 
 		final String actualCompXml = parser.encodeResourceToString(this.comp);
 
-		assertEquals(3, this.comp.getContained().getContainedResources().size());
+		assertEquals(0, this.comp.getContained().getContainedResources().size());
 
 		// second encoding - xml could not be parsed back to compositon - i.e.: patient content 4 times! should be the same
 		// as after first encoding!
@@ -145,7 +145,7 @@ public class ContainedResourceEncodingTest {
 
 		final String thirdCompXml = parser.encodeResourceToString(this.comp);
 
-		assertEquals(3, this.comp.getContained().getContainedResources().size());
+		assertEquals(0, this.comp.getContained().getContainedResources().size());
 
 		// third encoding - xml could not be parsed back to compositon i.e.: patient content 4 times! should be the same as
 		// afterfirst encoding!

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

@@ -11,6 +11,7 @@ import java.io.StringReader;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import net.sf.json.JSON;
@@ -88,6 +89,30 @@ public class JsonParserTest {
 
 	}
 	
+	@Test
+	public void testEncodeNonContained() {
+		Organization org = new Organization();
+		org.setId("Organization/65546");
+		org.getName().setValue("Contained Test Organization");
+
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier("urn:mrns", "253345");
+		patient.getManagingOrganization().setResource(org);
+		
+		Bundle b = Bundle.withResources(Collections.singletonList((IResource)patient), ourCtx, "http://foo");
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(encoded);
+		assertThat(encoded, not(containsString("contained")));
+		assertThat(encoded, containsString("\"reference\":\"Organization/65546\""));
+		
+		encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, not(containsString("contained")));
+		assertThat(encoded, containsString("\"reference\":\"Organization/65546\""));
+	}
+	
+	
 	@Test
 	public void testEncodeIds() {
 		Patient pt =new Patient();
@@ -437,6 +462,38 @@ public class JsonParserTest {
 
 	}
 
+	@Test
+	public void testEncodeContained() {
+		// Create an organization
+		Organization org = new Organization();
+		org.getName().setValue("Contained Test Organization");
+
+		// Create a patient
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier("urn:mrns", "253345");
+		patient.getManagingOrganization().setResource(org);
+		
+		// Create a bundle with just the patient resource
+		List<IResource> resources = new ArrayList<IResource>();
+		resources.add(patient);
+		Bundle b = Bundle.withResources(resources, ourCtx, "http://example.com/base");
+		
+		// Encode the buntdle
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(encoded);
+		assertThat(encoded, stringContainsInOrder(Arrays.asList("\"contained\"", "resourceType\":\"Organization", "id\":\"1\"")));
+		assertThat(encoded, containsString("reference\":\"#1\""));
+		
+		encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, stringContainsInOrder(Arrays.asList("\"contained\"", "resourceType\":\"Organization", "id\":\"1\"")));
+		assertThat(encoded, containsString("reference\":\"#1\""));
+		
+		
+	}
+
+	
 	@Test
 	public void testEncodeContainedResources() throws IOException {
 

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

@@ -12,6 +12,7 @@ import java.io.StringReader;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import java.util.UUID;
 
@@ -78,6 +79,77 @@ public class XmlParserTest {
 		 System.setProperty("file.encoding", "ISO-8859-1");
 	}
 	
