Merge branch 'master' of github.com:jamesagnew/hapi-fhir into hl7org_structs

Conflicts:
	hapi-fhir-android/pom.xml
	hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
	hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
	hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java
	hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
	hapi-fhir-testpage-overlay/.gitignore
	src/changes/changes.xml

.gitignore

@@ -12,6 +12,7 @@ Servers/
 *.log*
 nohup.out
 .DS_Store
+*.orig
 
 # Vagrant stuff.
 .vagrant

examples/src/main/java/example/GenericClientExample.java

@@ -74,30 +74,30 @@ public class GenericClientExample {
          // END SNIPPET: create
       }
       {
-         Patient patient = new Patient();
+          Patient patient = new Patient();
-         // START SNIPPET: createConditional
+          // START SNIPPET: createConditional
-         // One form
+          // One form
-         MethodOutcome outcome = client.create()
+          MethodOutcome outcome = client.create()
-            .resource(patient)
+                  .resource(patient)
-            .conditionalByUrl("Patient?identifier=system%7C00001")
+                  .conditionalByUrl("Patient?identifier=system%7C00001")
-            .execute();
+                  .execute();
 
-         // Another form
+          // Another form
-         MethodOutcome outcome2 = client.create()
+          MethodOutcome outcome2 = client.create()
-            .resource(patient)
+                  .resource(patient)
-            .conditional()
+                  .conditional()
-            .where(Patient.IDENTIFIER.exactly().systemAndIdentifier("system", "00001"))
+                  .where(Patient.IDENTIFIER.exactly().systemAndIdentifier("system", "00001"))
-            .execute();
+                  .execute();
-         
+
-         // This will return true if the server responded with an HTTP 201 created,
+          // This will return true if the server responded with an HTTP 201 created,
-         // otherwise it will return null.
+          // otherwise it will return null.
-         Boolean created = outcome.getCreated();
+          Boolean created = outcome.getCreated();
-         
+
-         // The ID of the created, or the pre-existing resource
+          // The ID of the created, or the pre-existing resource
-         IdDt id = outcome.getId();
+          IdDt id = outcome.getId();
-         // END SNIPPET: createConditional
+          // END SNIPPET: createConditional
       }
-      {
+       {
          // START SNIPPET: update
          Patient patient = new Patient();
          // ..populate the patient object..
@@ -125,21 +125,21 @@ public class GenericClientExample {
          // END SNIPPET: update
       }
       {
-         Patient patient = new Patient();
+          Patient patient = new Patient();
-         // START SNIPPET: updateConditional
+          // START SNIPPET: updateConditional
-         client.update()
+          client.update()
-            .resource(patient)
+                  .resource(patient)
-            .conditionalByUrl("Patient?identifier=system%7C00001")
+                  .conditionalByUrl("Patient?identifier=system%7C00001")
-            .execute();
+                  .execute();
-   
+
-         client.update()
+          client.update()
-            .resource(patient)
+                  .resource(patient)
-            .conditional()
+                  .conditional()
-            .where(Patient.IDENTIFIER.exactly().systemAndIdentifier("system", "00001"))
+                  .where(Patient.IDENTIFIER.exactly().systemAndIdentifier("system", "00001"))
-            .execute();
+                  .execute();
-         // END SNIPPET: updateConditional
+          // END SNIPPET: updateConditional
       }
-      {
+       {
          // START SNIPPET: etagupdate
          // First, let's retrive the latest version of a resource
          // from the server
@@ -176,26 +176,26 @@ public class GenericClientExample {
       }
       {
          // START SNIPPET: delete
-         BaseOperationOutcome resp = client.delete().resourceById(new IdDt("Patient", "1234")).execute();
+          BaseOperationOutcome resp = client.delete().resourceById(new IdDt("Patient", "1234")).execute();
 
          // outcome may be null if the server didn't return one
-         if (resp != null) {
+          if (resp != null) {
-            OperationOutcome outcome = (OperationOutcome) resp;
+              OperationOutcome outcome = (OperationOutcome) resp;
             System.out.println(outcome.getIssueFirstRep().getDetailsElement().getValue());
          }
          // END SNIPPET: delete
       }
-      {
+       {
-         // START SNIPPET: deleteConditional
+           // START SNIPPET: deleteConditional
-         client.delete()
+           client.delete()
-               .resourceConditionalByUrl("Patient?identifier=system%7C00001")
+                   .resourceConditionalByUrl("Patient?identifier=system%7C00001")
-               .execute();
+                   .execute();
-         
+
-         client.delete()
+           client.delete()
-               .resourceConditionalByType("Patient")
+                   .resourceConditionalByType("Patient")
-               .where(Patient.IDENTIFIER.exactly().systemAndIdentifier("system", "00001"))
+                   .where(Patient.IDENTIFIER.exactly().systemAndIdentifier("system", "00001"))
-               .execute();
+                   .execute();
-         // END SNIPPET: deleteConditional
+           // END SNIPPET: deleteConditional
       }
       {
          // START SNIPPET: search

hapi-fhir-android/pom.xml

@@ -63,20 +63,22 @@
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-android</artifactId>
 			<version>${slf4j_version}</version>
-			<scope>provided</scope>
 		</dependency>
-		<!-- <dependency> <groupId>org.codehaus.woodstox</groupId> <artifactId>stax2-api</artifactId> 
+		<dependency>
-			<version>3.1.4</version> </dependency> -->
+			<groupId>org.slf4j</groupId>
-
+			<artifactId>slf4j-api</artifactId>
+			<version>${slf4j_version}</version>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
 			<version>${commons_io_version}</version>
+			<scope>test</scope>
 		</dependency>
 
-		<!-- 
+		<!-- Android does not come with the Servlet API bundled, and MethodUtil 
-		Android does not come with the Servlet API bundled, and MethodUtil requires it
+			requires it -->
-		-->
 		<dependency>
 			<groupId>javax.servlet</groupId>
 			<artifactId>javax.servlet-api</artifactId>
@@ -135,11 +137,10 @@
 						</goals>
 						<configuration>
 							<createDependencyReducedPom>true</createDependencyReducedPom>
-							<!--<minimizeJar>true</minimizeJar>-->
+							<!-- <minimizeJar>true</minimizeJar>  -->
 							<artifactSet>
 								<includes>
 									<include>commons-codec:commons-codec</include>
-									<include>commons-io:commons-io</include>
 									<include>ca.uhn.hapi.fhir:hapi-fhir-base</include>
 									<include>ca.uhn.hapi.fhir:hapi-fhir-structures-dstu</include>
 									<include>ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2</include>
@@ -148,7 +149,7 @@
 									<include>javax.xml.stream:stax-api</include>
 									<include>javax.servlet:javax.servlet-api</include>
 									<include>org.codehaus.woodstox:stax2-api</include>
-									<!--<include>org.slf4j:slf4j*</include>-->
+									<!-- <include>org.slf4j:slf4j*</include> -->
 									<include>org.apache.commons:*</include>
 									<include>org.apache.httpcomponents:*</include>
 									<include>org.glassfish:javax.json</include>
@@ -179,7 +180,7 @@
 			</plugin>
 		</plugins>
 	</build>
-	
+
 	<profiles>
 		<profile>
 			<id>DIST</id>
@@ -208,5 +209,5 @@
 			</build>
 		</profile>
 	</profiles>
-	
+
 </project>

hapi-fhir-android/src/main/java/ca/uhn/fhir/android/AndroidLoader.java

@@ -0,0 +1,14 @@
+package ca.uhn.fhir.android;
+
+import ca.uhn.fhir.context.FhirContext;
+
+public class AndroidLoader {
+
+	public static void main(String[] theArgs) {
+		FhirContext ctx = FhirContext.forDstu2();
+		ctx.newJsonParser();
+		ctx.newXmlParser();
+		ctx.newRestfulGenericClient("");
+	}
+	
+}

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

@@ -85,29 +85,34 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
 		for (Class<? extends IBase> next : myChoiceTypes) {
 
 			String elementName;
-			String alternateElementName = null;
 			BaseRuntimeElementDefinition<?> nextDef;
 			if (IBaseResource.class.isAssignableFrom(next)) {
 				elementName = getElementName() + StringUtils.capitalize(next.getSimpleName());
-				alternateElementName = getElementName() + "Reference";
 				List<Class<? extends IBaseResource>> types = new ArrayList<Class<? extends IBaseResource>>();
 				types.add((Class<? extends IBaseResource>) next);
 				nextDef = new RuntimeResourceReferenceDefinition(elementName, types);
 				nextDef.sealAndInitialize(theContext, theClassToElementDefinitions);
+				
+				myNameToChildDefinition.put(getElementName() + "Reference", nextDef);
+				myNameToChildDefinition.put(getElementName() + "Resource", nextDef);
+				
 			} else {
 				nextDef = theClassToElementDefinitions.get(next);
 				elementName = getElementName() + StringUtils.capitalize(nextDef.getName());
 			}
 
 			myNameToChildDefinition.put(elementName, nextDef);
-			if (alternateElementName != null) {
-				myNameToChildDefinition.put(alternateElementName, nextDef);
-			}
 			
 			if (IBaseResource.class.isAssignableFrom(next)) {
 				Class<? extends IBase> refType = theContext.getVersion().getResourceReferenceType();
 				myDatatypeToElementDefinition.put(refType, nextDef);
-				alternateElementName = getElementName() + "Reference";
+				
+				String alternateElementName;
+				if (theContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU1)) {
+					alternateElementName = getElementName() + "Resource";
+				} else {
+					alternateElementName = getElementName() + "Reference";
+				}
 				myDatatypeToElementName.put(refType, alternateElementName);
 			}
 			

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

@@ -38,6 +38,8 @@ import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
 
 public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildDefinition {
 
+	private static final String VALUE_REFERENCE = "valueReference";
+	private static final String VALUE_RESOURCE = "valueResource";
 	private Map<String, BaseRuntimeElementDefinition<?>> myAttributeNameToDefinition;
 	private Map<Class<? extends IBase>, String> myDatatypeToAttributeName;
 	private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myDatatypeToDefinition;
@@ -53,7 +55,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 			public List<IBase> getValues(Object theTarget) {
 				ExtensionDt target = (ExtensionDt) theTarget;
 				if (target.getValue() != null) {
-					return Collections.singletonList((IBase)target.getValue());
+					return Collections.singletonList((IBase) target.getValue());
 				}
 				ArrayList<IBase> retVal = new ArrayList<IBase>(target.getUndeclaredExtensions());
 				return retVal;
@@ -118,10 +120,10 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 
 		for (BaseRuntimeElementDefinition<?> next : theClassToElementDefinitions.values()) {
 			if (next instanceof IRuntimeDatatypeDefinition) {
-//				if (next.getName().equals("CodeableConcept")) {
+				// if (next.getName().equals("CodeableConcept")) {
-//					System.out.println();
+				// System.out.println();
-//				}
+				// }
-				
+
 				if (!((IRuntimeDatatypeDefinition) next).isSpecialization()) {
 					String attrName = createExtensionChildName(next);
 					datatypeAttributeNameToDefinition.put(attrName, next);
@@ -142,22 +144,29 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		}
 
 		/*
-		 * Resource reference - The correct name is 'valueReference', but 
+		 * Resource reference - The correct name is 'valueReference' in DSTU2 and 'valueResource' in DSTU1
-		 * we allow for valueResource because some incorrect parsers may use this
 		 */
-		addReferenceBinding(theContext, theClassToElementDefinitions, "valueResource");
+		addReferenceBinding(theContext, theClassToElementDefinitions, VALUE_RESOURCE);
-		addReferenceBinding(theContext, theClassToElementDefinitions, "valueReference");
+		addReferenceBinding(theContext, theClassToElementDefinitions, VALUE_REFERENCE);
 	}
 
 	private void addReferenceBinding(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions, String value) {
-		myDatatypeToAttributeName.put(theContext.getVersion().getResourceReferenceType(), value);
 		List<Class<? extends IBaseResource>> types = new ArrayList<Class<? extends IBaseResource>>();
 		types.add(IBaseResource.class);
 		RuntimeResourceReferenceDefinition def = new RuntimeResourceReferenceDefinition(value, types);
 		def.sealAndInitialize(theContext, theClassToElementDefinitions);
+
 		myAttributeNameToDefinition.put(value, def);
-		myDatatypeToDefinition.put(BaseResourceReferenceDt.class, def);
+		/*
-		myDatatypeToDefinition.put(theContext.getVersion().getResourceReferenceType(), def);
+		 * Resource reference - The correct name is 'valueReference' in DSTU2 and 'valueResource' in DSTU1
+		 */
+		boolean dstu1 = (theContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU1));
+		if ((dstu1 && (value != VALUE_REFERENCE)) || (!dstu1 && (value != VALUE_RESOURCE))) {
+			myDatatypeToAttributeName.put(theContext.getVersion().getResourceReferenceType(), value);
+			myDatatypeToDefinition.put(BaseResourceReferenceDt.class, def);
+			myDatatypeToDefinition.put(theContext.getVersion().getResourceReferenceType(), def);
+		}
+
 	}
 
 	public static String createExtensionChildName(BaseRuntimeElementDefinition<?> next) {

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

@@ -293,6 +293,7 @@ public class Bundle extends BaseBundle /* implements IElement */{
 		return myLinkSelf;
 	}
 
+	/*
 	public InstantDt getPublished() {
 		InstantDt retVal = (InstantDt) getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED);
 		if (retVal == null) {
@@ -301,6 +302,7 @@ public class Bundle extends BaseBundle /* implements IElement */{
 		}
 		return retVal;
 	}
+	*/
 
 	/**
 	 * Retrieves a resource from a bundle given its logical ID.
@@ -394,9 +396,11 @@ public class Bundle extends BaseBundle /* implements IElement */{
 		myCategories = theCategories;
 	}
 
+	/*
 	public void setPublished(InstantDt thePublished) {
 		getResourceMetadata().put(ResourceMetadataKeyEnum.PUBLISHED, thePublished);
 	}
+	/*
 
 	public void setType(BoundCodeDt<BundleTypeEnum> theType) {
 		myType = theType;

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

@@ -20,7 +20,7 @@ package ca.uhn.fhir.model.api;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.*;
 
 import java.util.ArrayList;
 import java.util.Collections;

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

@@ -95,19 +95,20 @@ import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseContainedDt;
 import ca.uhn.fhir.model.base.composite.BaseNarrativeDt;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
+import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.DecimalDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.primitive.UriDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.UrlUtil;
 
 /**
- * This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use
+ * This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use {@link FhirContext#newJsonParser()} to get an instance.
- * {@link FhirContext#newJsonParser()} to get an instance.
  */
 public class JsonParser extends BaseParser implements IParser {
 
@@ -196,7 +197,6 @@ public class JsonParser extends BaseParser implements IParser {
 		writeTagWithTextNode(eventWriter, "title", theBundle.getTitle());
 		writeTagWithTextNode(eventWriter, "id", theBundle.getBundleId());
 		writeOptionalTagWithTextNode(eventWriter, "updated", theBundle.getUpdated());
-		writeOptionalTagWithTextNode(eventWriter, "published", theBundle.getPublished());
 
 		boolean linkStarted = false;
 		linkStarted = writeAtomLinkInDstu1Format(eventWriter, "self", theBundle.getLinkSelf(), linkStarted);
@@ -353,7 +353,8 @@ public class JsonParser extends BaseParser implements IParser {
 		theEventWriter.writeEnd();
 	}
 
-	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonGenerator theWriter, IBase theNextValue, BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theIsSubElementWithinResource) throws IOException {
+	private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonGenerator theWriter, IBase theNextValue,
+			BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theContainedResource) throws IOException {
 
 		switch (theChildDef.getChildType()) {
 		case ID_DATATYPE: {
@@ -414,7 +415,7 @@ public class JsonParser extends BaseParser implements IParser {
 			if (theNextValue instanceof IBaseExtension) {
 				theWriter.write("url", ((IBaseExtension<?>) theNextValue).getUrl());
 			}
-			encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theWriter, childCompositeDef, theIsSubElementWithinResource);
+			encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theWriter, childCompositeDef, theContainedResource);
 			theWriter.writeEnd();
 			break;
 		}
@@ -488,7 +489,8 @@ public class JsonParser extends BaseParser implements IParser {
 
