HL7org unit tests all pass

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

@@ -156,8 +156,11 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		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);
+		
+		Class<? extends IBase> versionReferenceType = theContext.getVersion().getResourceReferenceType();
+		myDatatypeToDefinition.put(versionReferenceType, def);
 	}
 
 	public static String createExtensionChildName(BaseRuntimeElementDefinition<?> next) {

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

@@ -678,7 +678,7 @@ public class JsonParser extends BaseParser implements IParser {
 			}
 		} else if (theResource instanceof IAnyResource) {
 			IAnyResource res = (IAnyResource) theResource;
-			if (theContainedResource && StringUtils.isNotBlank(res.getId().getIdPart())) {
+			if (/*theContainedResource && */ StringUtils.isNotBlank(res.getId().getIdPart())) {
 				resourceId = res.getId().getIdPart();
 			}
 		}

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

@@ -1959,8 +1959,10 @@ class ParserState<T> {
 				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);
+					// nothing
+				} else if (StringUtils.isNotBlank(versionId)) {
+					elem.getIdElement().setValue(resourceName + "/" + elem.getId().getIdPart() + "/_history/" + versionId);
 				} else {
 					elem.getIdElement().setValue(resourceName + "/" + elem.getId().getIdPart());
 				}

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

@@ -35,7 +35,7 @@ import ca.uhn.fhir.model.primitive.UriDt;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.api.IRestfulClient;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
-import ca.uhn.fhir.rest.client.exceptions.FhirClientInnapropriateForServerException;
+import ca.uhn.fhir.rest.client.exceptions.FhirClientInappropriateForServerException;
 import ca.uhn.fhir.rest.gclient.ICreate;
 import ca.uhn.fhir.rest.gclient.IDelete;
 import ca.uhn.fhir.rest.gclient.IFetchConformanceUntyped;
@@ -116,7 +116,7 @@ public interface IGenericClient extends IRestfulClient {
 	 * 
 	 * @throws FhirClientConnectionException
 	 *             if the conformance statement cannot be read, or if the client
-	 * @throws FhirClientInnapropriateForServerException
+	 * @throws FhirClientInappropriateForServerException
 	 *             If the conformance statement indicates that the server is inappropriate for this client (e.g. it implements the wrong version of FHIR)
 	 */
 	void forceConformanceCheck() throws FhirClientConnectionException;

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

@@ -51,7 +51,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.rest.client.api.IRestfulClient;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
-import ca.uhn.fhir.rest.client.exceptions.FhirClientInnapropriateForServerException;
+import ca.uhn.fhir.rest.client.exceptions.FhirClientInappropriateForServerException;
 import ca.uhn.fhir.rest.method.BaseMethodBinding;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.util.FhirTerser;
@@ -316,7 +316,7 @@ public class RestfulClientFactory implements IRestfulClientFactory {
 		if (serverFhirVersionEnum != null) {
 			FhirVersionEnum contextFhirVersion = myContext.getVersion().getVersion();
 			if (!contextFhirVersion.isEquivalentTo(serverFhirVersionEnum)) {
-				throw new FhirClientInnapropriateForServerException(myContext.getLocalizer().getMessage(RestfulClientFactory.class, "wrongVersionInConformance", theServerBase + Constants.URL_TOKEN_METADATA, serverFhirVersionString, serverFhirVersionEnum, contextFhirVersion));
+				throw new FhirClientInappropriateForServerException(myContext.getLocalizer().getMessage(RestfulClientFactory.class, "wrongVersionInConformance", theServerBase + Constants.URL_TOKEN_METADATA, serverFhirVersionString, serverFhirVersionEnum, contextFhirVersion));
 			}
 		}
 		

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

@@ -27,19 +27,19 @@ import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
  * communicate with a server which is a valid FHIR server but is incompatible
  * with this client for some reason.
  */
-public class FhirClientInnapropriateForServerException extends BaseServerResponseException {
+public class FhirClientInappropriateForServerException extends BaseServerResponseException {
 
 	private static final long serialVersionUID = 1L;
 
-	public FhirClientInnapropriateForServerException(Throwable theCause) {
+	public FhirClientInappropriateForServerException(Throwable theCause) {
 		super(0, theCause);
 	}
 
