Merge branch 'master' into hl7org_dstu21

.gitignore

@@ -16,6 +16,7 @@ nohup.out
 tmp.txt
 *.hprof
 tmp.txt
+ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString/
 
 # Vagrant stuff.
 .vagrant

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

@@ -192,7 +192,7 @@ class ModelScanner {
 		Map<String, Class<? extends IBaseResource>> resourceTypes = myNameToResourceType;
 
 		myVersionTypes = scanVersionPropertyFile(theDatatypes, resourceTypes, myVersion);
-
+		
 		// toScan.add(DateDt.class);
 		// toScan.add(CodeDt.class);
 		// toScan.add(DecimalDt.class);

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

@@ -109,22 +109,26 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
 			} else {
 				nextDef = theClassToElementDefinitions.get(next);
 				BaseRuntimeElementDefinition<?> nextDefForChoice = nextDef;
-				if (nextDef instanceof IRuntimeDatatypeDefinition) {
+				/*
-					IRuntimeDatatypeDefinition nextDefDatatype = (IRuntimeDatatypeDefinition) nextDef;
+				 * In HAPI 1.3 the following applied:
-					if (nextDefDatatype.getProfileOf() != null) {
+				 * Elements which are called foo[x] and have a choice which is a profiled datatype must use the
-						/*
+				 * unprofiled datatype as the element name. E.g. if foo[x] allows markdown as a datatype, it calls the
-						 * Elements which are called foo[x] and have a choice which is a profiled datatype must use the
+				 * element fooString when encoded, because markdown is a profile of string. This is according to the
-						 * unprofiled datatype as the element name. E.g. if foo[x] allows markdown as a datatype, it calls the
+				 * FHIR spec
-						 * element fooString when encoded, because markdown is a profile of string. This is according to the
+				 * 
-						 * FHIR spec
+				 * As of HAPI 1.4 this has been disabled after conversation with Grahame. It appears
-						 */
+				 * that it is not correct behaviour.
-						nextDefForChoice = null;
+				 */
-						nonPreferred = true;
+//				if (nextDef instanceof IRuntimeDatatypeDefinition) {
-						Class<? extends IBaseDatatype> profileType = nextDefDatatype.getProfileOf();
+//					IRuntimeDatatypeDefinition nextDefDatatype = (IRuntimeDatatypeDefinition) nextDef;
-						BaseRuntimeElementDefinition<?> elementDef = theClassToElementDefinitions.get(profileType);
+//					if (nextDefDatatype.getProfileOf() != null) {
-						elementName = getElementName() + StringUtils.capitalize(elementDef.getName());
+//						nextDefForChoice = null;
-					}
+//						nonPreferred = true;
-				}
+//						Class<? extends IBaseDatatype> profileType = nextDefDatatype.getProfileOf();
+//						BaseRuntimeElementDefinition<?> elementDef = theClassToElementDefinitions.get(profileType);
+//						elementName = getElementName() + StringUtils.capitalize(elementDef.getName());
+//					}
+//				}
 				if (nextDefForChoice != null) {
 					elementName = getElementName() + StringUtils.capitalize(nextDefForChoice.getName());
 				}

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

@@ -26,6 +26,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeSet;
 
 import org.apache.commons.lang3.text.WordUtils;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -34,6 +35,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.model.api.IDatatype;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
+import ca.uhn.fhir.model.primitive.CodeDt;
 
 public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildDefinition {
 
@@ -153,13 +155,8 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		myDatatypeToAttributeName = new HashMap<Class<? extends IBase>, String>();
 		myDatatypeToDefinition = new HashMap<Class<? extends IBase>, BaseRuntimeElementDefinition<?>>();
 
-//		for (theContext.get)
-		
 		for (BaseRuntimeElementDefinition<?> next : theClassToElementDefinitions.values()) {
 			if (next instanceof IRuntimeDatatypeDefinition) {
-				// if (next.getName().equals("CodeableConcept")) {
-				// System.out.println();
-				// }
 
 				myDatatypeToDefinition.put(next.getImplementingClass(), next);
 
@@ -178,7 +175,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 					 * type.
 					 */
 					if (!qualifiedName.startsWith("ca.uhn.fhir.model")) {
-						if (!qualifiedName.startsWith("org.hl7.fhir.instance.model")) {
+						if (!qualifiedName.startsWith("org.hl7.fhir")) {
 							continue;
 						}
 					}
@@ -198,12 +195,6 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		myAttributeNameToDefinition = datatypeAttributeNameToDefinition;
 