 	}
 
-	private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonGenerator theEventWriter, List<? extends BaseRuntimeChildDefinition> theChildren, boolean theIsSubElementWithinResource) throws IOException {
+	private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonGenerator theEventWriter,
+			List<? extends BaseRuntimeChildDefinition> theChildren, boolean theContainedResource) throws IOException {
 		for (BaseRuntimeChildDefinition nextChild : theChildren) {
 			if (nextChild.getElementName().equals("extension") || nextChild.getElementName().equals("modifierExtension")) {
 				continue;
@@ -507,15 +509,15 @@ 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, theIsSubElementWithinResource);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, narr, type, childName, theContainedResource);
 						continue;
 					}
 				}
 			} else if (nextChild instanceof RuntimeChildContainedResources) {
-				if (theIsSubElementWithinResource == false) {
+				if (theContainedResource == false) {
 					String childName = nextChild.getValidChildNames().iterator().next();
 					BaseRuntimeElementDefinition<?> child = nextChild.getChildByName(childName);
-					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, null, child, childName, theIsSubElementWithinResource);
+					encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, null, child, childName, theContainedResource);
 				}
 				continue;
 			}
@@ -535,7 +537,7 @@ public class JsonParser extends BaseParser implements IParser {
 			for (IBase nextValue : values) {
 				if (nextValue == null || nextValue.isEmpty()) {
 					if (nextValue instanceof BaseContainedDt) {
-						if (theIsSubElementWithinResource || getContainedResources().isEmpty()) {
+						if (theContainedResource || getContainedResources().isEmpty()) {
 							continue;
 						}
 					} else {
@@ -551,7 +553,7 @@ public class JsonParser extends BaseParser implements IParser {
 				}
 				boolean primitive = childDef.getChildType() == ChildTypeEnum.PRIMITIVE_DATATYPE;
 
-				if ((childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES||childDef.getChildType()==ChildTypeEnum.CONTAINED_RESOURCE_LIST) && theIsSubElementWithinResource) {
+				if ((childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES||childDef.getChildType()==ChildTypeEnum.CONTAINED_RESOURCE_LIST) && theContainedResource) {
 					continue;
 				}
 
@@ -573,15 +575,15 @@ 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, theIsSubElementWithinResource);
+							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource);
-						} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theIsSubElementWithinResource) {
+						} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
 							// suppress narratives from contained resources
 						} else {
-							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theIsSubElementWithinResource);
+							encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theContainedResource);
 						}
 						currentChildName = childName;
 					} else {
-						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theIsSubElementWithinResource);
+						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource);
 					}
 
 					if (primitive) {
@@ -655,13 +657,15 @@ public class JsonParser extends BaseParser implements IParser {
 		}
 	}
 
-	private void encodeCompositeElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonGenerator theEventWriter, BaseRuntimeElementCompositeDefinition<?> resDef, boolean theIsSubElementWithinResource) throws IOException, DataFormatException {
+	private void encodeCompositeElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonGenerator theEventWriter,
+			BaseRuntimeElementCompositeDefinition<?> resDef, boolean theContainedResource) throws IOException, DataFormatException {
 		extractAndWriteExtensionsAsDirectChild(theNextValue, theEventWriter, resDef, theResDef, theResource, null);
-		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, resDef.getExtensions(), theIsSubElementWithinResource);
+		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, resDef.getExtensions(), theContainedResource);
-		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, resDef.getChildren(), theIsSubElementWithinResource);
+		encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, resDef.getChildren(), theContainedResource);
 	}
 
-	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull, boolean theContainedResource) throws IOException {
+	private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonGenerator theEventWriter, String theObjectNameOrNull, boolean theContainedResource)
+			throws IOException {
 		String resourceId = null;
 		if (theResource instanceof IResource) {
 			IResource res = (IResource) theResource;
@@ -702,20 +706,22 @@ public class JsonParser extends BaseParser implements IParser {
 
 		if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1) && theResource instanceof IResource) {
 			IResource resource = (IResource) theResource;
+			// Object securityLabelRawObj =
 
+			List<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
+			List<IdDt> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
+			TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(resource);
 			InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
 			IdDt resourceId = resource.getId();
 			String versionIdPart = resourceId.getVersionIdPart();
 			if (isBlank(versionIdPart)) {
 				versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
 			}
-			List<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
+
-			List<IdDt> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
-			TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(resource);
 			if (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, profiles) == false) {
 				theEventWriter.writeStartObject("meta");
-				writeOptionalTagWithTextNode(theEventWriter, "versionId", resource.getId().getVersionIdPart());
+				writeOptionalTagWithTextNode(theEventWriter, "versionId", versionIdPart);
-				writeOptionalTagWithTextNode(theEventWriter, "lastUpdated", ResourceMetadataKeyEnum.UPDATED.get(resource));
+				writeOptionalTagWithTextNode(theEventWriter, "lastUpdated", updated);
 
 				if (profiles != null && profiles.isEmpty() == false) {
 					theEventWriter.writeStartArray("profile");
@@ -1175,31 +1181,30 @@ public class JsonParser extends BaseParser implements IParser {
 		}
 	}
 
-	private void parseExtensionInDstu2Style(boolean theModifier, ParserState<?> theState, String theParentExtensionUrl, String theExtensionUrl, JsonArray theValues) {
+	// private void parseExtensionInDstu2Style(boolean theModifier, ParserState<?> theState, String theParentExtensionUrl, String theExtensionUrl, JsonArray theValues) {
-		String extUrl = UrlUtil.constructAbsoluteUrl(theParentExtensionUrl, theExtensionUrl);
+	// String extUrl = UrlUtil.constructAbsoluteUrl(theParentExtensionUrl, theExtensionUrl);
-		theState.enteringNewElementExtension(null, extUrl, theModifier);
+	// theState.enteringNewElementExtension(null, extUrl, theModifier);
-
+	//
-		for (int extIdx = 0; extIdx < theValues.size(); extIdx++) {
+	// for (int extIdx = 0; extIdx < theValues.size(); extIdx++) {
-			JsonObject nextExt = theValues.getJsonObject(extIdx);
+	// JsonObject nextExt = theValues.getJsonObject(extIdx);
-			for (String nextKey : nextExt.keySet()) {
+	// for (String nextKey : nextExt.keySet()) {
-				// if (nextKey.startsWith("value") && nextKey.length() > 5 &&
+	// // if (nextKey.startsWith("value") && nextKey.length() > 5 &&
-				// myContext.getRuntimeChildUndeclaredExtensionDefinition().getChildByName(nextKey) != null) {
+	// // myContext.getRuntimeChildUndeclaredExtensionDefinition().getChildByName(nextKey) != null) {
-				JsonValue jsonVal = nextExt.get(nextKey);
+	// JsonValue jsonVal = nextExt.get(nextKey);
-				if (jsonVal.getValueType() == ValueType.ARRAY) {
+	// if (jsonVal.getValueType() == ValueType.ARRAY) {
-					/*
+	// /*
-					 * Extension children which are arrays are sub-extensions. Any other value type should be treated as
+	// * Extension children which are arrays are sub-extensions. Any other value type should be treated as a value.
-					 * a value.
+	// */
-					 */
+	// JsonArray arrayValue = (JsonArray) jsonVal;
-					JsonArray arrayValue = (JsonArray) jsonVal;
+	// parseExtensionInDstu2Style(theModifier, theState, extUrl, nextKey, arrayValue);
-					parseExtensionInDstu2Style(theModifier, theState, extUrl, nextKey, arrayValue);
+	// } else {
-				} else {
+	// parseChildren(theState, nextKey, jsonVal, null, null);
-					parseChildren(theState, nextKey, jsonVal, null, null);
+	// }
-				}
+	// }
-			}
+	// }
-		}
+	//
-
+	// theState.endingElement();
-		theState.endingElement();
+	// }
-	}
 
 	@Override
 	public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {

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

@@ -683,8 +683,6 @@ class ParserState<T> {
 		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
 			if ("entry".equals(theLocalPart) && verifyNamespace(XmlParser.ATOM_NS, theNamespaceURI)) {
 				push(new AtomEntryState(myInstance, myResourceType));
-			} else if (theLocalPart.equals("published")) {
-				push(new AtomPrimitiveState(myInstance.getPublished()));
 			} else if (theLocalPart.equals("title")) {
 				push(new AtomPrimitiveState(myInstance.getTitle()));
 			} else if ("id".equals(theLocalPart)) {
@@ -900,7 +898,7 @@ class ParserState<T> {
 				if (myInstance instanceof IIdentifiableElement) {
 					((IIdentifiableElement) myInstance).setElementSpecificId((theValue));
 				} else {
-					((IResource)myInstance).setId(new IdDt(theValue));
+					((IResource) myInstance).setId(new IdDt(theValue));
 				}
 			} else if ("contentType".equals(theName)) {
 				myInstance.setContentType(theValue);
@@ -1393,7 +1391,7 @@ class ParserState<T> {
 					res.getId().setValue('#' + res.getId().getIdPart());
 				}
 			}
-			
+
 			IBaseResource preResCurrentElement = getPreResourceState().getCurrentElement();
 			RuntimeResourceDefinition def = myContext.getResourceDefinition(preResCurrentElement);
 			def.getChildByName("contained").getMutator().addValue(preResCurrentElement, res);
@@ -1496,6 +1494,7 @@ class ParserState<T> {
 	private class ElementCompositeState extends BaseState {
 
 		private BaseRuntimeElementCompositeDefinition<?> myDefinition;
+
 		public BaseRuntimeElementCompositeDefinition<?> getDefinition() {
 			return myDefinition;
 		}
@@ -1623,8 +1622,8 @@ class ParserState<T> {
 					ParserState<T>.PreResourceStateHapi state = new PreResourceStateHapi(myInstance, child.getMutator(), null);
 					push(state);
 				} else {
-				ParserState<T>.PreResourceStateHl7Org state = new PreResourceStateHl7Org(myInstance, child.getMutator(), null);
+					ParserState<T>.PreResourceStateHl7Org state = new PreResourceStateHl7Org(myInstance, child.getMutator(), null);
-				push(state);
+					push(state);
 				}
 				return;
 			}
@@ -1729,10 +1728,9 @@ class ParserState<T> {
 
 	}
 
-
 	private class SecurityLabelElementStateHapi extends ElementCompositeState {
 
-		public SecurityLabelElementStateHapi(ParserState<T>.PreResourceState thePreResourceState,BaseRuntimeElementCompositeDefinition<?> theDef, BaseCodingDt codingDt) {
+		public SecurityLabelElementStateHapi(ParserState<T>.PreResourceState thePreResourceState, BaseRuntimeElementCompositeDefinition<?> theDef, BaseCodingDt codingDt) {
 			super(thePreResourceState, theDef, codingDt);
 		}
 
@@ -1741,7 +1739,6 @@ class ParserState<T> {
 			pop();
 		}
 
-
 	}
 
 	private class MetaElementState extends BaseState {
@@ -1761,8 +1758,8 @@ class ParserState<T> {
 		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
 			if (theLocalPart.equals("versionId")) {
 				push(new MetaVersionElementState(getPreResourceState(), myMap));
-//			} else if (theLocalPart.equals("profile")) {
+				// } else if (theLocalPart.equals("profile")) {
-//				
+				//
 			} else if (theLocalPart.equals("lastUpdated")) {
 				InstantDt updated = new InstantDt();
 				push(new PrimitiveState(getPreResourceState(), updated));
@@ -1774,7 +1771,7 @@ class ParserState<T> {
 					securityLabels = new ArrayList<BaseCodingDt>();
 					myMap.put(ResourceMetadataKeyEnum.SECURITY_LABELS, securityLabels);
 				}
-				BaseCodingDt securityLabel= myContext.getVersion().newCodingDt();
+				BaseCodingDt securityLabel = myContext.getVersion().newCodingDt();
 				BaseRuntimeElementCompositeDefinition<?> codinfDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(securityLabel.getClass());
 				push(new SecurityLabelElementStateHapi(getPreResourceState(), codinfDef, securityLabel));
 				securityLabels.add(securityLabel);
@@ -1903,33 +1900,30 @@ class ParserState<T> {
 			if (myEntry == null) {
 				myObject = (T) getCurrentElement();
 			}
-			
+
 			IResource nextResource = (IResource) getCurrentElement();
 			String version = ResourceMetadataKeyEnum.VERSION.get(nextResource);
 			String resourceName = myContext.getResourceDefinition(nextResource).getName();
 			String bundleIdPart = nextResource.getId().getIdPart();
 			if (isNotBlank(bundleIdPart)) {
-//				if (isNotBlank(entryBaseUrl)) {
+				// if (isNotBlank(entryBaseUrl)) {
-//					nextResource.setId(new IdDt(entryBaseUrl, resourceName, bundleIdPart, version));
+				// nextResource.setId(new IdDt(entryBaseUrl, resourceName, bundleIdPart, version));
-//				} else {
+				// } else {
-					nextResource.setId(new IdDt(null, resourceName, bundleIdPart, version));
+				nextResource.setId(new IdDt(null, resourceName, bundleIdPart, version));
-//				}
+				// }
 			}
 
-
 		}
 
-		
-
 		@Override
 		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
 			super.enteringNewElement(theNamespaceURI, theLocalPart);
 			if (myEntry != null) {
 				myEntry.setResource((IResource) getCurrentElement());
 			}
-				if (myMutator != null) {
+			if (myMutator != null) {
-					myMutator.addValue(myTarget, getCurrentElement());
+				myMutator.addValue(myTarget, getCurrentElement());
-				}
+			}
 		}
 
 	}
@@ -1956,13 +1950,15 @@ class ParserState<T> {
 			if (myTarget == null) {
 				myObject = (T) getCurrentElement();
 			}
-			
+
 			if (getCurrentElement() instanceof IDomainResource) {
 				IDomainResource elem = (IDomainResource) getCurrentElement();
 				String resourceName = myContext.getResourceDefinition(elem).getName();
 				String versionId = elem.getMeta().getVersionId();
-				if (StringUtils.isNotBlank(versionId)) {
+				if (StringUtils.isBlank(elem.getId().getIdPart())) {
-				elem.getIdElement().setValue(resourceName + "/" + elem.getId().getIdPart() + "/_history/" + versionId);
+					// Resource has no ID
+				} else if (StringUtils.isNotBlank(versionId)) {
+					elem.getIdElement().setValue(resourceName + "/" + elem.getId().getIdPart() + "/_history/" + versionId);
 				} else {
 					elem.getIdElement().setValue(resourceName + "/" + elem.getId().getIdPart());
 				}
@@ -2063,12 +2059,12 @@ class ParserState<T> {
 		@Override
 		public void wereBack() {
 			final boolean bundle = "Bundle".equals(myContext.getResourceDefinition(myInstance).getName());
-			
+
 			FhirTerser terser = myContext.newTerser();
 			terser.visit(myInstance, new IModelVisitor() {
 
 				@Override
-				public void acceptElement(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
+				public void acceptElement(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
 					if (theElement instanceof BaseResourceReferenceDt) {
 						BaseResourceReferenceDt nextRef = (BaseResourceReferenceDt) theElement;
 						String ref = nextRef.getReference().getValue();
@@ -2082,7 +2078,7 @@ class ParserState<T> {
 								}
 							}
 						}
-					}else					if (theElement instanceof IReference) {
+					} else if (theElement instanceof IReference) {
 						IReference nextRef = (IReference) theElement;
 						String ref = nextRef.getReference().getValue();
 						if (isNotBlank(ref)) {
@@ -2099,8 +2095,8 @@ class ParserState<T> {
 				}
 
 				@Override
-				public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
+				public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
-					acceptElement(theNextExt.getValue(), null, null);
+					acceptElement(theNextExt.getValue(), null, null, null);
 				}
 			});
 
@@ -2132,7 +2128,7 @@ class ParserState<T> {
 				}
 
 			}
-			
+
 		}
 
 	}
@@ -2547,13 +2543,12 @@ class ParserState<T> {
 			// TODO: this is not very efficient
 			String value = getDt().getValueAsString();
 			myHl7OrgDatatype.setValueAsString(value);
-			
+
 			super.doPop();
 		}
-		
+
-		
 	}
-	
+
 	private class XhtmlState extends BaseState {
 		private int myDepth;
 		private XhtmlDt myDt;
@@ -2583,7 +2578,7 @@ class ParserState<T> {
 		protected void doPop() {
 			pop();
 		}
-		
+
 		@Override
 		public void endingElement() throws DataFormatException {
 			if (myJsonMode) {

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

@@ -271,7 +271,6 @@ public class XmlParser extends BaseParser implements IParser {
 		}
 
 		writeOptionalTagWithTextNode(eventWriter, "updated", theBundle.getUpdated());
-		writeOptionalTagWithTextNode(eventWriter, "published", theBundle.getPublished());
 
 		if (StringUtils.isNotBlank(theBundle.getAuthorName().getValue())) {
 			eventWriter.writeStartElement("author");
@@ -804,6 +803,7 @@ public class XmlParser extends BaseParser implements IParser {
 					if (updated != null) {
 						writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
 					}
+
 					for (IdDt profile : profiles) {
 						theEventWriter.writeStartElement("profile");
 						theEventWriter.writeAttribute("value", profile.getValue());