-	public FhirClientInnapropriateForServerException(String theMessage, Throwable theCause) {
+	public FhirClientInappropriateForServerException(String theMessage, Throwable theCause) {
 		super(0, theMessage, theCause);
 	}
 
-	public FhirClientInnapropriateForServerException(String theMessage) {
+	public FhirClientInappropriateForServerException(String theMessage) {
 		super(0, theMessage);
 	}
 

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

@@ -127,8 +127,8 @@ public class FhirTerser {
                 if (theElement == null || theElement.isEmpty()) {
                     return;
                 }
-                if (BaseResourceReferenceDt.class.isAssignableFrom(theElement.getClass())) {
+                if (IReference.class.isAssignableFrom(theElement.getClass())) {
-                    retVal.add(new ResourceReferenceInfo(theResource, thePathToElement, (BaseResourceReferenceDt)theElement));
+                    retVal.add(new ResourceReferenceInfo(myContext, theResource, thePathToElement, (IReference)theElement));
                 }
             }
 
@@ -136,7 +136,7 @@ public class FhirTerser {
             public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition,
                                                   ExtensionDt theNextExt) {
                 if (theNextExt.getValue() != null && BaseResourceReferenceDt.class.isAssignableFrom(theNextExt.getValue().getClass())) {
-                    retVal.add(new ResourceReferenceInfo(theResource, thePathToElement, (BaseResourceReferenceDt)theNextExt.getValue()));
+                    retVal.add(new ResourceReferenceInfo(myContext, theResource, thePathToElement, (BaseResourceReferenceDt)theNextExt.getValue()));
                 }
             }
         });

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

@@ -20,79 +20,82 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
-import ca.uhn.fhir.model.api.Include;
+import java.util.Iterator;
-import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import java.util.List;
-import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
+import java.util.Set;
 
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hl7.fhir.instance.model.IBaseResource;
+import org.hl7.fhir.instance.model.api.IReference;
 
-import java.util.Iterator;
+import ca.uhn.fhir.context.FhirContext;
-import java.util.List;
+import ca.uhn.fhir.model.api.Include;
-import java.util.Set;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
 
 /**
  * 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 IReference myResource;
 
-    public ResourceReferenceInfo(IBaseResource theOwningResource, List<String> thePathToElement, BaseResourceReferenceDt theResource) {
+	public ResourceReferenceInfo(FhirContext theContext, IBaseResource theOwningResource, List<String> thePathToElement, IReference theElement) {
-        myOwningResource = theOwningResource.getClass().getAnnotation(ResourceDef.class).name();
-        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
+		myOwningResource = theContext.getResourceDefinition(theOwningResource).getName();
-    public String toString() {
-        ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
-        b.append("name", myName);
-        b.append("resource", myResource.getReference());
-        return b.build();
-    }
 
-    public String getName() {
+		myResource = theElement;
-        return myName;
+		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;
+		}
+	}
 
-    public BaseResourceReferenceDt getResourceReference() {
+	@Override
-        return myResource;
+	public String toString() {
-    }
+		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+		b.append("name", myName);
+		b.append("resource", myResource.getReference());
+		return b.build();
+	}
 
-    public boolean matchesIncludeSet(Set<Include> theIncludes) {
+	public String getName() {
-        if (theIncludes == null)
+		return myName;
-            return false;
+	}
-        for (Include include : theIncludes) {
-            if (matchesInclude(include))
-                return true;
-        }
-        return false;
-    }
 
-    public boolean matchesInclude(Include theInclude) {
+	public IReference getResourceReference() {
-        if (theInclude.getValue().equals("*")) {
+		return myResource;
-            return true;
+	}
-        }
+
-        if (theInclude.getValue().indexOf(':') != -1) {
+	public boolean matchesIncludeSet(Set<Include> theIncludes) {
-            // DSTU2 style
+		if (theIncludes == null)
-            return (theInclude.getValue().equals(myOwningResource + ':' + myName));
+			return false;
-        } else {
+		for (Include include : theIncludes) {
-            // DSTU1 style
+			if (matchesInclude(include))
-            return (theInclude.getValue().equals(myOwningResource + '.' + myName));
+				return true;
-        }
+		}
-    }
+		return false;
+	}
+
+	public boolean matchesInclude(Include theInclude) {
+		if (theInclude.getValue().equals("*")) {
+			return true;
+		}
+		if (theInclude.getValue().indexOf(':') != -1) {
+			// DSTU2 style
+			return (theInclude.getValue().equals(myOwningResource + ':' + myName));
+		} else {
+			// DSTU1 style
+			return (theInclude.getValue().equals(myOwningResource + '.' + myName));
+		}
+	}
 }

hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IReference.java

@@ -22,9 +22,10 @@ package org.hl7.fhir.instance.model.api;
 
 import org.hl7.fhir.instance.model.IBase;
 import org.hl7.fhir.instance.model.IBaseResource;
+import org.hl7.fhir.instance.model.ICompositeType;
 import org.hl7.fhir.instance.model.IPrimitiveType;
 
-public interface IReference extends IBase {
+public interface IReference extends ICompositeType {
 
 	IBaseResource getResource();
 

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2hl7org/Dstu2Hl7OrgBundleFactory.java

@@ -99,15 +99,15 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 				}
 			}
 
-            List<ResourceReferenceInfo> references = myContext.newTerser().getAllResourceReferences(next);
+			List<ResourceReferenceInfo> references = myContext.newTerser().getAllResourceReferences(next);
 			do {
 				List<IBaseResource> addedResourcesThisPass = new ArrayList<IBaseResource>();
 
-                for (ResourceReferenceInfo nextRefInfo : references) {
+				for (ResourceReferenceInfo nextRefInfo : references) {
-                    if (!theBundleInclusionRule.shouldIncludeReferencedResource(nextRefInfo, theIncludes))
+					if (!theBundleInclusionRule.shouldIncludeReferencedResource(nextRefInfo, theIncludes))
-                        continue;
+						continue;
 
-                    IBaseResource nextRes = (IBaseResource) nextRefInfo.getResourceReference().getResource();
+					IBaseResource nextRes = (IBaseResource) nextRefInfo.getResourceReference().getResource();
 					if (nextRes != null) {
 						if (nextRes.getId().hasIdPart()) {
 							if (containedIds.contains(nextRes.getId().getValue())) {
@@ -130,22 +130,22 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 					}
 				}
 
-                includedResources.addAll(addedResourcesThisPass);
+				includedResources.addAll(addedResourcesThisPass);
 
 				// Linked resources may themselves have linked resources
-                references = new ArrayList<ResourceReferenceInfo>();
+				references = new ArrayList<ResourceReferenceInfo>();
 				for (IBaseResource iResource : addedResourcesThisPass) {
-                    List<ResourceReferenceInfo> newReferences = myContext.newTerser().getAllResourceReferences(iResource);
+					List<ResourceReferenceInfo> newReferences = myContext.newTerser().getAllResourceReferences(iResource);
 					references.addAll(newReferences);
 				}
 			} while (references.isEmpty() == false);
 
 			BundleEntryComponent entry = myBundle.addEntry().setResource((Resource) next);
-			
+
-//			BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next);
+			// BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next);
-//			if (searchMode != null) {
+			// if (searchMode != null) {
-//				entry.getSearch().getModeElement().setValue(searchMode.getCode());
+			// entry.getSearch().getModeElement().setValue(searchMode.getCode());
-//			}
+			// }
 		}
 
 		/*
@@ -157,7 +157,7 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 
 	}
 
-    @Override
+	@Override
 	public void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theCompleteUrl, Integer theTotalResults, BundleTypeEnum theBundleType) {
 
 		if (myBundle.getId().isEmpty()) {
@@ -194,7 +194,8 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 	}
 