 
-//		for (Entry<String, BaseRuntimeElementDefinition<?>> next : myAttributeNameToDefinition.entrySet()) {
-//			@SuppressWarnings("unchecked")
-//			Class<? extends IDatatype> type = (Class<? extends IDatatype>) next.getValue().getImplementingClass();
-//			myDatatypeToDefinition.put(type, next.getValue());
-//		}
-
 		/*
 		 * Resource reference - The correct name is 'valueReference' in DSTU2 and 'valueResource' in DSTU1
 		 */

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

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.model.api;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 import org.apache.commons.lang3.builder.ToStringBuilder;
 
 /*
@@ -32,9 +35,9 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
  */
 public class Include {
 
+	private final boolean myImmutable;
 	private boolean myRecurse;
 	private String myValue;
-	private boolean myImmutable;
 
 	/**
 	 * Constructor for <b>non-recursive</b> include
@@ -44,10 +47,11 @@ public class Include {
 	 */
 	public Include(String theValue) {
 		myValue = theValue;
+		myImmutable = false;
 	}
 
 	/**
-	 * Constructor for <b>non-recursive</b> include
+	 * Constructor for an include
 	 * 
 	 * @param theValue
 	 *           The <code>_include</code> value, e.g. "Patient:name"
@@ -57,6 +61,21 @@ public class Include {
 	public Include(String theValue, boolean theRecurse) {
 		myValue = theValue;
 		myRecurse = theRecurse;
+		myImmutable = false;
+	}
+
+	/**
+	 * Constructor for an include
+	 * 
+	 * @param theValue
+	 *           The <code>_include</code> value, e.g. "Patient:name"
+	 * @param theRecurse
+	 *           Should the include recurse
+	 */
+	public Include(String theValue, boolean theRecurse, boolean theImmutable) {
+		myValue = theValue;
+		myRecurse = theRecurse;
+		myImmutable = theImmutable;
 	}
 
 	/**
@@ -73,22 +92,6 @@ public class Include {
 		return new Include(myValue, true);
 	}
 
-	public String getValue() {
-		return myValue;
-	}
-
-	/**
-	 * See the note on equality on the {@link Include class documentation}
-	 */
-	@Override
-	public int hashCode() {
-		final int prime = 31;
-		int result = 1;
-		result = prime * result + (myRecurse ? 1231 : 1237);
-		result = prime * result + ((myValue == null) ? 0 : myValue.hashCode());
-		return result;
-	}
-
 	/**
 	 * See the note on equality on the {@link Include class documentation}
 	 */
@@ -117,6 +120,73 @@ public class Include {
 		return true;
 	}
 
+	/**
+	 * Returns the portion of the value before the first colon
+	 */
+	public String getParamType() {
+		int firstColon = myValue.indexOf(':');
+		if (firstColon == -1 || firstColon == myValue.length() - 1) {
+			return null;
+		}
+		return myValue.substring(0, firstColon);
+	}
+
+	/**
+	 * Returns the portion of the value after the first colon but before the second colon
+	 */
+	public String getParamName() {
+		int firstColon = myValue.indexOf(':');
+		if (firstColon == -1 || firstColon == myValue.length() - 1) {
+			return null;
+		}
+		int secondColon = myValue.indexOf(':', firstColon + 1);
+		if (secondColon != -1) {
+			return myValue.substring(firstColon + 1, secondColon);
+		} else {
+			return myValue.substring(firstColon + 1);
+		}
+	}
+
+	/**
+	 * Returns the portion of the string after the second colon, or null if there are not two colons in the value.
+	 */
+	public String getParamTargetType() {
+		int firstColon = myValue.indexOf(':');
+		if (firstColon == -1 || firstColon == myValue.length() - 1) {
+			return null;
+		}
+		int secondColon = myValue.indexOf(':', firstColon + 1);
+		if (secondColon != -1) {
+			return myValue.substring(secondColon + 1);
+		} else {
+			return null;
+		}
+
+	}
+
+	public String getValue() {
+		return myValue;
+	}
+
+	/**
+	 * See the note on equality on the {@link Include class documentation}
+	 */
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + (myRecurse ? 1231 : 1237);
+		result = prime * result + ((myValue == null) ? 0 : myValue.hashCode());
+		return result;
+	}
+
+	/**
+	 * Is this object {@link #toLocked() locked}?
+	 */
+	public boolean isLocked() {
+		return myImmutable;
+	}
+
 	public boolean isRecurse() {
 		return myRecurse;
 	}
@@ -132,12 +202,14 @@ public class Include {
 		myValue = theValue;
 	}
 