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/MethodOutcome.java

@@ -135,7 +135,7 @@ public class MethodOutcome {
 	}
 
 	/**
-	 * This will be set to {@link Boolean#TRUE} for instance of MethodOutcome which are 
+	 * This will be set to {@link Boolean#TRUE} for instance of MethodOutcome which are
 	 * returned to client instances, if the server has responded with an HTTP 201 Created.
 	 */
 	public Boolean getCreated() {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/GenericClient.java

@@ -20,8 +20,7 @@ package ca.uhn.fhir.rest.client;
  * #L%
  */
 
-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.IOException;
 import java.io.Reader;
@@ -1413,7 +1412,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 						+ "the bundle return type for the client by adding \".returnBundle(org.hl7.fhir.instance.model.Bundle.class)\" to your search method call before the \".execute()\" method");
 			}
 
-			IClientResponseHandler binding;
+			IClientResponseHandler<? extends IBase> binding;
 			if (myReturnBundleType != null) {
 				binding = new ResourceResponseHandler(myReturnBundleType, null);
 			} else {
@@ -1581,8 +1580,8 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			myBundle = theResources;
 		}
 
-		public TransactionExecutable(List<IBaseResource> theResources) {
+		public TransactionExecutable(List<? extends IBaseResource> theResources) {
-			myResources = theResources;
+			myResources = new ArrayList<IBaseResource>(theResources);
 		}
 
 		public TransactionExecutable(IBaseBundle theBundle) {
@@ -1619,7 +1618,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		}
 
 		@Override
-		public ITransactionTyped<List<IBaseResource>> withResources(List<IBaseResource> theResources) {
+		public ITransactionTyped<List<IBaseResource>> withResources(List<? extends IBaseResource> theResources) {
 			Validate.notNull(theResources, "theResources must not be null");
 			return new TransactionExecutable<List<IBaseResource>>(theResources);
 		}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/ITransaction.java

@@ -32,7 +32,7 @@ public interface ITransaction {
 	/**
 	 * Use a list of resources as the transaction input
 	 */
-	ITransactionTyped<List<IBaseResource>> withResources(List<IBaseResource> theResources);
+	ITransactionTyped<List<IBaseResource>> withResources(List<? extends IBaseResource> theResources);
 	
 	/**
 	 * Use a DSTU1 Bundle (Atom) as the transaction input

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseResourceReturningMethodBinding.java

@@ -279,7 +279,7 @@ abstract class BaseResourceReturningMethodBinding extends BaseMethodBinding<Obje
 						return;
 					}
 				}
-				RestfulServerUtils.streamResponseAsResource(theServer, response, resource, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, respondGzip, theRequest.getFhirServerBase());
+				RestfulServerUtils.streamResponseAsResource(theServer, response, resource, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, Constants.STATUS_HTTP_200_OK, respondGzip, theRequest.getFhirServerBase(), isAddContentLocationHeader());
 				break;
 			} else {
 				Set<Include> includes = getRequestIncludesFromParams(params);
@@ -312,7 +312,7 @@ abstract class BaseResourceReturningMethodBinding extends BaseMethodBinding<Obje
 							return;
 						}
 					}
-					RestfulServerUtils.streamResponseAsResource(theServer, response, (IResource) resBundle, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, Constants.STATUS_HTTP_200_OK, theRequest.isRespondGzip(), theRequest.getFhirServerBase());
+					RestfulServerUtils.streamResponseAsResource(theServer, response, (IResource) resBundle, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, Constants.STATUS_HTTP_200_OK, theRequest.isRespondGzip(), theRequest.getFhirServerBase(), isAddContentLocationHeader());
 				}
 
 				break;
@@ -336,12 +336,19 @@ abstract class BaseResourceReturningMethodBinding extends BaseMethodBinding<Obje
 				}
 			}
 
-			RestfulServerUtils.streamResponseAsResource(theServer, response, resource, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, respondGzip, theRequest.getFhirServerBase());
+			RestfulServerUtils.streamResponseAsResource(theServer, response, resource, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, Constants.STATUS_HTTP_200_OK, respondGzip, theRequest.getFhirServerBase(), isAddContentLocationHeader());
 			break;
 		}
 		}
 	}
 
+	/**
+	 * Should the response include a Content-Location header. Search method bunding (and any others?) may override this to disable the content-location, since it doesn't make sense
+	 */
+	protected boolean isAddContentLocationHeader() {
+		return true;
+	}
+
 	/**
 	 * Subclasses may override
 	 * 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/SearchMethodBinding.java

@@ -132,6 +132,11 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 		return RestfulOperationTypeEnum.SEARCH_TYPE;
 	}
 
+	@Override
+	protected BundleTypeEnum getResponseBundleType() {
+		return BundleTypeEnum.SEARCHSET;
+	}
+
 	@Override
 	public ReturnTypeEnum getReturnType() {
 		return ReturnTypeEnum.BUNDLE;
@@ -289,13 +294,9 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 
 	}
 
-	public void setResourceType(Class<? extends IResource> resourceType) {
-		this.myDeclaredResourceType = resourceType;
-	}
-
 	@Override
-	public String toString() {
+	protected boolean isAddContentLocationHeader() {
-		return getMethod().toString();
+		return false;
 	}
 
 	private List<String> processWhitelistAndBlacklist(List<String> theQualifiedNames, Set<String> theQualifierWhitelist, Set<String> theQualifierBlacklist) {
@@ -313,6 +314,15 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 		return retVal;
 	}
 
+	public void setResourceType(Class<? extends IResource> resourceType) {
+		this.myDeclaredResourceType = resourceType;
+	}
+
+	@Override
+	public String toString() {
+		return getMethod().toString();
+	}
+
 	public static BaseHttpClientInvocation createSearchInvocation(FhirContext theContext, String theResourceName, Map<String, List<String>> theParameters, IdDt theId, String theCompartmentName,
 			SearchStyleEnum theSearchStyle) {
 		SearchStyleEnum searchStyle = theSearchStyle;
@@ -473,9 +483,4 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 
 	}
 
-	@Override
-	protected BundleTypeEnum getResponseBundleType() {
-		return BundleTypeEnum.SEARCHSET;
-	}
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/Dstu1BundleFactory.java

@@ -203,8 +203,6 @@ public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 		addResourcesToBundle(new ArrayList<IBaseResource>(resourceList), theBundleType, theServerBase, theServer.getBundleInclusionRule(), theIncludes);
 		addRootPropertiesToBundle(null, theServerBase, theCompleteUrl, theResult.size(), theBundleType);
 
-		myBundle.setPublished(theResult.getPublished());
-	
 		if (theServer.getPagingProvider() != null) {
 			int limit;
 			limit = theLimit != null ? theLimit : theServer.getPagingProvider().getDefaultPageSize();
@@ -232,10 +230,6 @@ public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 			myBundle.getBundleId().setValue(UUID.randomUUID().toString());
 		}
 		
-		if (myBundle.getPublished().isEmpty()) {
-			myBundle.getPublished().setToCurrentTimeInLocalTimeZone();
-		}
-		
 		if (myBundle.getLinkBase().isEmpty()) {
 			myBundle.getLinkBase().setValue(theServerBase);
 		}
@@ -269,7 +263,6 @@ public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 		
 		myBundle.getAuthorName().setValue(theAuthor);
 		myBundle.getBundleId().setValue(UUID.randomUUID().toString());
-		myBundle.getPublished().setToCurrentTimeInLocalTimeZone();
 		myBundle.getLinkBase().setValue(theServerBase);
 		myBundle.getLinkSelf().setValue(theCompleteUrl);
 		myBundle.getType().setValueAsEnum(theBundleType);

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

@@ -30,10 +30,19 @@ import org.apache.commons.lang3.StringUtils;
  */
 public class IncomingRequestAddressStrategy implements IServerAddressStrategy {
 
+	private String myServletPath;
+
 	@Override
 	public String determineServerBase(ServletContext theServletContext, HttpServletRequest theRequest) {
 		String requestFullPath = StringUtils.defaultString(theRequest.getRequestURI());
-		String servletPath = StringUtils.defaultString(theRequest.getServletPath());
+		
+		String servletPath;
+		if (myServletPath != null) {
+			servletPath = myServletPath;
+		} else {
+			servletPath = StringUtils.defaultString(theRequest.getServletPath());
+		}
+		
 		StringBuffer requestUrl = theRequest.getRequestURL();
 		String servletContextPath = "";
 		if (theServletContext != null) {
@@ -48,7 +57,9 @@ public class IncomingRequestAddressStrategy implements IServerAddressStrategy {
 		}
 
 		int startOfPath = requestUrl.indexOf("//");
-		if (startOfPath != -1 && (startOfPath + 2) < requestUrl.length()) {
+		int requestUrlLength = requestUrl.length();
+
+		if (startOfPath != -1 && (startOfPath + 2) < requestUrlLength) {
 			startOfPath = requestUrl.indexOf("/", startOfPath + 2);
 		}
 		if (startOfPath == -1) {
@@ -56,9 +67,9 @@ public class IncomingRequestAddressStrategy implements IServerAddressStrategy {
 		}
 
 		int contextIndex;
-		if (servletPath.length() == 0) {
+		if (servletPath.length() == 0 || servletPath.equals("/")) {
 			if (requestPath.length() == 0) {
-				contextIndex = requestUrl.length();
+				contextIndex = requestUrlLength;
 			} else {
 				contextIndex = requestUrl.indexOf(requestPath, startOfPath);
 			}
@@ -68,8 +79,30 @@ public class IncomingRequestAddressStrategy implements IServerAddressStrategy {
 
 		String fhirServerBase;
 		int length = contextIndex + servletPath.length();
+		if (length > requestUrlLength) {
+			length = requestUrlLength;
+		}
 		fhirServerBase = requestUrl.substring(0, length);
 		return fhirServerBase;
 	}
 
+	/**
+	 * If set to a non-null value (default is <code>null</code>), this address strategy assumes that the FHIR endpoint is deployed to the given servlet path within the context. This is useful in some
+	 * deployments where it isn't obvious to the servlet which part of the path is actually the root path to reach the servlet.
+	 * <p>
+	 * Example values could be:
+	 * <ul>
+	 * <li>null</li>
+	 * <li>/</li>
+	 * <li>/base</li>
+	 * </ul>
+	 * </p>
+	 * <p>
+	 * <b>Wildcards are not supported!</b>
+	 * </p>
+	 */
+	public void setServletPath(String theServletPath) {
+		myServletPath = theServletPath;
+	}
+
 }

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

@@ -490,7 +490,7 @@ public class RestfulServer extends HttpServlet {
 					return;
 				}
 			}
-			RestfulServerUtils.streamResponseAsResource(this, theResponse, (IResource) resBundle, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, Constants.STATUS_HTTP_200_OK, theRequest.isRespondGzip(), theRequest.getFhirServerBase());
+			RestfulServerUtils.streamResponseAsResource(this, theResponse, (IResource) resBundle, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, Constants.STATUS_HTTP_200_OK, theRequest.isRespondGzip(), theRequest.getFhirServerBase(), false);
 		}
 	}
 

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

@@ -76,10 +76,10 @@ public class RestfulServerUtils {
 	}
 
 	public static void streamResponseAsResource(RestfulServer theServer, HttpServletResponse theHttpResponse, IBaseResource theResource, EncodingEnum theResponseEncoding, boolean thePrettyPrint,
-			boolean theRequestIsBrowser, RestfulServer.NarrativeModeEnum theNarrativeMode, int stausCode, boolean theRespondGzip, String theServerBase) throws IOException {
+			boolean theRequestIsBrowser, RestfulServer.NarrativeModeEnum theNarrativeMode, int stausCode, boolean theRespondGzip, String theServerBase, boolean theAddContentLocationHeader) throws IOException {
 		theHttpResponse.setStatus(stausCode);
 
-		if (theResource.getId() != null && theResource.getId().hasIdPart() && isNotBlank(theServerBase)) {
+		if (theAddContentLocationHeader && theResource.getId() != null && theResource.getId().hasIdPart() && isNotBlank(theServerBase)) {
 			String resName = theServer.getFhirContext().getResourceDefinition(theResource).getName();
 			IIdType fullId = theResource.getId().withServerBase(theServerBase, resName);
 			theHttpResponse.addHeader(Constants.HEADER_CONTENT_LOCATION, fullId.getValue());
@@ -413,12 +413,12 @@ public class RestfulServerUtils {
 		}
 	}
 
-	public static void streamResponseAsResource(RestfulServer theServer, HttpServletResponse theHttpResponse, IBaseResource theResource, EncodingEnum theResponseEncoding, boolean thePrettyPrint,
+//	public static void streamResponseAsResource(RestfulServer theServer, HttpServletResponse theHttpResponse, IResource theResource, EncodingEnum theResponseEncoding, boolean thePrettyPrint,
-			boolean theRequestIsBrowser, RestfulServer.NarrativeModeEnum theNarrativeMode, boolean theRespondGzip, String theServerBase) throws IOException {
+//			boolean theRequestIsBrowser, RestfulServer.NarrativeModeEnum theNarrativeMode, boolean theRespondGzip, String theServerBase) throws IOException {
-		int stausCode = 200;
+//		int stausCode = 200;
-		RestfulServerUtils.streamResponseAsResource(theServer, theHttpResponse, theResource, theResponseEncoding, thePrettyPrint, theRequestIsBrowser, theNarrativeMode, stausCode, theRespondGzip,
+//		RestfulServerUtils.streamResponseAsResource(theServer, theHttpResponse, theResource, theResponseEncoding, thePrettyPrint, theRequestIsBrowser, theNarrativeMode, stausCode, theRespondGzip,
-				theServerBase);
+//				theServerBase);
-	}
+//	}
 
 	public static void validateResourceListNotNull(List<? extends IBaseResource> theResourceList) {
 		if (theResourceList == null) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/ExceptionHandlingInterceptor.java

@@ -129,7 +129,7 @@ public class ExceptionHandlingInterceptor extends InterceptorAdapter {
 		boolean requestIsBrowser = RestfulServer.requestIsBrowser(theRequest);
 		String fhirServerBase = ((Request) theRequestDetails).getFhirServerBase();
 		RestfulServerUtils.streamResponseAsResource(theRequestDetails.getServer(), theResponse, oo, RestfulServerUtils.determineResponseEncodingNoDefault(theRequest), true, requestIsBrowser,
-				NarrativeModeEnum.NORMAL, statusCode, false, fhirServerBase);
+				NarrativeModeEnum.NORMAL, statusCode, false, fhirServerBase, false);
 
 //		theResponse.setStatus(statusCode);
 //		theRequestDetails.getServer().addHeadersToResponse(theResponse);

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/ExceptionHandlingInterceptor.java.orig