 	@Override
-	public void initializeBundleFromBundleProvider(RestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl, boolean thePrettyPrint, int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
+	public void initializeBundleFromBundleProvider(RestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
+			boolean thePrettyPrint, int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
 		int numToReturn;
 		String searchId = null;
 		List<IBaseResource> resourceList;
@@ -252,11 +253,13 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 
 			if (searchId != null) {
 				if (theOffset + numToReturn < theResult.size()) {
-					myBundle.addLink().setRelation(Constants.LINK_NEXT).setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
+					myBundle.addLink().setRelation(Constants.LINK_NEXT)
+							.setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
 				}
 				if (theOffset > 0) {
 					int start = Math.max(0, theOffset - limit);
-					myBundle.addLink().setRelation(Constants.LINK_PREVIOUS).setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
+					myBundle.addLink().setRelation(Constants.LINK_PREVIOUS)
+							.setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
 				}
 			}
 		}
@@ -273,7 +276,8 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 	}
 
 	@Override
-	public void initializeBundleFromResourceList(String theAuthor, List<IBaseResource> theResources, String theServerBase, String theCompleteUrl, int theTotalResults, BundleTypeEnum theBundleType) {
+	public void initializeBundleFromResourceList(String theAuthor, List<? extends IBaseResource> theResources, String theServerBase, String theCompleteUrl, int theTotalResults,
+			BundleTypeEnum theBundleType) {
 		myBundle = new Bundle();
 
 		myBundle.setId(UUID.randomUUID().toString());
@@ -286,7 +290,7 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 
 		if (theBundleType.equals(BundleTypeEnum.TRANSACTION)) {
 			for (IBaseResource nextBaseRes : theResources) {
-				IBaseResource next = (IBaseResource)nextBaseRes;
+				IBaseResource next = (IBaseResource) nextBaseRes;
 				BundleEntryComponent nextEntry = myBundle.addEntry();
 
 				nextEntry.setResource((Resource) next);
@@ -309,7 +313,7 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 		myBundle.getTotalElement().setValue(theTotalResults);
 	}
 
-	private void addResourcesForSearch(List<IBaseResource> theResult) {
+	private void addResourcesForSearch(List<? extends IBaseResource> theResult) {
 		List<IBaseResource> includedResources = new ArrayList<IBaseResource>();
 		Set<IIdType> addedResourceIds = new HashSet<IIdType>();
 
@@ -320,7 +324,7 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 		}
 
 		for (IBaseResource nextBaseRes : theResult) {
-			IDomainResource next = (IDomainResource)nextBaseRes;
+			IDomainResource next = (IDomainResource) nextBaseRes;
 			Set<String> containedIds = new HashSet<String>();
 			for (IBaseResource nextContained : next.getContained()) {
 				if (nextContained.getId().isEmpty() == false) {
@@ -388,7 +392,7 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
 	public List<IBaseResource> toListOfResources() {
 		ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
 		for (BundleEntryComponent next : myBundle.getEntry()) {
-			if (next.getResource()!=null) {
+			if (next.getResource() != null) {
 				retVal.add(next.getResource());
 			} else if (next.getTransactionResponse().getLocationElement().isEmpty() == false) {
 				IdType id = new IdType(next.getTransactionResponse().getLocation());

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java

@@ -85,6 +85,9 @@ public class XhtmlNode implements IBaseXhtml {
   }
 
   public List<XhtmlNode> getChildNodes() {
+	  if (childNodes == null) {
+		  childNodes = new ArrayList<XhtmlNode>();
+	  }
     return childNodes;
   }
 

hapi-fhir-structures-hl7org-dstu2/src/main/resources/org/hl7/fhir/instance/model/fhirversion.properties

@@ -92,8 +92,8 @@ resource.Supply=org.hl7.fhir.instance.model.Supply
 resource.ValueSet=org.hl7.fhir.instance.model.ValueSet
 resource.VisionPrescription=org.hl7.fhir.instance.model.VisionPrescription
 
-datatype.Address=org.hl7.fhir.instance.model.AddressType
+datatype.Address=org.hl7.fhir.instance.model.Address
-datatype.Attachment=org.hl7.fhir.instance.model.AttachmentType
+datatype.Attachment=org.hl7.fhir.instance.model.Attachment
 datatype.CodeableConcept=org.hl7.fhir.instance.model.CodeableConceptType
 datatype.Coding=org.hl7.fhir.instance.model.CodingType
 datatype.ContactPoint=org.hl7.fhir.instance.model.ContactPointType
@@ -125,3 +125,4 @@ datatype.time=org.hl7.fhir.instance.model.TimeType
 datatype.unsignedInt=org.hl7.fhir.instance.model.UnsignedIntType
 datatype.uri=org.hl7.fhir.instance.model.UriType
 datatype.xhtml=org.hl7.fhir.instance.model.XhtmlType
+datatype.reference=org.hl7.fhir.instance.model.Reference