+	/**
+	 * Return a new
+	 */
 	public Include toLocked() {
-		Include retVal = new Include(myValue, myRecurse);
+		Include retVal = new Include(myValue, myRecurse, true);
-		retVal.myImmutable = true;
 		return retVal;
 	}
-	
+
 	@Override
 	public String toString() {
 		ToStringBuilder builder = new ToStringBuilder(this);
@@ -145,4 +217,56 @@ public class Include {
 		builder.append("recurse", myRecurse);
 		return builder.toString();
 	}
+
+	/**
+	 * Creates and returns a new copy of this Include with the given type. The following table shows what will be
+	 * returned:
+	 * <table>
+	 * <tr>
+	 * <th>Initial Contents</th>
+	 * <th>theResourceType</th>
+	 * <th>Output</th>
+	 * </tr>
+	 * <tr>
+	 * <td>Patient:careProvider</th>
+	 * <th>Organization</th>
+	 * <th>Patient:careProvider:Organization</th>
+	 * </tr>
+	 * <tr>
+	 * <td>Patient:careProvider:Practitioner</th>
+	 * <th>Organization</th>
+	 * <th>Patient:careProvider:Organization</th>
+	 * </tr>
+	 * <tr>
+	 * <td>Patient</th>
+	 * <th>(any)</th>
+	 * <th>{@link IllegalStateException}</th>
+	 * </tr>
+	 * </table>
+	 * 
+	 * @param theResourceType
+	 *           The resource type (e.g. "Organization")
+	 * @return A new copy of the include. Note that if this include is {@link #toLocked() locked}, the returned include
+	 *         will be too
+	 */
+	public Include withType(String theResourceType) {
+		StringBuilder b = new StringBuilder();
+		
+		String paramType = getParamType();
+		String paramName = getParamName();
+		if (isBlank(paramType) || isBlank(paramName)) {
+			throw new IllegalStateException("This include does not contain a value in the format [ResourceType]:[paramName]");
+		}
+		b.append(paramType);
+		b.append(":");
+		b.append(paramName);
+		
+		if (isNotBlank(theResourceType)) {
+			b.append(':');
+			b.append(theResourceType);
+		}
+		Include retVal = new Include(b.toString(), myRecurse, myImmutable);
+		return retVal;
+	}
+
 }

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

@@ -28,6 +28,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeSet;
 
 import javax.xml.stream.events.StartElement;
 import javax.xml.stream.events.XMLEvent;

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

@@ -853,10 +853,10 @@ public class GenericClient extends BaseClient implements IGenericClient {
 		}
 
 		@Override
-		public IDeleteTyped resource(IResource theResource) {
+		public IDeleteTyped resource(IBaseResource theResource) {
 			Validate.notNull(theResource, "theResource can not be null");
-			IdDt id = theResource.getId();
+			IIdType id = theResource.getIdElement();
-			Validate.notNull(id, "theResource.getId() can not be null");
+			Validate.notNull(id, "theResource.getIdElement() can not be null");
 			if (id.hasResourceType() == false || id.hasIdPart() == false) {
 				throw new IllegalArgumentException("theResource.getId() must contain a resource type and logical ID at a minimum (e.g. Patient/1234), found: " + id.getValue());
 			}

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.client.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 java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.util.zip.GZIPOutputStream;

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

@@ -3,8 +3,6 @@ package ca.uhn.fhir.rest.gclient;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 
-import ca.uhn.fhir.model.api.IResource;
-
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -27,7 +25,7 @@ import ca.uhn.fhir.model.api.IResource;
 
 public interface IDelete {
 
-	IDeleteTyped resource(IResource theResource);
+	IDeleteTyped resource(IBaseResource theResource);
 	
 	IDeleteTyped resourceById(IIdType theId);
 	

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsConformanceProvider.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 java.io.IOException;
 import java.lang.annotation.Annotation;
 import java.lang.reflect.Method;

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsPageProvider.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 java.io.IOException;
 import java.util.Collections;
 import java.util.List;