@@ -1,172 +0,0 @@
-package ca.uhn.fhir.rest.server.interceptor;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2015 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.io.IOException;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.lang3.exception.ExceptionUtils;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
-import ca.uhn.fhir.model.base.resource.BaseOperationOutcome.BaseIssue;
-import ca.uhn.fhir.rest.method.Request;
-import ca.uhn.fhir.rest.method.RequestDetails;
-import ca.uhn.fhir.rest.server.Constants;
-import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.RestfulServer.NarrativeModeEnum;
-import ca.uhn.fhir.rest.server.RestfulServerUtils;
-import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-
-public class ExceptionHandlingInterceptor extends InterceptorAdapter {
-
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExceptionHandlingInterceptor.class);
-	private Class<?>[] myReturnStackTracesForExceptionTypes;
-
-	/**
-	 * If any server methods throw an exception which extends any of the given exception types, the exception 
-	 * stack trace will be returned to the user. This can be useful for helping to diagnose issues, but may
-	 * not be desirable for production situations.
-	 * 
-	 * @param theExceptionTypes The exception types for which to return the stack trace to the user.
-	 * @return Returns an instance of this interceptor, to allow for easy method chaining.
-	 */
-	public ExceptionHandlingInterceptor setReturnStackTracesForExceptionTypes(Class<?>... theExceptionTypes) {
-		myReturnStackTracesForExceptionTypes = theExceptionTypes;
-		return this;
-	}
-
-	@Override
-<<<<<<< HEAD
-	public boolean handleException(RequestDetails theRequestDetails, Throwable theException, HttpServletRequest theRequest, HttpServletResponse theResponse) throws ServletException, IOException {
-=======
-	public boolean handleException(RestfulServer theRestfulServer, RequestDetails theRequestDetails, Throwable theException, HttpServletRequest theRequest, HttpServletResponse theResponse) throws ServletException, IOException {
-		ourLog.error("AA", theException);
->>>>>>> 5956ab75fd9186ccc8b9836b60bc421b19d3d288
-		BaseOperationOutcome oo = null;
-		int statusCode = Constants.STATUS_HTTP_500_INTERNAL_ERROR;
-
-        FhirContext ctx = theRestfulServer.getFhirContext();
-
-		if (theException instanceof BaseServerResponseException) {
-			oo = ((BaseServerResponseException) theException).getOperationOutcome();
-			statusCode = ((BaseServerResponseException) theException).getStatusCode();
-		}
-
-		/*
-		 * Generate an OperationOutcome to return, unless the exception throw by the resource provider had one
-		 */
-		if (oo == null) {
-			try {
-				oo = (BaseOperationOutcome) ctx.getResourceDefinition("OperationOutcome").getImplementingClass().newInstance();
-			} catch (Exception e1) {
-				ourLog.error("Failed to instantiate OperationOutcome resource instance", e1);
-				throw new ServletException("Failed to instantiate OperationOutcome resource instance", e1);
-			}
-
-			BaseIssue issue = oo.addIssue();
-			issue.getSeverityElement().setValue("error");
-			if (theException instanceof InternalErrorException) {
-				ourLog.error("Failure during REST processing", theException);
-				populateDetails(theException, issue);
-			} else if (theException instanceof BaseServerResponseException) {
-				ourLog.warn("Failure during REST processing: {}", theException);
-				BaseServerResponseException baseServerResponseException = (BaseServerResponseException) theException;
-				statusCode = baseServerResponseException.getStatusCode();
-				populateDetails(theException, issue);
-				if (baseServerResponseException.getAdditionalMessages() != null) {
-					for (String next : baseServerResponseException.getAdditionalMessages()) {
-						BaseIssue issue2 = oo.addIssue();
-						issue2.getSeverityElement().setValue("error");
-						issue2.setDetails(next);
-					}
-				}
-			} else {
-				ourLog.error("Failure during REST processing: " + theException.toString(), theException);
-				populateDetails(theException, issue);
-				statusCode = Constants.STATUS_HTTP_500_INTERNAL_ERROR;
-			}
-		} else {
-			ourLog.error("Unknown error during processing", theException);
-		}
-
-		// Add headers associated with the specific error code
-		if (theException instanceof BaseServerResponseException) {
-			Map<String, String[]> additional = ((BaseServerResponseException) theException).getAssociatedHeaders();
-			if (additional != null) {
-				for (Entry<String, String[]> next : additional.entrySet()) {
-					if (isNotBlank(next.getKey()) && next.getValue() != null) {
-						String nextKey = next.getKey();
-						for (String nextValue : next.getValue()) {
-							theResponse.addHeader(nextKey, nextValue);
-						}
-					}
-				}
-			}
-		}
-
-		boolean requestIsBrowser = RestfulServer.requestIsBrowser(theRequest);
-        String fhirServerBase = theRestfulServer.getServerBaseForRequest(theRequest);
-
-		RestfulServerUtils.streamResponseAsResource(theRestfulServer, theResponse, oo, RestfulServerUtils.determineResponseEncodingNoDefault(theRequest), true, requestIsBrowser,
-				NarrativeModeEnum.NORMAL, statusCode, false, fhirServerBase);
-
-<<<<<<< HEAD
-//		theResponse.setStatus(statusCode);
-//		theRequestDetails.getServer().addHeadersToResponse(theResponse);
-//		theResponse.setContentType("text/plain");
-//		theResponse.setCharacterEncoding("UTF-8");
-//		theResponse.getWriter().append(theException.getMessage());
-//		theResponse.getWriter().close();
-=======
-		theResponse.setStatus(statusCode);
-		theRestfulServer.addHeadersToResponse(theResponse);
-		theResponse.setContentType("text/plain");
-		theResponse.setCharacterEncoding("UTF-8");
-		theResponse.getWriter().append(theException.getMessage());
-		theResponse.getWriter().close();
->>>>>>> 5956ab75fd9186ccc8b9836b60bc421b19d3d288
-
-		return false;
-	}
-
-	private void populateDetails(Throwable theException, BaseIssue issue) {
-		if (myReturnStackTracesForExceptionTypes != null) {
-			for (Class<?> next : myReturnStackTracesForExceptionTypes) {
-				if (next.isAssignableFrom(theException.getClass())) {
-					issue.getDetailsElement().setValue(theException.getMessage() + "\n\n" + ExceptionUtils.getStackTrace(theException));
-					return;
-				}
-			}
-		}
-
-		issue.getDetailsElement().setValue(theException.getMessage());
-	}
-
-}

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

@@ -61,7 +61,7 @@ public class FhirTerser {
 		if (theElement instanceof ISupportsUndeclaredExtensions) {
 			ISupportsUndeclaredExtensions containingElement = (ISupportsUndeclaredExtensions) theElement;
 			for (ExtensionDt nextExt : containingElement.getUndeclaredExtensions()) {
-				theCallback.acceptUndeclaredExtension(containingElement, theChildDefinition, theDefinition, nextExt);
+				theCallback.acceptUndeclaredExtension(containingElement, null, theChildDefinition, theDefinition, nextExt);
 				addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
 			}
 		}
@@ -90,10 +90,10 @@ public class FhirTerser {
 	public <T extends IBase> List<T> getAllPopulatedChildElementsOfType(IBaseResource theResource, final Class<T> theType) {
 		final ArrayList<T> retVal = new ArrayList<T>();
 		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
-		visit(theResource, null, def, new IModelVisitor() {
+		visit(theResource, null, null, def, new IModelVisitor() {
 			@SuppressWarnings("unchecked")
 			@Override
-			public void acceptElement(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
+			public void acceptElement(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
 				if (theElement == null || theElement.isEmpty()) {
 					return;
 				}
@@ -105,7 +105,8 @@ public class FhirTerser {
 
 			@SuppressWarnings("unchecked")
 			@Override
-			public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
+			public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition,
+					ExtensionDt theNextExt) {
 				if (theType.isAssignableFrom(theNextExt.getClass())) {
 					retVal.add((T) theNextExt);
 				}
@@ -117,39 +118,34 @@ public class FhirTerser {
 		return retVal;
 	}
 
-	public List<ResourceReferenceInfo> getAllResourceReferences(final IBaseResource theResource) {
+    public <T extends IBase> List<ResourceReferenceInfo> getAllResourceReferences(final IBaseResource theResource) {
-		final ArrayList<ResourceReferenceInfo> retVal = new ArrayList<ResourceReferenceInfo>();
+        final ArrayList<ResourceReferenceInfo> retVal = new ArrayList<ResourceReferenceInfo>();
-		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
+        BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
-		visit(theResource, null, def, new IModelVisitor() {
+        visit(theResource, null, null, def, new IModelVisitor() {
-			@Override
+            @SuppressWarnings("unchecked")
-			public void acceptElement(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
+            @Override
-				if (theElement == null || theElement.isEmpty()) {
+            public void acceptElement(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
-					return;
+                if (theElement == null || theElement.isEmpty()) {
-				}
+                    return;
-				String name = null;
+                }
-				if (theChildDefinition != null) {
+                if (BaseResourceReferenceDt.class.isAssignableFrom(theElement.getClass())) {
-					name = theChildDefinition.getElementName();
+                    retVal.add(new ResourceReferenceInfo(theResource, thePathToElement, (BaseResourceReferenceDt)theElement));
-				}
+                }
-				if (BaseResourceReferenceDt.class.isAssignableFrom(theElement.getClass())) {
+            }
-					retVal.add(new ResourceReferenceInfo(theResource, name, (BaseResourceReferenceDt) theElement));
-				}
-			}
 
-			@Override
+            @SuppressWarnings("unchecked")
-			public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
+            @Override
-				String name = null;
+            public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition,
-				if (theChildDefinition != null) {
+                                                  ExtensionDt theNextExt) {
-					name = theChildDefinition.getElementName();
+                if (theNextExt.getValue() != null && BaseResourceReferenceDt.class.isAssignableFrom(theNextExt.getValue().getClass())) {
-				}
+                    retVal.add(new ResourceReferenceInfo(theResource, thePathToElement, (BaseResourceReferenceDt)theNextExt.getValue()));
-				if (theNextExt.getValue() != null && BaseResourceReferenceDt.class.isAssignableFrom(theNextExt.getValue().getClass())) {
+                }
-					retVal.add(new ResourceReferenceInfo(theResource, name, (BaseResourceReferenceDt) theNextExt.getValue()));
+            }
-				}
+        });
-			}
+        return retVal;
-		});
+    }
-		return retVal;
-	}
 
-	private BaseRuntimeChildDefinition getDefinition(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, List<String> theSubList) {
+    private BaseRuntimeChildDefinition getDefinition(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, List<String> theSubList) {
 		BaseRuntimeChildDefinition nextDef = theCurrentDef.getChildByNameOrThrowDataFormatException(theSubList.get(0));
 
 		if (theSubList.size() == 1) {
@@ -222,8 +218,19 @@ public class FhirTerser {
 
 	}
 
-	private void visit(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
+    private List<String> addNameToList(List<String> theCurrentList, BaseRuntimeChildDefinition theChildDefinition) {
-		theCallback.acceptElement(theElement, theChildDefinition, theDefinition);
+        if (theChildDefinition == null)
+            return null;
+        if (theCurrentList== null || theCurrentList.isEmpty())
+            return new ArrayList<String>(Arrays.asList(theChildDefinition.getElementName()));
+        List<String> newList = new ArrayList<String>(theCurrentList);
+        newList.add(theChildDefinition.getElementName());
+        return newList;
+    }
+
+	private void visit(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
+        List<String> pathToElement = addNameToList(thePathToElement, theChildDefinition);
+		theCallback.acceptElement(theElement, pathToElement, theChildDefinition, theDefinition);
 		addUndeclaredExtensions(theElement, theDefinition, theChildDefinition, theCallback);
 
 		// if (theElement.isEmpty()) {
@@ -243,7 +250,7 @@ public class FhirTerser {
 				IBaseResource theResource = resRefDt.getResource();
 				if (theResource.getId() == null || theResource.getId().isEmpty() || theResource.getId().isLocal()) {
 					BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
-					visit(theResource, null, def, theCallback);
+					visit(theResource, pathToElement, null, def, theCallback);
 				}
 			}
 			break;
@@ -285,9 +292,9 @@ public class FhirTerser {
 
 						if (nextChild instanceof RuntimeChildDirectResource) {
 							// Don't descend into embedded resources
-							theCallback.acceptElement(nextValue, nextChild, childElementDef);
+							theCallback.acceptElement(nextValue, null, nextChild, childElementDef);
 						} else {
-							visit(nextValue, nextChild, childElementDef, theCallback);
+							visit(nextValue, pathToElement, nextChild, childElementDef, theCallback);
 						}
 					}
 				}
@@ -298,7 +305,7 @@ public class FhirTerser {
 			BaseContainedDt value = (BaseContainedDt) theElement;
 			for (IResource next : value.getContainedResources()) {
 				BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(next);
-				visit(next, null, def, theCallback);
+				visit(next, pathToElement, null, def, theCallback);
 			}
 			break;
 		}
@@ -309,7 +316,7 @@ public class FhirTerser {
 		case CONTAINED_RESOURCE_LIST:
 			if (theElement != null) {
 				BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theElement.getClass());
-				visit(theElement, null, def, theCallback);
+				visit(theElement, pathToElement, null, def, theCallback);
 			}
 			break;
 		}
@@ -454,7 +461,7 @@ public class FhirTerser {
 	 */
 	public void visit(IBaseResource theResource, IModelVisitor theVisitor) {
 		BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
-		visit(theResource, null, def, theVisitor);
+		visit(theResource, null, null, def, theVisitor);
 	}
 
 	/**

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

@@ -28,6 +28,8 @@ import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
 
+import java.util.List;
+
 /**
  * @see FhirTerser#visit(IBaseResource, IModelVisitor)
  */
@@ -39,7 +41,7 @@ public interface IModelVisitor {
 	 * @param theChildDefinition May be null if this is a root element
 	 * @param theDefinition
 	 */
-	void acceptElement(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition);
+	void acceptElement(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition);
 
 	/**
 	 * 
@@ -48,7 +50,7 @@ public interface IModelVisitor {
 	 * @param theDefinition
 	 * @param theNextExt
 	 */
-	void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt);
+	void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt);
 
 	
 	

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

@@ -28,58 +28,71 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hl7.fhir.instance.model.IBaseResource;
 
+import java.util.Iterator;
+import java.util.List;
 import java.util.Set;
 
 /**
  * Created by Bill de Beaubien on 2/26/2015.
  */
 public class ResourceReferenceInfo {
-	private String myOwningResource;
+    private String myOwningResource;
-	private String myName;
+    private String myName;
-	private BaseResourceReferenceDt myResource;
+    private BaseResourceReferenceDt myResource;
 
-	public ResourceReferenceInfo(IBaseResource theOwningResource, String theName, BaseResourceReferenceDt theResource) {
+    public ResourceReferenceInfo(IBaseResource theOwningResource, List<String> thePathToElement, BaseResourceReferenceDt theResource) {
-		myOwningResource = theOwningResource.getClass().getAnnotation(ResourceDef.class).name();
+        myOwningResource = theOwningResource.getClass().getAnnotation(ResourceDef.class).name();
-		myName = theName;
+        myResource = theResource;
-		myResource = theResource;
+        if (thePathToElement != null && !thePathToElement.isEmpty()) {
-	}
+            StringBuilder sb = new StringBuilder();
+            thePathToElement.iterator();
+            for (Iterator<String> iterator = thePathToElement.iterator(); iterator.hasNext(); ) {
+                sb.append(iterator.next());
+                if (iterator.hasNext())
+                    sb.append(".");
+            }
+            myName = sb.toString();
+        } else {
+            myName = null;
+        }
+    }
 
-	@Override
+    @Override
-	public String toString() {
+    public String toString() {
-		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+        ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
-		b.append("name", myName);
+        b.append("name", myName);
-		b.append("resource", myResource.getReference());
+        b.append("resource", myResource.getReference());
-		return b.build();
+        return b.build();
-	}
+    }
 
-	public String getName() {
+    public String getName() {
-		return myName;
+        return myName;
-	}
+    }
 
-	public BaseResourceReferenceDt getResourceReference() {
+    public BaseResourceReferenceDt getResourceReference() {
-		return myResource;
+        return myResource;
-	}
+    }
 
-	public boolean matchesIncludeSet(Set<Include> theIncludes) {
+    public boolean matchesIncludeSet(Set<Include> theIncludes) {
-		if (theIncludes == null)
+        if (theIncludes == null)
-			return false;
+            return false;
-		for (Include include : theIncludes) {
+        for (Include include : theIncludes) {
-			if (matchesInclude(include))
+            if (matchesInclude(include))
-				return true;
+                return true;
-		}
+        }
-		return false;
+        return false;
-	}
+    }
 
-	public boolean matchesInclude(Include theInclude) {
+    public boolean matchesInclude(Include theInclude) {
-		if (theInclude.getValue().equals("*")) {
+        if (theInclude.getValue().equals("*")) {
-			return true;
+            return true;
-		}
+        }
-		if (theInclude.getValue().indexOf(':') != -1) {
+        if (theInclude.getValue().indexOf(':') != -1) {
-			// DSTU2 style
+            // DSTU2 style
-			return (theInclude.getValue().equals(myOwningResource + ':' + myName));
+            return (theInclude.getValue().equals(myOwningResource + ':' + myName));
-		} else {
+        } else {
-			// DSTU1 style
+            // DSTU1 style
-			return (theInclude.getValue().equals(myOwningResource + '.' + myName));
+            return (theInclude.getValue().equals(myOwningResource + '.' + myName));
-		}
+        }
-	}
+    }
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirDao.java

@@ -20,8 +20,7 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
-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.UnsupportedEncodingException;
 import java.net.URI;
@@ -444,12 +443,12 @@ public abstract class BaseFhirDao implements IDao {
 			}
 
 			@Override
-			public List<IResource> getResources(final int theFromIndex, final int theToIndex) {
+			public List<IBaseResource> getResources(final int theFromIndex, final int theToIndex) {
 				final StopWatch timer = new StopWatch();
 				TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-				return template.execute(new TransactionCallback<List<IResource>>() {
+				return template.execute(new TransactionCallback<List<IBaseResource>>() {
 					@Override
-					public List<IResource> doInTransaction(TransactionStatus theStatus) {
+					public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
 						List<BaseHasResource> resEntities = Lists.newArrayList();
 
 						List<HistoryTuple> tupleSubList = tuples.subList(theFromIndex, theToIndex);
@@ -471,7 +470,7 @@ public abstract class BaseFhirDao implements IDao {
 							resEntities = resEntities.subList(0, limit);
 						}
 
-						ArrayList<IResource> retVal = new ArrayList<IResource>();
+						ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
 						for (BaseHasResource next : resEntities) {
 							RuntimeResourceDefinition type;
 							try {
@@ -514,7 +513,7 @@ public abstract class BaseFhirDao implements IDao {
 		return true;
 	}
 