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

@@ -3,7 +3,9 @@ package ca.uhn.fhir.parser;
 import static org.junit.Assert.*;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
+import java.util.Set;
 import java.util.UUID;
 
 import org.hl7.fhir.instance.model.CodeableConcept;
@@ -29,7 +31,11 @@ import org.slf4j.LoggerFactory;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.model.valueset.BundleTypeEnum;
+import ca.uhn.fhir.rest.server.BundleInclusionRule;
 import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.provider.dstu2hl7org.Dstu2Hl7OrgBundleFactory;
 
 /**
  * Initially contributed by Alexander Kley for bug #29
@@ -38,26 +44,26 @@ public class ContainedResourceEncodingTest {
 
 	private static Logger logger = LoggerFactory.getLogger(ContainedResourceEncodingTest.class);
 
-	private FhirContext ctx;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ContainedResourceEncodingTest.class);
-
-	private Composition comp;
 
 	private Practitioner author;
 
-	private Patient patient;
+	private Composition comp;
+
+	private FhirContext ctx;
 
 	private final String patFamName1 = "FirstFamilyName";
 
 	private final String patGivName1 = "FirstGivenName";
 
-	@Before
+	private Patient patient;
-	public void initTest() {
-		logger.info("[initTest]");
 
-		initPatient();
+	private void initAuthor() {
-		initAuthor();
+		this.author = new Practitioner();
-		initComposition();
+		this.author.setId((UUID.randomUUID().toString()));
-		this.ctx = new FhirContext();
+		this.author.addIdentifier().setSystem("DoctorID").setValue("4711");
+		this.author.addPractitionerRole().getRole().addCoding().setCode("doctor");
+		this.author.setName(new HumanName().addFamily("Mueller").addGiven("Klaus").addPrefix("Prof. Dr."));
 
 	}
 
@@ -99,40 +105,109 @@ public class ContainedResourceEncodingTest {
 
 	}
 
-	private void initAuthor() {
+	@Before
-		this.author = new Practitioner();
+	public void initTest() {
-		this.author.setId((UUID.randomUUID().toString()));
+		logger.info("[initTest]");
-		this.author.addIdentifier().setSystem("DoctorID").setValue("4711");
+
-		this.author.addPractitionerRole().getRole().addCoding().setCode("doctor");
+		initPatient();
-		this.author.setName(new HumanName().addFamily("Mueller").addGiven("Klaus").addPrefix("Prof. Dr."));
+		initAuthor();
+		initComposition();
+		this.ctx = new FhirContext();
 
 	}
 
 	@Test
-	public void testPatient() {
+	public void testBundleWithContained() {
-		logger.debug("[xmlEncoding] encode resource to xml.");
 
-		/**
+		DiagnosticReport dr = new DiagnosticReport();
-		 * This works fine, although patient instance is modifing from encoder
+		dr.setId(("123"));
-		 */
-		final String expectedPatientXml = this.ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(this.patient);
-		logger.debug("[xmlEncoding] first encoding: {}", expectedPatientXml);
-		final String actualPatientXml = this.ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(this.patient);
-		// second encoding - xml is corrupt - i.e.: patient content 4 times! should be the same as after first encoding!
-		logger.debug("[xmlEncoding] second encoding: {}", actualPatientXml);
 