+	@Test
+	public void testEncodeNonContained() {
+		// Create an organization
+		Organization org = new Organization();
+		org.setId("Organization/65546");
+		org.getName().setValue("Contained Test Organization");
+
+		// Create a patient
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier("urn:mrns", "253345");
+		patient.getManagingOrganization().setResource(org);
+		
+		// Create a list containing both resources. In a server method, you might just
+		// return this list, but here we will create a bundle to encode.
+		List<IResource> resources = new ArrayList<IResource>();
+		resources.add(org);
+		resources.add(patient);		
+		
+		// Create a bundle with both
+		Bundle b = Bundle.withResources(resources, ourCtx, "http://example.com/base");
+		
+		// Encode the buntdle
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(encoded);
+		assertThat(encoded, not(containsString("<contained>")));
+		assertThat(encoded, containsString("<reference value=\"Organization/65546\"/>"));
+		
+		encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, not(containsString("<contained>")));
+		assertThat(encoded, containsString("<reference value=\"Organization/65546\"/>"));
+		
+		
+	}
+	
+	
+	@Test
+	public void testEncodeContained() {
+		// Create an organization, note that the organization does not have an ID
+		Organization org = new Organization();
+		org.getName().setValue("Contained Test Organization");
+
+		// Create a patient
+		Patient patient = new Patient();
+		patient.setId("Patient/1333");
+		patient.addIdentifier("urn:mrns", "253345");
+		
+		// Put the organization as a reference in the patient resource
+		patient.getManagingOrganization().setResource(org);
+		
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+		ourLog.info(encoded);
+		assertThat(encoded, containsString("<contained>"));
+		assertThat(encoded, containsString("<reference value=\"#1\"/>"));
+		
+		// Create a bundle with just the patient resource
+		List<IResource> resources = new ArrayList<IResource>();
+		resources.add(patient);
+		Bundle b = Bundle.withResources(resources, ourCtx, "http://example.com/base");
+		
+		// Encode the buntdle
+		encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
+		ourLog.info(encoded);
+		assertThat(encoded, containsString("<contained>"));
+		assertThat(encoded, containsString("<reference value=\"#1\"/>"));
+		
+		
+	}
+	
+	
 	/**
 	 * Thanks to Alexander Kley!
 	 */
@@ -85,9 +157,9 @@ public class XmlParserTest {
 	public void testParseContainedBinaryResource() {
 		byte[] bin = new byte[] {0,1,2,3,4};
 	    final Binary binary = new Binary("PatientConsent", bin);
-	    binary.setId(UUID.randomUUID().toString());
+//	    binary.setId(UUID.randomUUID().toString());
 	    DocumentManifest manifest = new DocumentManifest();
-	    manifest.setId(UUID.randomUUID().toString());
+//	    manifest.setId(UUID.randomUUID().toString());
 	    manifest.setType(new CodeableConceptDt("mySystem", "PatientDocument"));
 	    manifest.setMasterIdentifier("mySystem", UUID.randomUUID().toString());
 	    manifest.addContent().setResource(binary);

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/SearchTest.java

@@ -1,7 +1,8 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -25,6 +26,8 @@ import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import com.google.common.net.UrlEscapers;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
@@ -42,6 +45,7 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenOrListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.util.PortUtil;
 
 /**
@@ -121,6 +125,23 @@ public class SearchTest {
 		assertEquals("bbb", p.getIdentifier().get(1).getValue().getValue());
 	}
 	
+	@Test
+	public void testSearchWithTokenParameter() throws Exception {
+		String token = UrlEscapers.urlFragmentEscaper().asFunction().apply("http://www.dmix.gov/vista/2957|301");
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?tokenParam="+token);
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
+		assertEquals(1, bundle.getEntries().size());
+
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals("http://www.dmix.gov/vista/2957", p.getNameFirstRep().getFamilyAsSingleString());
+		assertEquals("301", p.getNameFirstRep().getGivenAsSingleString());
+	}
+	
+	
 	@Test
 	public void testSearchByPost() throws Exception {
 		HttpPost filePost = new HttpPost("http://localhost:" + ourPort + "/Patient/_search");
@@ -325,6 +346,18 @@ public class SearchTest {
 		}
 
 		
+		@Search()
+		public List<Patient> findPatientWithToken(@RequiredParam(name = "tokenParam") TokenParam theParam) {
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+
+			Patient patient = new Patient();
+			patient.setId("1");
+			patient.addName().addFamily(theParam.getSystem()).addGiven(theParam.getValue());
+			retVal.add(patient);
+			return retVal;
+		}
+
+		
 		@Search(queryName = "findWithLinks")
 		public List<Patient> findWithLinks() {
 			ArrayList<Patient> retVal = new ArrayList<Patient>();