-	protected List<IResource> loadResourcesById(Set<IdDt> theIncludePids) {
+	protected List<IBaseResource> loadResourcesById(Set<IdDt> theIncludePids) {
 		Set<Long> pids = new HashSet<Long>();
 		for (IdDt next : theIncludePids) {
 			if (next.isIdPartValidLong()) {
@@ -528,6 +527,10 @@ public abstract class BaseFhirDao implements IDao {
 			}
 		}
 
+		if (pids.isEmpty()) {
+			return new ArrayList<IBaseResource>();
+		}
+		
 		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
 		CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
 		Root<ResourceTable> from = cq.from(ResourceTable.class);
@@ -538,7 +541,7 @@ public abstract class BaseFhirDao implements IDao {
 		// }
 		TypedQuery<ResourceTable> q = myEntityManager.createQuery(cq);
 
-		ArrayList<IResource> retVal = new ArrayList<IResource>();
+		ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
 		for (ResourceTable next : q.getResultList()) {
 			IResource resource = (IResource) toResource(next);
 			retVal.add(resource);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirResourceDao.java

@@ -20,8 +20,7 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
-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.math.BigDecimal;
 import java.util.ArrayList;
@@ -660,12 +659,12 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return new HashSet<Long>(q.getResultList());
 	}
 
-	private List<IResource> addResourcesAsIncludesById(List<IResource> theListToPopulate, Set<IdDt> includePids, List<IResource> resources) {
+	private List<IBaseResource> addResourcesAsIncludesById(List<IBaseResource> theListToPopulate, Set<IdDt> includePids, List<IBaseResource> resources) {
 		if (!includePids.isEmpty()) {
 			ourLog.info("Loading {} included resources", includePids.size());
 			resources = loadResourcesById(includePids);
-			for (IResource next : resources) {
+			for (IBaseResource next : resources) {
-				ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(next, BundleEntrySearchModeEnum.INCLUDE);
+				ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IResource) next, BundleEntrySearchModeEnum.INCLUDE);
 			}
 			theListToPopulate.addAll(resources);
 		}
@@ -1000,7 +999,7 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return tags;
 	}
 
-	protected abstract List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IResource theResource, RuntimeResourceDefinition theResourceDef);
+	protected abstract List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IBaseResource theResource, RuntimeResourceDefinition theResourceDef);
 
 	public Class<T> getResourceType() {
 		return myResourceType;
@@ -1074,8 +1073,8 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 			}
 
 			@Override
-			public List<IResource> getResources(int theFromIndex, int theToIndex) {
+			public List<IBaseResource> getResources(int theFromIndex, int theToIndex) {
-				ArrayList<IResource> retVal = new ArrayList<IResource>();
+				List<IBaseResource> retVal = new ArrayList<IBaseResource>();
 				if (theFromIndex == 0 && current != null) {
 					retVal.add(current);
 				}
@@ -1128,7 +1127,7 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return retVal;
 	}
 
-	private void loadResourcesByPid(Collection<Long> theIncludePids, List<IResource> theResourceListToPopulate, BundleEntrySearchModeEnum theBundleEntryStatus) {
+	private void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, BundleEntrySearchModeEnum theBundleEntryStatus) {
 		if (theIncludePids.isEmpty()) {
 			return;
 		}
@@ -1520,15 +1519,15 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 			}
 
 			@Override
-			public List<IResource> getResources(final int theFromIndex, final int theToIndex) {
+			public List<IBaseResource> getResources(final int theFromIndex, final int theToIndex) {
 				TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
-				return template.execute(new TransactionCallback<List<IResource>>() {
+				return template.execute(new TransactionCallback<List<IBaseResource>>() {
 					@Override
-					public List<IResource> doInTransaction(TransactionStatus theStatus) {
+					public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
 						List<Long> pidsSubList = pids.subList(theFromIndex, theToIndex);
 
 						// Execute the query and make sure we return distinct results
-						List<IResource> retVal = new ArrayList<IResource>();
+						List<IBaseResource> retVal = new ArrayList<IBaseResource>();
 						loadResourcesByPid(pidsSubList, retVal, BundleEntrySearchModeEnum.MATCH);
 
 						/*
@@ -1538,18 +1537,18 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 						 */
 						if (theParams.getIncludes() != null && theParams.getIncludes().isEmpty() == false) {
 							Set<IdDt> previouslyLoadedPids = new HashSet<IdDt>();
-							for (IResource next : retVal) {
+							for (IBaseResource next : retVal) {
-								previouslyLoadedPids.add(next.getId().toUnqualifiedVersionless());
+								previouslyLoadedPids.add((IdDt) next.getId().toUnqualifiedVersionless());
 							}
 
 							Set<IdDt> includePids = new HashSet<IdDt>();
-							List<IResource> resources = retVal;
+							List<IBaseResource> resources = retVal;
 							do {
 								includePids.clear();
 
 								FhirTerser t = getContext().newTerser();
 								for (Include next : theParams.getIncludes()) {
-									for (IResource nextResource : resources) {
+									for (IBaseResource nextResource : resources) {
 										RuntimeResourceDefinition def = getContext().getResourceDefinition(nextResource);
 										List<Object> values = getIncludeValues(t, next, nextResource, def);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu1.java

@@ -24,6 +24,8 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
+import org.hl7.fhir.instance.model.IBaseResource;
+
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
@@ -32,7 +34,7 @@ import ca.uhn.fhir.util.FhirTerser;
 
 public class FhirResourceDaoDstu1<T extends IResource> extends BaseFhirResourceDao<T> {
 
-	protected List<Object> getIncludeValues(FhirTerser t, Include next, IResource nextResource, RuntimeResourceDefinition def) {
+	protected List<Object> getIncludeValues(FhirTerser t, Include next, IBaseResource nextResource, RuntimeResourceDefinition def) {
 		List<Object> values;
 		if ("*".equals(next.getValue())) {
 			values = new ArrayList<Object>();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java

@@ -24,6 +24,8 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
+import org.hl7.fhir.instance.model.IBaseResource;
+
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.model.api.IResource;
@@ -33,7 +35,7 @@ import ca.uhn.fhir.util.FhirTerser;
 
 public class FhirResourceDaoDstu2<T extends IResource> extends BaseFhirResourceDao<T> {
 
-	protected List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IResource theResource, RuntimeResourceDefinition theResourceDef) {
+	protected List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IBaseResource theResource, RuntimeResourceDefinition theResourceDef) {
 		List<Object> values;
 		if ("*".equals(theInclude.getValue())) {
 			values = new ArrayList<Object>();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -31,6 +31,7 @@ import java.util.Set;
 
 import javax.persistence.TypedQuery;
 
+import org.hl7.fhir.instance.model.IBaseResource;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
@@ -241,9 +242,9 @@ public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
 						if (bundle.size() > configuredMax) {
 							oo.addIssue().setSeverity(IssueSeverityEnum.WARNING).setDetails("Search nested within transaction found more than " + configuredMax + " matches, but paging is not supported in nested transactions");
 						}
-						List<IResource> resourcesToAdd = bundle.getResources(0, Math.min(bundle.size(), configuredMax));
+						List<IBaseResource> resourcesToAdd = bundle.getResources(0, Math.min(bundle.size(), configuredMax));
-						for (IResource next : resourcesToAdd) {
+						for (IBaseResource next : resourcesToAdd) {
-							searchBundle.addEntry().setResource(next);
+							searchBundle.addEntry().setResource((IResource) next);
 						}
 
 						response.addEntry().setResource(searchBundle);

hapi-fhir-jpaserver-base/src/main/resources/fhir-spring-config.xml

@@ -39,9 +39,11 @@
 			</bean>
 		</property>
 	</bean>
+
 	<bean id="myTxManager" class="org.springframework.orm.jpa.JpaTransactionManager">
 		<property name="entityManagerFactory" ref="myEntityManagerFactory" />
 	</bean>
+
 	<tx:annotation-driven transaction-manager="myTxManager" />
 
 </beans>

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2Test.java

@@ -27,6 +27,7 @@ import java.util.Set;
 
 import org.apache.commons.lang3.RandomStringUtils;
 import org.hamcrest.core.StringContains;
+import org.hl7.fhir.instance.model.IBaseResource;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -453,8 +454,8 @@ public class FhirResourceDaoDstu2Test {
 
 		IBundleProvider history = ourPatientDao.history(null);
 		assertEquals(4 + initialHistory, history.size());
-		List<IResource> resources = history.getResources(0, 4);
+		List<IBaseResource> resources = history.getResources(0, 4);
-		assertNotNull(resources.get(0).getResourceMetadata().get(ResourceMetadataKeyEnum.DELETED_AT));
+		assertNotNull(((IResource) resources.get(0)).getResourceMetadata().get(ResourceMetadataKeyEnum.DELETED_AT));
 
 		try {
 			ourPatientDao.delete(id2);
@@ -534,9 +535,9 @@ public class FhirResourceDaoDstu2Test {
 		IBundleProvider history = ourPatientDao.history(id, null);
 		assertEquals(2, history.size());
 
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(0, 0).get(0)));
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 0).get(0)));
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(0, 0).get(0)).getValue());
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 0).get(0)).getValue());
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(1, 1).get(0)));
+		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(1, 1).get(0)));
 
 	}
 
@@ -879,7 +880,7 @@ public class FhirResourceDaoDstu2Test {
 		map.setRevIncludes(Collections.singleton(Patient.INCLUDE_ORGANIZATION));
 		IBundleProvider resultsP = ourOrganizationDao.search(map);
 		assertEquals(2, resultsP.size());
-		List<IResource> results = resultsP.getResources(0, resultsP.size());
+		List<IBaseResource> results = resultsP.getResources(0, resultsP.size());
 		assertEquals(2, results.size());
 		assertEquals(Organization.class, results.get(0).getClass());
 		assertEquals(Patient.class, results.get(1).getClass());
@@ -2162,15 +2163,15 @@ public class FhirResourceDaoDstu2Test {
 
 		assertEquals(2, historyBundle.size());
 
-		List<IResource> history = historyBundle.getResources(0, 2);
+		List<IBaseResource> history = historyBundle.getResources(0, 2);
 		assertEquals("1", history.get(1).getId().getVersionIdPart());
 		assertEquals("2", history.get(0).getId().getVersionIdPart());
-		assertEquals(published, history.get(1).getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED));
+		assertEquals(published, ((IResource)history.get(1)).getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED));
-		assertEquals(published, history.get(1).getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED));
+		assertEquals(published, ((IResource)history.get(1)).getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED));
-		assertEquals(updated, history.get(1).getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
+		assertEquals(updated, ((IResource)history.get(1)).getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
 		assertEquals("001", ((Patient) history.get(1)).getIdentifierFirstRep().getValue());
-		assertEquals(published2, history.get(0).getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED));
+		assertEquals(published2, ((IResource)history.get(0)).getResourceMetadata().get(ResourceMetadataKeyEnum.PUBLISHED));
-		assertEquals(updated2, history.get(0).getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
+		assertEquals(updated2, ((IResource)history.get(0)).getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED));
 		assertEquals("002", ((Patient) history.get(0)).getIdentifierFirstRep().getValue());
 
 	}
@@ -2313,8 +2314,8 @@ public class FhirResourceDaoDstu2Test {
 
 	private List<IdDt> toUnqualifiedVersionlessIds(IBundleProvider theFound) {
 		List<IdDt> retVal = new ArrayList<IdDt>();
-		for (IResource next : theFound.getResources(0, theFound.size())) {
+		for (IBaseResource next : theFound.getResources(0, theFound.size())) {
-			retVal.add(next.getId().toUnqualifiedVersionless());
+			retVal.add((IdDt) next.getId().toUnqualifiedVersionless());
 		}
 		return retVal;
 	}
@@ -2353,9 +2354,9 @@ public class FhirResourceDaoDstu2Test {
 		
 		IBundleProvider value = ourDeviceDao.search(new SearchParameterMap());
 		ourLog.info("Initial size: " + value.size());
-		for (IResource next : value.getResources(0, value.size())) {
+		for (IBaseResource next : value.getResources(0, value.size())) {
 			ourLog.info("Deleting: {}", next.getId());
-			ourDeviceDao.delete(next.getId());
+			ourDeviceDao.delete((IdDt) next.getId());
 		}
 
 		value = ourDeviceDao.search(new SearchParameterMap());
@@ -2365,7 +2366,7 @@ public class FhirResourceDaoDstu2Test {
 		}
 		assertEquals(0, value.size());
 
-		List<IResource> res = value.getResources(0, 0);
+		List<IBaseResource> res = value.getResources(0, 0);
 		assertTrue(res.isEmpty());
 
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1Test.java

@@ -11,6 +11,7 @@ import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
+import org.hl7.fhir.instance.model.IBaseResource;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -93,7 +94,7 @@ public class FhirSystemDaoDstu1Test {
         IBundleProvider values = ourSystemDao.history(start);
         assertEquals(4, values.size());
 
-        List<IResource> res = values.getResources(0, 4);
+        List<IBaseResource> res = values.getResources(0, 4);
         assertEquals(newpid3, res.get(0).getId());
         assertEquals(newpid2, res.get(1).getId());
         assertEquals(newpid, res.get(2).getId());
@@ -146,7 +147,7 @@ public class FhirSystemDaoDstu1Test {
         IBundleProvider patResults = ourPatientDao.search(Patient.SP_IDENTIFIER, new IdentifierDt("urn:system", "testPersistWithSimpleLinkP01"));
         assertEquals(1, obsResults.size());
 
-        IdDt foundPatientId = patResults.getResources(0, 1).get(0).getId();
+        IdDt foundPatientId = (IdDt) patResults.getResources(0, 1).get(0).getId();
         ResourceReferenceDt subject = obs.getSubject();
         assertEquals(foundPatientId.getIdPart(), subject.getReference().getIdPart());
 
@@ -371,7 +372,7 @@ public class FhirSystemDaoDstu1Test {
 		 */
 
         res = new ArrayList<IResource>();
-        List<IResource> existing = results.getResources(0, 3);
+        List<IBaseResource> existing = results.getResources(0, 3);
 
         p1 = new Patient();
         p1.setId(existing.get(0).getId());
@@ -391,7 +392,7 @@ public class FhirSystemDaoDstu1Test {
 
         IBundleProvider results2 = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system", "testTransactionWithDelete"));
         assertEquals(1, results2.size());
-        List<IResource> existing2 = results2.getResources(0, 1);
+        List<IBaseResource> existing2 = results2.getResources(0, 1);
         assertEquals(existing2.get(0).getId(), existing.get(2).getId());
 
     }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2Test.java

@@ -14,6 +14,7 @@ import static org.junit.Assert.fail;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.hl7.fhir.instance.model.IBaseResource;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -262,9 +263,9 @@ public class FhirSystemDaoDstu2Test {
 		IBundleProvider history = ourPatientDao.history(id, null);
 		assertEquals(2, history.size());
 
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(0, 0).get(0)));
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 0).get(0)));
-		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(0, 0).get(0)).getValue());
+		assertNotNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(0, 0).get(0)).getValue());
-		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get(history.getResources(1, 1).get(0)));
+		assertNull(ResourceMetadataKeyEnum.DELETED_AT.get((IResource) history.getResources(1, 1).get(0)));
 
 	}
 
@@ -769,9 +770,9 @@ public class FhirSystemDaoDstu2Test {
 
 	static void doDeleteEverything(IFhirSystemDao<Bundle> systemDao) {
 		IBundleProvider all = systemDao.history(null);
-		List<IResource> allRes = all.getResources(0, all.size());
+		List<IBaseResource> allRes = all.getResources(0, all.size());
-		for (IResource iResource : allRes) {
+		for (IBaseResource iResource : allRes) {
-			if (ResourceMetadataKeyEnum.DELETED_AT.get(iResource) == null) {
+			if (ResourceMetadataKeyEnum.DELETED_AT.get((IResource) iResource) == null) {
 				ourLog.info("Deleting: {}", iResource.getId());
 				
 				Bundle b = new Bundle();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -26,6 +26,7 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.instance.model.IBaseResource;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -126,12 +127,7 @@ public class ResourceProviderDstu2Test {
 
 		CloseableHttpResponse response = ourHttpClient.execute(post);
 		try {
-
+			assertEquals(400, response.getStatusLine().getStatusCode());
-			assertEquals(201, response.getStatusLine().getStatusCode());
-			assertThat(response.getFirstHeader(Constants.HEADER_LOCATION_LC).getValue(), startsWith(ourServerBase + "/Patient/"));
-			assertThat(response.getFirstHeader(Constants.HEADER_LOCATION_LC).getValue(), endsWith("/_history/1"));
-			assertThat(response.getFirstHeader(Constants.HEADER_LOCATION_LC).getValue(), not(containsString("1777")));
-
 		} finally {
 			response.close();
 		}
@@ -452,7 +448,7 @@ public class ResourceProviderDstu2Test {
 		// NB this does not get used- The paging provider has its own limits built in
 		ourDaoConfig.setHardSearchLimit(100);
 
-		List<IResource> resources = new ArrayList<IResource>();
+		List<IBaseResource> resources = new ArrayList<IBaseResource>();
 		for (int i = 0; i < 100; i++) {
 			Organization org = new Organization();
 			org.setName("rpdstu2_testCountParam_01");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderTest.java

@@ -7,6 +7,7 @@ import java.util.List;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.instance.model.IBaseResource;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;

hapi-fhir-jpaserver-example/pom.xml

@@ -2,22 +2,25 @@
 	<modelVersion>4.0.0</modelVersion>
 
 	<!-- 
-	Note: HAPI projects use the Sonatype OSS parent project to
+	Note: HAPI projects use the "hapi-fhir" POM as their base to provide
-	facilitate deployment to the global Maven repos.
+	easy management.
 	 