-		Assert.assertEquals(expectedPatientXml.length(), actualPatientXml.length());
+		Observation observation = new Observation();
-		Assert.assertArrayEquals(expectedPatientXml.getBytes(), actualPatientXml.getBytes());
+
+		CodeableConcept obsName = new CodeableConcept();
+		obsName.setText("name");
+		observation.setCode(obsName);
+
+		Reference result = dr.addResult();
+		result.setResource(observation);
+
+		ArrayList<Reference> performers = new ArrayList<Reference>();
+		Reference performer = new Reference();
+
+		Practitioner p = new Practitioner();
+		p.setId((UUID.randomUUID().toString()));
+		p.addIdentifier().setSystem("DoctorID").setValue("4711");
+		p.addPractitionerRole().getRole().setText("Doctor");
+		p.setName(new HumanName().addFamily("Mueller").addGiven("Klaus").addPrefix("Prof. Dr."));
+
+		performer.setResource(p);
+		performers.add(performer);
+		observation.getPerformer().addAll(performers);
+
+		List<IBaseResource> list = new ArrayList<IBaseResource>();
+		list.add(dr);
+
+		Dstu2Hl7OrgBundleFactory builder = new Dstu2Hl7OrgBundleFactory(ctx);
+		Set<Include> inc2 = Collections.emptySet();
+		builder.addResourcesToBundle(list, BundleTypeEnum.TRANSACTION, "http://foo", BundleInclusionRule.BASED_ON_RESOURCE_PRESENCE, inc2);
+		IBaseResource bundle = builder.getResourceBundle();
+
+		IParser parser = this.ctx.newXmlParser().setPrettyPrint(true);
+		String xml = parser.encodeResourceToString(bundle);
+		ourLog.info(xml);
+		Assert.assertTrue(xml.contains("Mueller"));
 
 	}
-	
+
+	@Test
+	public void testBundleWithContainedWithNoIdDt() {
+
+		DiagnosticReport dr = new DiagnosticReport();
+		dr.setId("123");
+
+		Observation observation = new Observation();
+
+		CodeableConcept obsName = new CodeableConcept();
+		obsName.setText("name");
+		observation.setCode(obsName);
+
+		Reference result = dr.addResult();
+		result.setResource(observation);
+
+		ArrayList<Reference> performers = new ArrayList<Reference>();
+		Reference performer = new Reference();
+
+		Practitioner p = new Practitioner();
+		// no idDt on practitioner p
+		p.addIdentifier().setSystem("DoctorID").setValue("4711");
+		p.addPractitionerRole().getRole().setText("Doctor");
+		p.setName(new HumanName().addFamily("Mueller").addGiven("Klaus").addPrefix("Prof. Dr."));
+
+		performer.setResource(p);
+		performers.add(performer);
+		observation.getPerformer().addAll(performers);
+
+		List<IBaseResource> list = new ArrayList<IBaseResource>();
+		list.add(dr);
+
+		Dstu2Hl7OrgBundleFactory builder = new Dstu2Hl7OrgBundleFactory(ctx);
+		Set<Include> inc2 = Collections.emptySet();
+		builder.addResourcesToBundle(list, BundleTypeEnum.TRANSACTION, "http://foo", BundleInclusionRule.BASED_ON_RESOURCE_PRESENCE, inc2);
+		IBaseResource bundle = builder.getResourceBundle();
+
+		IParser parser = this.ctx.newXmlParser().setPrettyPrint(true);
+		String xml = parser.encodeResourceToString(bundle);
+		Assert.assertTrue(xml.contains("Mueller"));
+
+	}
+
 	@Test
 	public void testComposition() {
 
 		IParser parser = this.ctx.newXmlParser().setPrettyPrint(true);
-		
+
 		assertEquals(0, this.comp.getContained().size());
-		
+
 		/**
 		 * This doesn't works, secund encoding creates corrupt xml
 		 */
@@ -161,84 +236,23 @@ public class ContainedResourceEncodingTest {
 		Assert.assertArrayEquals(expectedCompXml.getBytes(), actualCompXml.getBytes());
 
 	}
-	
+
-	
 	@Test
-	public void testBundleWithContained() {	
+	public void testPatient() {
-		
+		logger.debug("[xmlEncoding] encode resource to xml.");
-		DiagnosticReport dr = new DiagnosticReport();
-		dr.setId(("123"));
-		
-		Observation observation = new Observation();
-		 
-        CodeableConcept obsName = new CodeableConcept();
-        obsName.setText("name");
-		observation.setCode(obsName);
 
-		Reference result = dr.addResult();
+		/**
-		result.setResource(observation);
+		 * This works fine, although patient instance is modifing from encoder
+		 */
+		final String expectedPatientXml = this.ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(this.patient);
+		logger.debug("[xmlEncoding] first encoding: {}", expectedPatientXml);
+		final String actualPatientXml = this.ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(this.patient);
+		// second encoding - xml is corrupt - i.e.: patient content 4 times! should be the same as after first encoding!
+		logger.debug("[xmlEncoding] second encoding: {}", actualPatientXml);
 
-		ArrayList<Reference> performers = new ArrayList<Reference>();
+		Assert.assertEquals(expectedPatientXml.length(), actualPatientXml.length());
-		Reference performer = new Reference();
+		Assert.assertArrayEquals(expectedPatientXml.getBytes(), actualPatientXml.getBytes());
-        
-        Practitioner p = new Practitioner();
-		p.setId((UUID.randomUUID().toString()));
-		p.addIdentifier().setSystem("DoctorID").setValue("4711");
-		p.addPractitionerRole().getRole().setText("Doctor");
-		p.setName(new HumanName().addFamily("Mueller").addGiven("Klaus").addPrefix("Prof. Dr."));
-        
-        performer.setResource(p);
-        performers.add(performer);
-        observation.getPerformer().addAll(performers);
-        
-        
-        List<IBaseResource> list = new ArrayList<IBaseResource>();
-		list.add(dr);
-		Bundle bundle = null; // RestfulServer.createBundleFromResourceList(new FhirContext(), null, list, null, null, 0);
-        
-        IParser parser = this.ctx.newXmlParser().setPrettyPrint(true);
-        String xml = parser.encodeBundleToString(bundle);
-        Assert.assertTrue(xml.contains("Mueller"));
-        
-	}
-	
-	@Test
-	public void testBundleWithContainedWithNoIdDt() {	
-		
-		DiagnosticReport dr = new DiagnosticReport();
-		dr.setId("123");
-		
-		Observation observation = new Observation();
-		 
-        CodeableConcept obsName = new CodeableConcept();
-        obsName.setText("name");
-		observation.setCode(obsName);
 
-		Reference result = dr.addResult();
-		result.setResource(observation);
-
-		ArrayList<Reference> performers = new ArrayList<Reference>();
-		Reference performer = new Reference();
-        
-        Practitioner p = new Practitioner();
-		// no idDt on practitioner p
-		p.addIdentifier().setSystem("DoctorID").setValue("4711");
-		p.addPractitionerRole().getRole().setText("Doctor");
-		p.setName(new HumanName().addFamily("Mueller").addGiven("Klaus").addPrefix("Prof. Dr."));
-        
-        performer.setResource(p);
-        performers.add(performer);
-        observation.getPerformer().addAll(performers);
-        
-        
-        List<IAnyResource> list = new ArrayList<IAnyResource>();
-		list.add(dr);
-		Bundle bundle = null; // RestfulServer.createBundleFromResourceList(new FhirContext(), null, list, null, null, 0);
-        
-        IParser parser = this.ctx.newXmlParser().setPrettyPrint(true);
-        String xml = parser.encodeBundleToString(bundle);
-        Assert.assertTrue(xml.contains("Mueller"));
-        
 	}
 
 }

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserHl7OrgTest.java

@@ -595,7 +595,7 @@ public class JsonParserHl7OrgTest {
 
 		String val = parser.encodeResourceToString(patient);
 		ourLog.info(val);
-		assertThat(val, StringContains.containsString("\"extension\":[{\"url\":\"urn:foo\",\"valueResource\":{\"reference\":\"Organization/123\"}}]"));
+		assertThat(val, StringContains.containsString("\"extension\":[{\"url\":\"urn:foo\",\"valueReference\":{\"reference\":\"Organization/123\"}}]"));
 
 		Patient actual = parser.parseResource(Patient.class, val);
 		assertEquals(AddressUse.HOME, patient.getAddress().get(0).getUse());
@@ -664,7 +664,7 @@ public class JsonParserHl7OrgTest {
 		out = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(b);
 		ourLog.info(out);
 		// Backslashes need to be escaped because they are in a JSON value
-		assertThat(out, containsString("<div>hello</div>"));
+		assertThat(out, containsString("<xhtml:div xmlns:xhtml=\\\"http://www.w3.org/1999/xhtml\\\">hello</xhtml:div>"));
 