 	You do not need to use this in your own projects, so the 
 	"parent" tag and it's contents below may be removed if you
 	are using this file as a basis for your own project.
 	-->
+	<!-- 
 	<parent>
-		<groupId>org.sonatype.oss</groupId>
+		<groupId>ca.uhn.hapi.fhir</groupId>
-		<artifactId>oss-parent</artifactId>
+		<artifactId>hapi-fhir</artifactId>
-		<version>7</version>
+		<version>1.0-SNAPSHOT</version>
+		<relativePath>../pom.xml</relativePath>
 	</parent>
+	-->
 	
 	<groupId>ca.uhn.hapi.example</groupId>
 	<artifactId>hapi-fhir-jpaserver-example</artifactId>
-	<version>0.9-SNAPSHOT</version>
+	<version>1.0-SNAPSHOT</version>
 	<packaging>war</packaging>
 
 	<name>HAPI FHIR JPA Server - Example</name>

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java

@@ -4,12 +4,11 @@ import java.util.List;
 
 import javax.servlet.ServletException;
 
-import ca.uhn.fhir.context.FhirVersionEnum;
-
 import org.springframework.web.context.ContextLoaderListener;
 import org.springframework.web.context.WebApplicationContext;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu1;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
@@ -23,7 +22,7 @@ import ca.uhn.fhir.rest.server.EncodingEnum;
 import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 
 public class JpaServerDemo extends RestfulServer {
 
@@ -123,12 +122,12 @@ public class JpaServerDemo extends RestfulServer {
 		setPagingProvider(new FifoMemoryPagingProvider(10));
 
 		/*
-		 * Do some fancy logging to create a nice access log that has details about each incoming request.
+		 * Load interceptors for the server from Spring (these are defined in hapi-fhir-server-config.xml
 		 */
-		LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
+		List<IServerInterceptor> interceptorBeans = myAppCtx.getBean("myServerInterceptors", List.class);
-		loggingInterceptor.setLoggerName("fhir.access");
+		for (IServerInterceptor interceptor : interceptorBeans) {
-		loggingInterceptor.setMessageFormat("Path[${servletPath}] Operation[${operationType} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}]");
+			this.registerInterceptor(interceptor);
-		this.registerInterceptor(loggingInterceptor);
+		}
 
 	}
 

hapi-fhir-jpaserver-example/src/main/webapp/WEB-INF/hapi-fhir-server-config.xml

@@ -21,4 +21,18 @@
 	</bean>
 	<tx:annotation-driven transaction-manager="myTxManager" />
 
+	<util:list id="myServerInterceptors">
+		<ref bean="myLoggingInterceptor"/>
+	</util:list>
+	
+	<!-- 
+	Do some fancy logging to create a nice access log that has details
+	about each incoming request.
+	-->
+	<bean id="myLoggingInterceptor" class="ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor">
+		<property name="loggerName" value="fhirtest.access"/>
+		<property name="messageFormat"
+				  value="Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}]"/>
+	</bean>
+	
 </beans>

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java

@@ -7,17 +7,16 @@ import javax.servlet.ServletContext;
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 
-import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
-
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.context.ApplicationContext;
 import org.springframework.web.context.ContextLoaderListener;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
-import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu1;
+import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1;
+import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.EncodingEnum;
@@ -25,7 +24,7 @@ import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
 import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 
 public class TestRestfulServer extends RestfulServer {
 
@@ -164,13 +163,12 @@ public class TestRestfulServer extends RestfulServer {
 		setPagingProvider(new FifoMemoryPagingProvider(10));
 
 		/*
-		 * Do some fancy logging to create a nice access log that has details
+		 * Load interceptors for the server from Spring (these are defined in hapi-fhir-server-config.xml
-		 * about each incoming request. 
 		 */
-		LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
+		List<IServerInterceptor> interceptorBeans = myAppCtx.getBean("myServerInterceptors", List.class);
-		loggingInterceptor.setLoggerName("fhirtest.access");
+		for (IServerInterceptor interceptor : interceptorBeans) {
-		loggingInterceptor.setMessageFormat("Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}]");
+			this.registerInterceptor(interceptor);
-		this.registerInterceptor(loggingInterceptor);
+		}
 
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/hapi-fhir-server-config.xml

@@ -21,4 +21,18 @@
 	</bean>
 	<tx:annotation-driven transaction-manager="myTxManager" />
 
+	<util:list id="myServerInterceptors">
+		<ref bean="myLoggingInterceptor"/>
+	</util:list>
+	
+	<!-- 
+	Do some fancy logging to create a nice access log that has details
+	about each incoming request.
+	-->
+	<bean id="myLoggingInterceptor" class="ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor">
+		<property name="loggerName" value="fhirtest.access"/>
+		<property name="messageFormat"
+				  value="Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}]"/>
+	</bean>
+
 </beans>

hapi-fhir-jpaserver-uhnfhirtest/src/test/java/ca/uhn/fhirtest/UhnFhirTestApp.java

@@ -1,10 +1,12 @@
 package ca.uhn.fhirtest;
 
+import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.commons.io.IOUtils;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.webapp.WebAppContext;
+import org.hl7.fhir.instance.model.IBaseResource;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IResource;
@@ -65,7 +67,8 @@ public class UhnFhirTestApp {
 			ResourceMetadataKeyEnum.TAG_LIST.put(p1, list);
 			client.create(p1);
 
-			List<IResource> resources = ctx.newJsonParser().parseBundle(IOUtils.toString(UhnFhirTestApp.class.getResourceAsStream("/test-server-seed-bundle.json"))).toListOfResources();
+			List<IBaseResource> resources;
+			resources = new ArrayList<IBaseResource>(ctx.newJsonParser().parseBundle(IOUtils.toString(UhnFhirTestApp.class.getResourceAsStream("/test-server-seed-bundle.json"))).toListOfResources());
 			client.transaction(resources);
 
 //			for (int i = 0; i < 1000; i++) {

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

@@ -782,13 +782,13 @@ public class JsonParserTest {
 
 	private void parseAndEncode(String name) throws IOException {
 		String msg = IOUtils.toString(XmlParser.class.getResourceAsStream(name));
-		ourLog.info(msg);
+//		ourLog.info(msg);
 
 		IParser p = ourCtx.newJsonParser();
 		Profile res = p.parseResource(Profile.class, msg);
 
 		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(res);
-		ourLog.info(encoded);
+//		ourLog.info(encoded);
 
 		JSON expected = JSONSerializer.toJSON(msg.trim());
 		JSON actual = JSONSerializer.toJSON(encoded.trim());
@@ -1219,7 +1219,6 @@ public class JsonParserTest {
 		Bundle b = new Bundle();
 
 		InstantDt pub = InstantDt.withCurrentTime();
-		b.setPublished(pub);
 		Thread.sleep(2);
 
 		Patient p1 = new Patient();
@@ -1245,7 +1244,6 @@ public class JsonParserTest {
 		ourLog.info(bundleString);
 
 		List<String> strings = new ArrayList<String>();
-		strings.addAll(Arrays.asList("\"published\":\"" + pub.getValueAsString() + "\""));
 		strings.addAll(Arrays.asList("\"id\":\"1\""));
 		strings.addAll(Arrays.asList("this is the summary"));
 		strings.addAll(Arrays.asList("\"id\":\"2\"", "\"rel\":\"alternate\"", "\"href\":\"http://foo/bar\""));

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

@@ -314,7 +314,6 @@ public class XmlParserTest {
 		b.getCategories().addTag("http://hl7.org/fhir/tag", "http://hl7.org/fhir/tag/message", "Message");
 
 		InstantDt pub = InstantDt.withCurrentTime();
-		b.setPublished(pub);
 		Thread.sleep(2);
 
 		Patient p1 = new Patient();
@@ -340,7 +339,6 @@ public class XmlParserTest {
 		ourLog.info(bundleString);
 
 		List<String> strings = new ArrayList<String>();
-		strings.addAll(Arrays.asList("<published>", pub.getValueAsString(), "</published>"));
 		strings.add("<category term=\"http://hl7.org/fhir/tag/message\" label=\"Message\" scheme=\"http://hl7.org/fhir/tag\"/>");
 		strings.addAll(Arrays.asList("<entry>", "<id>1</id>", "</Patient>", "<summary type=\"xhtml\">", "<div", "</entry>"));
 		strings.addAll(Arrays.asList("<entry>", "<id>2</id>", "<link rel=\"alternate\" href=\"http://foo/bar\"/>", "<link rel=\"search\" href=\"http://foo/bar/search\"/>", "</entry>"));
@@ -380,7 +378,6 @@ public class XmlParserTest {
 		b.getCategories().addTag("http://hl7.org/fhir/tag", "http://hl7.org/fhir/tag/message", "Message");
 
 		InstantDt pub = InstantDt.withCurrentTime();
-		b.setPublished(pub);
 		Thread.sleep(2);
 
 		Patient p1 = new Patient();
@@ -406,7 +403,6 @@ public class XmlParserTest {
 		ourLog.info(bundleString);
 
 		List<String> strings = new ArrayList<String>();
-		strings.addAll(Arrays.asList("<published>", pub.getValueAsString(), "</published>"));
 		strings.add("<category term=\"http://hl7.org/fhir/tag/message\" label=\"Message\" scheme=\"http://hl7.org/fhir/tag\"/>");
 		strings.addAll(Arrays.asList("<entry>", "<id>1</id>", "</Patient>", "<summary type=\"xhtml\">", "<div", "</entry>"));
 		strings.addAll(Arrays.asList("<entry>", "<id>2</id>", "<link rel=\"alternate\" href=\"http://foo/bar\"/>", "<link rel=\"search\" href=\"http://foo/bar/search\"/>", "</entry>"));

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/client/ClientTest.java

@@ -102,8 +102,7 @@ public class ClientTest {
 				"<title/>\n" + 
 				"<id>d039f91a-cc3c-4013-988e-af4d8d0614bd</id>\n" + 
 				"<os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">1</os:totalResults>\n" + 
-				"<published>2014-03-11T16:35:07-04:00</published>\n" + 
+				"<author>\n" +
-				"<author>\n" + 
 				"<name>ca.uhn.fhir.rest.server.DummyRestfulServer</name>\n" + 
 				"</author>\n" + 
 				"<entry>\n" + 
@@ -301,7 +300,6 @@ public class ClientTest {
 		String msg = "<feed xmlns=\"http://www.w3.org/2005/Atom\"><title/><id>6c1d93be-027f-468d-9d47-f826cd15cf42</id>"
 				+ "<link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history\"/>"
 				+ "<link rel=\"fhir-base\" href=\"http://localhost:51698\"/><os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults>"
-				+ "<published>2014-04-13T18:24:50-04:00</published>"
 				+ "<author><name>ca.uhn.fhir.rest.method.HistoryMethodBinding</name></author>"
 				+ "<entry><title>Patient 222</title><id>222</id>"
 				+ "<updated>"+date1.getValueAsString()+"</updated>"
@@ -374,7 +372,6 @@ public class ClientTest {
 		String msg = "<feed xmlns=\"http://www.w3.org/2005/Atom\"><title/><id>6c1d93be-027f-468d-9d47-f826cd15cf42</id>"
 				+ "<link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history\"/>"
 				+ "<link rel=\"fhir-base\" href=\"http://localhost:51698\"/><os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults>"
-				+ "<published>2014-04-13T18:24:50-04:00</published>"
 				+ "<author><name>ca.uhn.fhir.rest.method.HistoryMethodBinding</name></author>"
 				+ "<entry><title>Patient 222</title><id>222</id>"
 				+ "<updated>"+date1.getValueAsString()+"</updated>"
@@ -446,7 +443,6 @@ public class ClientTest {
 		String msg = "<feed xmlns=\"http://www.w3.org/2005/Atom\"><title/><id>6c1d93be-027f-468d-9d47-f826cd15cf42</id>"
 				+ "<link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history\"/>"
 				+ "<link rel=\"fhir-base\" href=\"http://localhost:51698\"/><os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults>"
-				+ "<published>2014-04-13T18:24:50-04:00</published>"
 				+ "<author><name>ca.uhn.fhir.rest.method.HistoryMethodBinding</name></author>"
 				+ "<entry><title>Patient 222</title><id>222</id>"
 				+ "<updated>"+date1.getValueAsString()+"</updated>"
@@ -511,7 +507,7 @@ public class ClientTest {
 	public void testHistoryWithParams() throws Exception {
 
 		//@formatter:off
-		final String msg = "<feed xmlns=\"http://www.w3.org/2005/Atom\"><title/><id>6c1d93be-027f-468d-9d47-f826cd15cf42</id><link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history\"/><link rel=\"fhir-base\" href=\"http://localhost:51698\"/><os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults><published>2014-04-13T18:24:50-04:00</published><author><name>ca.uhn.fhir.rest.method.HistoryMethodBinding</name></author><entry><title>Patient 222</title><id>222</id><updated>1969-12-31T19:00:20.000-05:00</updated><published>1969-12-31T19:00:10.000-05:00</published><link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history/1\"/><content type=\"text/xml\"><Patient xmlns=\"http://hl7.org/fhir\"><identifier><use value=\"official\"/><system value=\"urn:hapitest:mrns\"/><value value=\"00001\"/></identifier><name><family value=\"OlderFamily\"/><given value=\"PatientOne\"/></name><gender><text value=\"M\"/></gender></Patient></content></entry><entry><title>Patient 222</title><id>222</id><updated>1969-12-31T19:00:30.000-05:00</updated><published>1969-12-31T19:00:10.000-05:00</published><link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history/2\"/><content type=\"text/xml\"><Patient xmlns=\"http://hl7.org/fhir\"><identifier><use value=\"official\"/><system value=\"urn:hapitest:mrns\"/><value value=\"00001\"/></identifier><name><family value=\"NewerFamily\"/><given value=\"PatientOne\"/></name><gender><text value=\"M\"/></gender></Patient></content></entry></feed>";
+		final String msg = "<feed xmlns=\"http://www.w3.org/2005/Atom\"><title/><id>6c1d93be-027f-468d-9d47-f826cd15cf42</id><link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history\"/><link rel=\"fhir-base\" href=\"http://localhost:51698\"/><os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults><author><name>ca.uhn.fhir.rest.method.HistoryMethodBinding</name></author><entry><title>Patient 222</title><id>222</id><updated>1969-12-31T19:00:20.000-05:00</updated><published>1969-12-31T19:00:10.000-05:00</published><link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history/1\"/><content type=\"text/xml\"><Patient xmlns=\"http://hl7.org/fhir\"><identifier><use value=\"official\"/><system value=\"urn:hapitest:mrns\"/><value value=\"00001\"/></identifier><name><family value=\"OlderFamily\"/><given value=\"PatientOne\"/></name><gender><text value=\"M\"/></gender></Patient></content></entry><entry><title>Patient 222</title><id>222</id><updated>1969-12-31T19:00:30.000-05:00</updated><published>1969-12-31T19:00:10.000-05:00</published><link rel=\"self\" href=\"http://localhost:51698/Patient/222/_history/2\"/><content type=\"text/xml\"><Patient xmlns=\"http://hl7.org/fhir\"><identifier><use value=\"official\"/><system value=\"urn:hapitest:mrns\"/><value value=\"00001\"/></identifier><name><family value=\"NewerFamily\"/><given value=\"PatientOne\"/></name><gender><text value=\"M\"/></gender></Patient></content></entry></feed>";
 		//@formatter:on
 
 		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/client/GenericClientTest.java

@@ -85,8 +85,7 @@ public class GenericClientTest {
 				"<title/>\n" + 
 				"<id>d039f91a-cc3c-4013-988e-af4d8d0614bd</id>\n" + 
 				"<os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">1</os:totalResults>\n" + 
-				"<published>2014-03-11T16:35:07-04:00</published>\n" + 
+				"<author>\n" +
-				"<author>\n" + 
 				"<name>ca.uhn.fhir.rest.server.DummyRestfulServer</name>\n" + 
 				"</author>\n" + 
 				"<entry>\n" + 
@@ -132,7 +131,7 @@ public class GenericClientTest {
 