 	}
 

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

@@ -484,7 +484,7 @@ public class XmlParserHl7OrgDstu2Test {
 	public void testParseNarrative() throws Exception {
 		//@formatter:off
 		String htmlNoNs = "<div>AAA<b>BBB</b>CCC</div>";
-		String htmlNs = htmlNoNs.replace("<div>", "<div xmlns=\"http://www.w3.org/1999/xhtml\">"); 
+		String htmlNs = fixDivNodeText(htmlNoNs); 
 		String res= "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
 				"   <id value=\"1333\"/>\n" + 
 				"   <text>\n" + 
@@ -494,7 +494,14 @@ public class XmlParserHl7OrgDstu2Test {
 		//@formatter:on
 		
 		Patient p = ourCtx.newXmlParser().parseResource(Patient.class, res);
-		assertEquals(htmlNoNs, p.getText().getDivAsString());
+		assertEquals(htmlNs, p.getText().getDivAsString());
+	}
+
+	private String fixDivNodeText(String htmlNoNs) {
+		return htmlNoNs.replace("<div>", "<div xmlns=\"http://www.w3.org/1999/xhtml\">");
+	}
+	private String fixDivNodeTextJson(String htmlNoNs) {
+		return htmlNoNs.replace("<div>", "<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">");
 	}
 	
 	@Test
@@ -841,7 +848,7 @@ public class XmlParserHl7OrgDstu2Test {
 
 		String val = parser.encodeResourceToString(patient);
 		ourLog.info(val);
-		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueResource><reference value=\"Organization/123\"/></valueResource></extension>"));
+		assertThat(val, StringContains.containsString("<extension url=\"urn:foo\"><valueReference><reference value=\"Organization/123\"/></valueReference></extension>"));
 
 		Patient actual = parser.parseResource(Patient.class, val);
 		assertEquals(AddressUse.HOME, patient.getAddress().get(0).getUse());
@@ -1062,7 +1069,7 @@ 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 +1204,9 @@ public class XmlParserHl7OrgDstu2Test {
 		Patient patient1 = ourCtx.newXmlParser().parseResource(Patient.class, msg);
 		String encoded1 = ourCtx.newXmlParser().encodeResourceToString(patient1);
 
+		ourLog.info("Expected: {}", msg);
+		ourLog.info("Actual:   {}", encoded1);
+		
 		Diff d = new Diff(new StringReader(msg), new StringReader(encoded1));
 		assertTrue(d.toString(), d.identical());
 
@@ -1492,8 +1502,8 @@ public class XmlParserHl7OrgDstu2Test {
 		JSON actual = JSONSerializer.toJSON(encoded.trim());
 
 		// The encoded escapes quote marks using XML escaping instead of JSON escaping, which is probably nicer anyhow...
-		String exp = expected.toString().replace("\\\"Jim\\\"", "&quot;Jim&quot;");
+		String exp = fixDivNodeTextJson(expected.toString().replace("\\\"Jim\\\"", "&quot;Jim&quot;"));
-		String act = actual.toString();
+		String act = fixDivNodeTextJson(actual.toString());
 
 		ourLog.info("Expected: {}", exp);
 		ourLog.info("Actual  : {}", act);

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/rest/client/ClientServerValidationTestDstu2.java

@@ -34,6 +34,7 @@ import org.mockito.stubbing.Answer;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.primitive.UriDt;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
+import ca.uhn.fhir.rest.client.exceptions.FhirClientInappropriateForServerException;
 import ca.uhn.fhir.rest.server.Constants;
 
 public class ClientServerValidationTestDstu2 {
@@ -146,7 +147,7 @@ public class ClientServerValidationTestDstu2 {
 		try {
 			myCtx.newRestfulGenericClient("http://foo").read(new UriDt("http://foo/Patient/123"));
 			fail();
-		} catch (FhirClientConnectionException e) {
+		} catch (FhirClientInappropriateForServerException e) {
 			String out = e.toString();
 			String want = "The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"0.80\" which corresponds to DSTU1, but this client is configured to use DSTU2_HL7ORG (via the FhirContext)";
 			ourLog.info(out);