 		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
 		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
-		when(myHttpResponse.getAllHeaders()).thenReturn(new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "/Patient/44/_history/22") });
+		when(myHttpResponse.getAllHeaders()).thenReturn(new Header[]{new BasicHeader(Constants.HEADER_LOCATION, "/Patient/44/_history/22")});
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(""), Charset.forName("UTF-8")));
 
@@ -141,14 +140,14 @@ public class GenericClientTest {
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 201, "OK"));
 		MethodOutcome resp = client.create().resource(ourCtx.newXmlParser().encodeResourceToString(p1)).execute();
 		assertTrue(resp.getCreated());
-		
+
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		resp = client.create().resource(ourCtx.newXmlParser().encodeResourceToString(p1)).execute();
 		assertNull(resp.getCreated());
-		
+
 	}
-	
+
-	
+
 	@Test
 	public void testCreateWithStringAutoDetectsEncoding() throws Exception {
 

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/client/IncludedResourceStitchingClientTest.java

@@ -114,8 +114,7 @@ public class IncludedResourceStitchingClientTest {
 				"   <link rel=\"self\" href=\"http://localhost:49782/Patient?_query=declaredExtInclude&amp;_pretty=true\"/>\n" + 
 				"   <link rel=\"fhir-base\" href=\"http://localhost:49782\"/>\n" + 
 				"   <os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults>\n" + 
-				"   <published>2014-08-12T10:22:19.097-04:00</published>\n" + 
+				"   <author>\n" +
-				"   <author>\n" + 
 				"      <name>HAPI FHIR Server</name>\n" + 
 				"   </author>\n" + 
 				"   <entry>\n" + 
@@ -192,8 +191,7 @@ public class IncludedResourceStitchingClientTest {
 				"   <link rel=\"self\" href=\"http://localhost:49627/Patient?_query=extInclude&amp;_pretty=true\"/>\n" + 
 				"   <link rel=\"fhir-base\" href=\"http://localhost:49627\"/>\n" + 
 				"   <os:totalResults xmlns:os=\"http://a9.com/-/spec/opensearch/1.1/\">2</os:totalResults>\n" + 
-				"   <published>2014-08-05T15:22:08.512-04:00</published>\n" + 
+				"   <author>\n" +
-				"   <author>\n" + 
 				"      <name>HAPI FHIR Server</name>\n" + 
 				"   </author>\n" + 
 				"   <entry>\n" + 

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/Dstu1BundleFactoryTest.java

@@ -20,6 +20,7 @@ import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu.resource.DiagnosticReport;
+import ca.uhn.fhir.model.dstu.resource.Medication;
 import ca.uhn.fhir.model.dstu.resource.Observation;
 import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.dstu.resource.Practitioner;
@@ -86,6 +87,23 @@ public class Dstu1BundleFactoryTest {
         myBundleFactory = new Dstu1BundleFactory(ourCtx);
     }
 
+    @Test
+    public void whenMedicationHasIngredients_include_shouldIncludeThem() throws Exception {
+        Medication medication = new Medication();
+        medication.setName("Main Medication");
+        medication.setId("Medication/1");
+        Medication ingredientMedication = new Medication();
+        ingredientMedication.setName("Ingredient");
+        ingredientMedication.setId("Medication/2");
+        Medication.ProductIngredient ingredient = new Medication.ProductIngredient();
+        ingredient.setItem(new ResourceReferenceDt(ingredientMedication));
+        medication.getProduct().getIngredient().add(ingredient);
+
+        myResourceList = Arrays.asList(new IBaseResource[]{medication});
+        Bundle bundle = makeBundle(BundleInclusionRule.BASED_ON_INCLUDES, includes("Medication.product.ingredient.item"));
+        assertEquals(2, bundle.getEntries().size());
+    }
+
     @Test
     public void whenIncludeIsAsterisk_bundle_shouldContainAllReferencedResources() throws Exception {
         Bundle bundle = makeBundle(BundleInclusionRule.BASED_ON_INCLUDES, includes("*"));

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/IncomingRequestAddressStrategyTest.java

@@ -1,30 +1,236 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
+import java.io.IOException;
+import java.util.concurrent.TimeUnit;
+
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
 
+import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.Before;
+import org.junit.BeforeClass;
 import org.junit.Test;
 
+import ca.uhn.fhir.util.RandomServerPortProvider;
+
 public class IncomingRequestAddressStrategyTest {
 
+	private static CloseableHttpClient ourClient;
+	private static String ourLastBase;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(IncomingRequestAddressStrategyTest.class);
+	private static IncomingRequestAddressStrategy ourStrategy;
+
+	private Server myServer;
+
+	public void after() throws Exception {
+		if (myServer != null) {
+			myServer.stop();
+		}
+	}
+
+	@Before
+	public void before() {
+		ourLastBase = null;
+		ourStrategy = new IncomingRequestAddressStrategy();
+	}
+
+	private void httpGet(String url) throws IOException, ClientProtocolException {
+		ourLastBase = null;
+
+		HttpGet httpPost = new HttpGet(url);
+		HttpResponse status = ourClient.execute(httpPost);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+		ourLog.info(responseContent);
+	}
+
+	private void startServer(int port, String contextPath, String servletPath) throws Exception {
+		myServer = new Server(port);
+
+		org.eclipse.jetty.servlet.ServletContextHandler proxyHandler = new org.eclipse.jetty.servlet.ServletContextHandler();
+		proxyHandler.setContextPath(contextPath);
+
+		ServletHolder handler = new ServletHolder();
+		handler.setServlet(new MyServlet());
+		proxyHandler.addServlet(handler, servletPath);
+
+		myServer.setHandler(proxyHandler);
+		myServer.start();
+	}
+
 	/**
-	 * This is an incoming request from an instance of Tomcat on AWS, provided by 
+	 * This is an incoming request from an instance of Tomcat on AWS, provided by Simon Ling of Systems Made Simple
-	 * Simon Ling of Systems Made Simple
 	 */
 	@Test
 	public void testAwsUrl() {
-		
+
 		HttpServletRequest req = mock(HttpServletRequest.class);
 		when(req.getRequestURI()).thenReturn("/FhirStorm/fhir/Patient/_search");
 		when(req.getServletPath()).thenReturn("/fhir");
 		when(req.getRequestURL()).thenReturn(new StringBuffer().append("http://fhirstorm.dyndns.org:8080/FhirStorm/fhir/Patient/_search"));
 		when(req.getContextPath()).thenReturn("/FhirStorm");
-		
+
 		IncomingRequestAddressStrategy incomingRequestAddressStrategy = new IncomingRequestAddressStrategy();
-		String actual = incomingRequestAddressStrategy.determineServerBase(null,req);
+		String actual = incomingRequestAddressStrategy.determineServerBase(null, req);
 		assertEquals("http://fhirstorm.dyndns.org:8080/FhirStorm/fhir", actual);
 	}
+
+	@Test
+	public void testUnderJettyWithContextPathServletRoot() throws Exception {
+		int port = RandomServerPortProvider.findFreePort();
+
+		String contextPath = "/ctx";
+		String servletPath = "/*";
+
+		startServer(port, contextPath, servletPath);
+
+		httpGet("http://localhost:" + port + "/ctx");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/Patient?_pretty=true");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/Patient/123/_history/222");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port);
+		assertEquals(null, ourLastBase);
+		
+	}
+
+	@Test
+	public void testUnderJettyWithContextPathServletRootContextOnly() throws Exception {
+		int port = RandomServerPortProvider.findFreePort();
+
+		String contextPath = "/ctx";
+		String servletPath = "/";
+
+		startServer(port, contextPath, servletPath);
+		ourStrategy.setServletPath("");
+
+		httpGet("http://localhost:" + port + "/ctx");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/Patient?_pretty=true");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/Patient/123/_history/222");
+		assertEquals("http://localhost:" + port + "/ctx/", ourLastBase);
+
+		httpGet("http://localhost:" + port);
+		assertEquals(null, ourLastBase);
+		
+	}
+
 	
+	@Test
+	public void testUnderJettyWithContextPathServletRoot2() throws Exception {
+		int port = RandomServerPortProvider.findFreePort();
+
+		String contextPath = "/ctx";
+		String servletPath = "/foo/bar/*"; // not /* but still this should work
+
+		startServer(port, contextPath, servletPath);
+
+		httpGet("http://localhost:" + port + "/ctx/foo/bar/Patient?_pretty=true");
+		assertEquals("http://localhost:" + port + "/ctx/foo/bar", ourLastBase);
+		
+		httpGet("http://localhost:" + port + "/ctx/foo/bar");
+		assertEquals("http://localhost:" + port + "/ctx/foo/bar", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/foo/bar/");
+		assertEquals("http://localhost:" + port + "/ctx/foo/bar", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/foo/bar/Patient/123/_history/222");
+		assertEquals("http://localhost:" + port + "/ctx/foo/bar", ourLastBase);
+
+		httpGet("http://localhost:" + port);
+		assertEquals(null, ourLastBase);
+		
+	}
+
+	@Test
+	public void testUnderJettyWithContextPathServletPath() throws Exception {
+		int port = RandomServerPortProvider.findFreePort();
+
+		String contextPath = "/ctx";
+		String servletPath = "/servlet/*";
+
+		startServer(port, contextPath, servletPath);
+
+		httpGet("http://localhost:" + port);
+		assertEquals(null, ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/servlet/");
+		assertEquals("http://localhost:" + port + "/ctx/servlet", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/servlet/Patient?_pretty=true");
+		assertEquals("http://localhost:" + port + "/ctx/servlet", ourLastBase);
+
+		httpGet("http://localhost:" + port + "/ctx/servlet/Patient/123/_history/222");
+		assertEquals("http://localhost:" + port + "/ctx/servlet", ourLastBase);
+	}
+
+	@Test
+	public void testUnderJettyWithContextRootServletRoot() throws Exception {
+		int port = RandomServerPortProvider.findFreePort();
+
+		String contextPath = "/";
+		String servletPath = "/*";
+
+		startServer(port, contextPath, servletPath);
+
+		httpGet("http://localhost:" + port);
+		assertEquals("http://localhost:" + port + contextPath, ourLastBase);
+
+		httpGet("http://localhost:" + port + "/Patient?_pretty=true");
+		assertEquals("http://localhost:" + port + contextPath, ourLastBase);
+
+		httpGet("http://localhost:" + port + "/Patient/123/_history/222");
+		assertEquals("http://localhost:" + port + contextPath, ourLastBase);
+	}
+
+	@BeforeClass
+	public static void beforeClass() {
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+	}
+
+	private static class MyServlet extends HttpServlet {
+
+		@Override
+		protected void doGet(HttpServletRequest theReq, HttpServletResponse theResp) throws ServletException, IOException {
+			
+//			ourLog.info("Ctx: {}", theReq.)
+			
+			ourLastBase = ourStrategy.determineServerBase(getServletContext(), theReq);
+			theResp.setContentType("text/plain");
+			theResp.getWriter().append("Success");
+			theResp.getWriter().close();
+		}
+
+	}
+
 }

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/util/RandomServerPortProvider.java

@@ -0,0 +1,36 @@
+package ca.uhn.fhir.util;
+
+import java.io.IOException;
+import java.net.ServerSocket;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Provides server ports
+ */
+public class RandomServerPortProvider {
+
+	private static List<Integer> ourPorts = new ArrayList<Integer>(); 
+	
+	public static int findFreePort() {
+		ServerSocket server;
+		try {
+			server = new ServerSocket(0);
+			int port = server.getLocalPort();
+			ourPorts.add(port);
+			server.close();
+			Thread.sleep(500);
+			return port;
+		} catch (IOException e) {
+			throw new Error(e);
+		} catch (InterruptedException e) {
+			throw new Error(e);
+		}
+	}
+
+	public static List<Integer> list() {
+		return ourPorts;
+	}
+
+}
+ 

hapi-fhir-structures-dstu/src/test/resources/mixed-return-bundle.xml

@@ -4,7 +4,6 @@
    <link rel="self" href="http://localhost:8888/fhir/context/Patient?_pretty=true&amp;_include=Patient.managingOrganization&amp;_pretty=true"/>
    <link rel="fhir-base" href="http://localhost:8888/fhir/context"/>
    <os:totalResults xmlns:os="http://a9.com/-/spec/opensearch/1.1/">2</os:totalResults>
-   <published>2014-06-22T21:37:05-04:00</published>
    <author>
       <name>HAPI FHIR Server</name>
    </author>

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/model/dstu2/FhirDstu2.java

@@ -105,7 +105,7 @@ public class FhirDstu2 implements IFhirVersion {
 	public Class<? extends BaseContainedDt> getContainedType() {
 		return ContainedDt.class;
 	}
-	
+
 	@Override
 	public BaseCodingDt newCodingDt() {
 		return new CodingDt();

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -468,7 +468,7 @@ public class XmlParserDstu2Test {
 		//@formatter:on
 		
 		Patient p = ourCtx.newXmlParser().parseResource(Patient.class, res);
-		assertEquals(htmlNoNs, p.getText().getDiv().getValueAsString());
+		assertEquals(htmlNs, p.getText().getDiv().getValueAsString());
 	}
 	
 	/**

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/SearchDstu2Test.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
 
 import java.util.concurrent.TimeUnit;
 
@@ -49,6 +49,7 @@ public class SearchDstu2Test {
 		Patient patient = (Patient) ourCtx.newXmlParser().parseResource(Bundle.class, responseContent).getEntry().get(0).getResource();
 		String ref = patient.getManagingOrganization().getReference().getValue();
 		assertEquals("Organization/555", ref);
+		assertNull(status.getFirstHeader(Constants.HEADER_CONTENT_LOCATION));
 	}
 
 

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserHl7OrgDstu2Test.java

@@ -1062,7 +1062,7 @@ public class XmlParserHl7OrgDstu2Test {
 		Patient patient = ourCtx.newXmlParser().parseResource(Patient.class, msg);
 
 		assertEquals(NarrativeStatus.GENERATED, patient.getText().getStatus());
-		assertEquals("<div>John Cardinal:            444333333        </div>", patient.getText().getDiv().getValueAsString());
+		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">John Cardinal:            444333333        </div>", patient.getText().getDiv().getValueAsString());
 		assertEquals("PRP1660", patient.getIdentifier().get(0).getValue());
 
 		String encoded = ourCtx.newXmlParser().encodeResourceToString(patient);
@@ -1197,6 +1197,8 @@ public class XmlParserHl7OrgDstu2Test {
 		Patient patient1 = ourCtx.newXmlParser().parseResource(Patient.class, msg);
 		String encoded1 = ourCtx.newXmlParser().encodeResourceToString(patient1);
 
+		ourLog.info(encoded1);
+		
 		Diff d = new Diff(new StringReader(msg), new StringReader(encoded1));
 		assertTrue(d.toString(), d.identical());
 

hapi-fhir-testpage-overlay/.gitignore

@@ -1 +1,128 @@
+/target/
+
+# Created by https://www.gitignore.io
+
+### Java ###
+*.class
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.ear
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+
+### Maven ###
+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+buildNumber.properties
+
+
+### Vim ###
+[._]*.s[a-w][a-z]
+[._]s[a-w][a-z]
+*.un~
+Session.vim
+.netrwhist
+*~
+
+
+### Intellij ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm
+
+*.iml
+
+## Directory-based project format:
+.idea/
+# if you remove the above rule, at least ignore the following:
+
+# User-specific stuff:
+# .idea/workspace.xml
+# .idea/tasks.xml
+# .idea/dictionaries
+
+# Sensitive or high-churn files:
+# .idea/dataSources.ids
+# .idea/dataSources.xml
+# .idea/sqlDataSources.xml
+# .idea/dynamic.xml
+# .idea/uiDesigner.xml
+
+# Gradle:
+# .idea/gradle.xml
+# .idea/libraries
+
+# Mongo Explorer plugin:
+# .idea/mongoSettings.xml
+
+## File-based project format:
+*.ipr
+*.iws
+
+## Plugin-specific files:
+
+# IntelliJ
+/out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+
+
+
+### Eclipse ###
+*.pydevproject
+.metadata
+.gradle
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
+.loadpath
+
+# Eclipse Core
+.project
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# CDT-specific
+.cproject
+
+# JDT-specific (Eclipse Java Development Tools)
+.classpath
+
+# PDT-specific
+.buildpath
+
+# sbteclipse plugin
+.target
+
+# TeXlipse plugin
+.texlipse
+
 /build/

hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/Controller.java

@@ -1203,7 +1203,7 @@ public class Controller {
 
 	private String parseNarrative(HomeRequest theRequest, EncodingEnum theCtEnum, String theResultBody) {
 		try {
-			IResource resource = theCtEnum.newParser(getContext(theRequest)).parseResource(theResultBody);
+			IResource resource = (IResource) theCtEnum.newParser(getContext(theRequest)).parseResource(theResultBody);
 			String retVal = resource.getText().getDiv().getValueAsString();
 			return StringUtils.defaultString(retVal);
 		} catch (Exception e) {

hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/model/HomeRequest.java

@@ -49,7 +49,9 @@ public class HomeRequest {
 		}
 
 		if (retVal.contains("${serverBase}")) {
-			String base = new IncomingRequestAddressStrategy().determineServerBase(theRequest.getServletContext(), theRequest);
+			IncomingRequestAddressStrategy strategy = new IncomingRequestAddressStrategy();
+			strategy.setServletPath("");
+			String base = strategy.determineServerBase(theRequest.getServletContext(), theRequest);
 			if (base.endsWith("/")) {
 				base = base.substring(0, base.length() - 1);
 			}

hapi-fhir-testpage-overlay/src/test/java/ca/uhn/fhir/jpa/test/OverlayTestApp.java

@@ -8,6 +8,7 @@ import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.eclipse.jetty.webapp.WebAppContext;
+import org.hl7.fhir.instance.model.IBaseResource;
 import org.springframework.context.support.ClassPathXmlApplicationContext;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -129,7 +130,7 @@ public class OverlayTestApp {
 			client.create(p1);
 
 			List<IResource> resources = restServerDstu1.getFhirContext().newJsonParser().parseBundle(IOUtils.toString(OverlayTestApp.class.getResourceAsStream("/test-server-seed-bundle.json"))).toListOfResources();
-			client.transaction(resources);
+			client.transaction(new ArrayList<IBaseResource>(resources));
 
 			client.create(p1);
 			client.create(p1);

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/model/dstu2/resource/BaseResource.java

@@ -0,0 +1,175 @@
+package ca.uhn.fhir.model.dstu2.resource;
+
+/*
+ * #%L
+ * HAPI FHIR Structures - DSTU2 (FHIR v0.4.0)
+ * %%
+ * Copyright (C) 2014 - 2015 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import ca.uhn.fhir.model.api.BaseElement;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.SearchParamDefinition;
+import ca.uhn.fhir.model.base.resource.ResourceMetadataMap;
+import ca.uhn.fhir.model.dstu2.composite.ContainedDt;
+import ca.uhn.fhir.model.dstu2.composite.NarrativeDt;
+import ca.uhn.fhir.model.primitive.CodeDt;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.gclient.StringClientParam;
+import ca.uhn.fhir.util.ElementUtil;
+
+public abstract class BaseResource extends BaseElement implements IResource {
+
+	/**
+	 * Search parameter constant for <b>_language</b>
+	 */
+	@SearchParamDefinition(name="_language", path="", description="The language of the resource", type="string"  )
+	public static final String SP_RES_LANGUAGE = "_language";
+
+
+	/**
+	 * Search parameter constant for <b>_id</b>
+	 */
+	@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="string"  )
+	public static final String SP_RES_ID = "_id";
+
+	/**
+	 * <b>Fluent Client</b> search parameter constant for <b>_id</b>
+	 * <p>
+	 * Description: <b>the _id of a resource</b><br>
+	 * Type: <b>string</b><br>
+	 * Path: <b>Resource._id</b><br>
+	 * </p>
+	 */
+	public static final StringClientParam RES_ID = new StringClientParam(BaseResource.SP_RES_ID);
+
+
+	@Child(name = "contained", order = 2, min = 0, max = 1)
+	private ContainedDt myContained;
+
+	private IdDt myId;
+
+	@Child(name = "language", order = 0, min = 0, max = Child.MAX_UNLIMITED)
+	private CodeDt myLanguage;
+
+	private ResourceMetadataMap myResourceMetadata;
+
+	@Child(name = "text", order = 1, min = 0, max = 1)
+	private NarrativeDt myText;
+
+	@Override
+	public ContainedDt getContained() {
+		if (myContained == null) {
+			myContained = new ContainedDt();
+		}
+		return myContained;
+	}
+
+	public IdDt getId() {
+		if (myId == null) {
+			myId = new IdDt();
+		}
+		return myId;
+	}
+
+	@Override
+	public CodeDt getLanguage() {
+		if (myLanguage == null) {
+			myLanguage = new CodeDt();
+		}
+		return myLanguage;
+	}
+
+	@Override
+	public ResourceMetadataMap getResourceMetadata() {
+		if (myResourceMetadata == null) {
+			myResourceMetadata = new ResourceMetadataMap();
+		}
+		return myResourceMetadata;
+	}
+
+	@Override
+	public NarrativeDt getText() {
+		if (myText == null) {
+			myText = new NarrativeDt();
+		}
+		return myText;
+	}
+
+	public void setContained(ContainedDt theContained) {
+		myContained = theContained;
+	}
+
+	public void setId(IdDt theId) {
+		myId = theId;
+	}
+	
+	public BaseResource setId(IIdType theId) {
+		if (theId instanceof IdDt) {
+			myId = (IdDt) theId;
+		} else if (theId != null) {
+			myId = new IdDt(theId.getValue());
+		}
+		return this;
+	}
+
+	public BaseResource setId(String theId) {
+		if (theId == null) {
+			myId = null;
+		} else {
+			myId = new IdDt(theId);
+		}
+		return this;
+	}
+
+	@Override
+	public void setLanguage(CodeDt theLanguage) {
+		myLanguage = theLanguage;
+	}
+
+	@Override
+	public void setResourceMetadata(ResourceMetadataMap theMap) {
+		Validate.notNull(theMap, "The Map must not be null");
+		myResourceMetadata = theMap;
+	}
+
+	public void setText(NarrativeDt theText) {
+		myText = theText;
+	}
+
+	@Override
+	public String toString() {
+		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+		b.append("id", getId().toUnqualified());
+		return b.toString();
+	}
+
+	/**
+	 * Intended to be called by extending classes {@link #isEmpty()} implementations, returns <code>true</code> if all
+	 * content in this superclass instance is empty per the semantics of {@link #isEmpty()}.
+	 */
+	@Override
+	protected boolean isBaseEmpty() {
+		return super.isBaseEmpty() && ElementUtil.isEmpty(myLanguage, myText, myId);
+	}
+
+}

restful-server-example-test/pom.xml

@@ -21,7 +21,7 @@
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
-			<artifactId>hapi-fhir-structures-dstu</artifactId>
+			<artifactId>hapi-fhir-structures-dstu2</artifactId>
 			<version>1.0-SNAPSHOT</version>
 			<scope>test</scope>
 		</dependency>

restful-server-example-test/src/test/java/ca/uhn/example/ExampleTest.java

@@ -1,7 +1,6 @@
 package ca.uhn.example;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
-import static org.junit.Assert.assertThat;
 
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.webapp.WebAppContext;
@@ -12,7 +11,7 @@ import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
-import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.rest.client.IGenericClient;
 
 public class ExampleTest {

restful-server-example/pom.xml

@@ -14,7 +14,7 @@
 	
 	<groupId>ca.uhn.hapi.example</groupId>
 	<artifactId>restful-server-example</artifactId>
-	<version>0.8-SNAPSHOT</version>
+	<version>1.0-SNAPSHOT</version>
 	<packaging>war</packaging>
 
 	<name>HAPI FHIR Sample RESTful Server</name>
@@ -40,7 +40,7 @@
 		<!-- At least one "structures" JAR must also be included -->
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
-			<artifactId>hapi-fhir-structures-dstu</artifactId>
+			<artifactId>hapi-fhir-structures-dstu2</artifactId>
 			<version>1.0-SNAPSHOT</version>
 		</dependency>
 

restful-server-example/src/main/java/ca/uhn/example/model/MyOrganization.java

@@ -3,7 +3,6 @@ package ca.uhn.example.model;
 import java.util.ArrayList;
 import java.util.List;
 
-import ca.uhn.fhir.model.api.BaseElement;
 import ca.uhn.fhir.model.api.BaseIdentifiableElement;
 import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IExtension;
@@ -12,8 +11,8 @@ import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.api.annotation.Extension;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import ca.uhn.fhir.model.dstu.composite.ContactDt;
+import ca.uhn.fhir.model.dstu2.composite.ContactPointDt;
-import ca.uhn.fhir.model.dstu.resource.Organization;
+import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.primitive.BooleanDt;
 import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.util.ElementUtil;
@@ -115,7 +114,7 @@ public class MyOrganization extends Organization {
 		@Description(shortDefinition = "Contains the actual contact details")
 		@Extension(url = "http://foo#emergencyContactContact", isModifier = false, definedLocally = true)
 		@Child(name = "contact")
-		private ContactDt myContact;
+		private ContactPointDt myContact;
 
 		/* *****************************
 		 * Getters and setters
@@ -132,14 +131,14 @@ public class MyOrganization extends Organization {
 			myActive = theActive;
 		}
 
-		public ContactDt getContact() {
+		public ContactPointDt getContact() {
 			if (myContact == null) {
-				myContact = new ContactDt();
+				myContact = new ContactPointDt();
 			}
 			return myContact;
 		}
 
-		public void setContact(ContactDt theContact) {
+		public void setContact(ContactPointDt theContact) {
 			myContact = theContact;
 		}
 

restful-server-example/src/main/java/ca/uhn/example/provider/OrganizationResourceProvider.java

@@ -1,9 +1,8 @@
 package ca.uhn.example.provider;
 
 import ca.uhn.example.model.MyOrganization;
-import ca.uhn.example.model.MyOrganization.EmergencyContact;
+import ca.uhn.fhir.model.dstu2.composite.ContactPointDt;
-import ca.uhn.fhir.model.dstu.composite.ContactDt;
+import ca.uhn.fhir.model.dstu2.valueset.ContactPointUseEnum;
-import ca.uhn.fhir.model.dstu.valueset.ContactUseEnum;
 import ca.uhn.fhir.model.primitive.BooleanDt;
 import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -51,9 +50,9 @@ public class OrganizationResourceProvider implements IResourceProvider {
 		
 		MyOrganization retVal = new MyOrganization();
 		retVal.setId("1");
-		retVal.addIdentifier("urn:example:orgs", "FooOrganization");
+		retVal.addIdentifier().setSystem("urn:example:orgs").setValue("FooOrganization");
 		retVal.addAddress().addLine("123 Fake Street").setCity("Toronto");
-		retVal.addTelecom().setUse(ContactUseEnum.WORK).setValue("1-888-123-4567");
+		retVal.addTelecom().setUse(ContactPointUseEnum.WORK).setValue("1-888-123-4567");
 		
 		// Populate the first, primitive extension
 		retVal.setBillingCode(new CodeDt("00102-1"));
@@ -61,7 +60,7 @@ public class OrganizationResourceProvider implements IResourceProvider {
 		// The second extension is repeatable and takes a block type
 		MyOrganization.EmergencyContact contact = new MyOrganization.EmergencyContact();
 		contact.setActive(new BooleanDt(true));
-		contact.setContact(new ContactDt());
+		contact.setContact(new ContactPointDt());
 		retVal.getEmergencyContact().add(contact);
 		
 		return retVal;

restful-server-example/src/main/java/ca/uhn/example/provider/PatientResourceProvider.java

@@ -7,11 +7,11 @@ import java.util.List;
 import java.util.Map;
 
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-import ca.uhn.fhir.model.dstu.composite.HumanNameDt;
+import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
-import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
+import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
-import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.dstu.valueset.AdministrativeGenderCodesEnum;
+import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
-import ca.uhn.fhir.model.dstu.valueset.IssueSeverityEnum;
+import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.StringDt;
@@ -59,7 +59,7 @@ public class PatientResourceProvider implements IResourceProvider {
 		patient.getIdentifier().get(0).setValue("00002");
 		patient.addName().addFamily("Test");
 		patient.getName().get(0).addGiven("PatientOne");
-		patient.setGender(AdministrativeGenderCodesEnum.F);
+		patient.setGender(AdministrativeGenderEnum.FEMALE);
 
 		LinkedList<Patient> list = new LinkedList<Patient>();
 		list.add(patient);

restful-server-example/src/main/java/ca/uhn/example/servlet/ExampleRestfulServlet.java

@@ -5,6 +5,7 @@ import java.util.List;
 
 import ca.uhn.example.provider.OrganizationResourceProvider;
 import ca.uhn.example.provider.PatientResourceProvider;
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.rest.server.IResourceProvider;
@@ -23,6 +24,7 @@ public class ExampleRestfulServlet extends RestfulServer {
 	 */
 	@Override
 	public void initialize() {
+		setFhirContext(FhirContext.forDstu2());// Support DSTU2
 		
 		/*
 		 * Two resource providers are defined. Each one handles a specific

src/changes/changes.xml

@@ -136,6 +136,16 @@
 				configures the parser to preserve versions in resource reference links when
 				encoding. By default, these are removed.
 			</action>
+			<action type="fix" issue="155" dev="wdebeau1">
+				Terser's IModelVisitor now supplies to the path to the element. This is
+				an API change, but I don't think there are many users of the IModelVisitor yet.
+				Please let us know if this is a big hardship and we can find an alternate way
+				of making this change.
+			</action>
+			<action type="fix">
+				Prevent server from returning a Content-Location header for search
+				response when using the DSTU2 bundle format
+			</action>
 		</release>
 		<release version="0.9" date="2015-Mar-14">
 			<action type="add">

src/site/xdoc/doc_rest_client.xml

@@ -165,8 +165,10 @@
 
 				<h4>Search - Using HTTP POST</h4>
 				<p>
-					The FHIR specification allows the use of an HTTP POST to transmit a search to a server instead of using
+					The FHIR specification allows the use of an HTTP POST to transmit a search to a server instead of
-					an HTTP GET. With this style of search, the search parameters are included in the request body instead
+					using
+					an HTTP GET. With this style of search, the search parameters are included in the request body
+					instead
 					of the request URL, which can be useful if you need to transmit a search with a large number
 					of parameters.
 				</p>
@@ -176,7 +178,7 @@
 					case the client automatically switches to POST.
 				</p>
 				<p>
-					An alternate form of the search URL (using a URL ending with <code>_search</code>) was also
+					An alternate form of the search URL (using a URL ending with<code>_search</code>) was also
 					supported in FHIR DSTU1. This form is no longer valid in FHIR DSTU2, but HAPI retains support
 					for using this form in order to interoperate with servers which use it.
 				</p>
@@ -211,18 +213,18 @@
 					<param name="file"
 						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
-				
+
 				<h4>Conditional Creates</h4>
 				<p>
 					FHIR also specifies a type of update called "conditional create", where
 					a set of search parameters are provided and a new resource is only
-					created if no existing resource matches those parameters. See the 
+					created if no existing resource matches those parameters. See the
-					FHIR specification for more information on conditional creation. 
+					FHIR specification for more information on conditional creation.
 				</p>
 				<macro name="snippet">
-					<param name="id" value="updateConditional" />
+					<param name="id" value="updateConditional"/>
 					<param name="file"
-						value="examples/src/main/java/example/GenericClientExample.java" />
+						   value="examples/src/main/java/example/GenericClientExample.java"/>
 				</macro>
 			</subsection>			
 
@@ -276,7 +278,7 @@
 				</macro>
 				<h4>Conditional Deletes</h4>
 				<p>
-					Conditional deletions are also possible, which is a form where 
+					Conditional deletions are also possible, which is a form where
 					instead of deleting a resource using its logical ID, you specify
 					a set of search criteria and a single resource is deleted if
 					it matches that criteria. Note that this is not a mechanism
@@ -284,9 +286,9 @@
 					on conditional deletes and how they are used.
 				</p>
 				<macro name="snippet">
-					<param name="id" value="deleteConditional" />
+					<param name="id" value="deleteConditional"/>
 					<param name="file"
-						value="examples/src/main/java/example/GenericClientExample.java" />
+						   value="examples/src/main/java/example/GenericClientExample.java"/>
 				</macro>
 			</subsection>
 
@@ -305,19 +307,19 @@
 					<param name="file"
 						value="examples/src/main/java/example/GenericClientExample.java" />
 				</macro>
-				
+
 				<h4>Conditional Updates</h4>
 				<p>
 					FHIR also specifies a type of update called "conditional updates", where
 					insetad of using the logical ID of a resource to update, a set of
 					search parameters is provided. If a single resource matches that set of
-					parameters, that resource is updated. See the FHIR specification for 
+					parameters, that resource is updated. See the FHIR specification for
 					information on how conditional updates work.
 				</p>
 				<macro name="snippet">
-					<param name="id" value="updateConditional" />
+					<param name="id" value="updateConditional"/>
 					<param name="file"
-						value="examples/src/main/java/example/GenericClientExample.java" />
+						   value="examples/src/main/java/example/GenericClientExample.java"/>
 				</macro>
 
 				<h4>ETags and Resource Contention</h4>