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsProvider.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 java.util.HashMap;
 import java.util.List;
 import java.util.Map;

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsResourceProvider.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 java.io.IOException;
 import java.net.URL;
 import java.util.Collections;

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/interceptor/JaxRsExceptionInterceptor.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server.interceptor;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 java.io.IOException;
 
 import javax.interceptor.AroundInvoke;

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/interceptor/JaxRsResponseException.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server.interceptor;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 javax.ejb.ApplicationException;
 
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/util/JaxRsMethodBindings.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server.util;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 java.lang.reflect.Method;
 import java.util.concurrent.ConcurrentHashMap;
 

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/util/JaxRsRequest.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server.util;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 java.io.IOException;
 import java.io.InputStream;
 import java.io.Reader;

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/util/JaxRsResponse.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jaxrs.server.util;
 
+/*
+ * #%L
+ * HAPI FHIR JAX-RS Server
+ * %%
+ * 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 java.io.IOException;
 import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;

hapi-fhir-jpaserver-base/pom.xml

@@ -436,6 +436,7 @@
 				<skip-hib4>true</skip-hib4>
 			</properties>
 		</profile>
+			<!-- 
 		<profile>
 			<id>DIST</id>
 			<build>
@@ -448,9 +449,13 @@
 							<target>SCRIPT</target>
 							<skip>${skip-hib4}</skip>
 						</configuration>
-						<!-- This needs to be uncommented in order for this plugin to work with Hibernate 4.3+ (as of hibernate4-maven-plugin version 1.0.5) -->
+						<dependencies>
-						<dependencies> <dependency> <groupId>org.hibernate</groupId> <artifactId>hibernate-core</artifactId> 
+							<dependency>
-							<version>${hibernate_version}</version> </dependency> </dependencies>
+								<groupId>org.hibernate</groupId>
+								<artifactId>hibernate-core</artifactId>
+								<version>${hibernate_version}</version>
+							</dependency>
+						</dependencies>
 						<executions>
 							<execution>
 								<id>o10g</id>
@@ -501,6 +506,7 @@
 				</plugins>
 			</build>
 		</profile>
+		 -->
 	</profiles>
 
 </project>

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

@@ -1079,13 +1079,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return retVal;
 	}
 
-	protected IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation) {
+	@Override
+	public IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation) {
 		RuntimeResourceDefinition type = myContext.getResourceDefinition(theEntity.getResourceType());
 		return toResource(type.getImplementingClass(), theEntity, theForHistoryOperation);
 	}
 
+	@Override
 	@SuppressWarnings("unchecked")
-	protected <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation) {
+	public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation) {
 		String resourceText = null;
 		switch (theEntity.getEncoding()) {
 		case JSON:

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

@@ -33,10 +33,7 @@ import java.util.Map.Entry;
 import java.util.Set;
 
 import javax.annotation.PostConstruct;
-import javax.persistence.EntityManager;
 import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.PersistenceContextType;
 import javax.persistence.TemporalType;
 import javax.persistence.TypedQuery;
 
@@ -97,9 +94,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 	@Autowired
 	private DaoConfig myDaoConfig;
 
-	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
-	protected EntityManager myEntityManager;
-
 	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu21.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.dao;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * 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.util.ArrayList;

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

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.jpa.dao;
 
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import ca.uhn.fhir.jpa.entity.BaseHasResource;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 
@@ -40,5 +43,9 @@ public interface IDao {
 		}
 	};
 
+	IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation);
+
+	<R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation);
+
 	
 }

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

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.dao;
 
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -1322,7 +1324,7 @@ public class SearchBuilder {
 	 * 
 	 * @param theLastUpdated
 	 */
-	private HashSet<Long> loadReverseIncludes(Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode, EverythingModeEnum theEverythingModeEnum, DateRangeParam theLastUpdated) {
+	private HashSet<Long> loadReverseIncludes(Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode, DateRangeParam theLastUpdated) {
 		if (theMatches.size() == 0) {
 			return new HashSet<Long>();
 		}
@@ -1378,19 +1380,18 @@ public class SearchBuilder {
 					if (myContext.getVersion().getVersion() == FhirVersionEnum.DSTU1) {
 						paths = Collections.singletonList(nextInclude.getValue());
 					} else {
-						int colonIdx = nextInclude.getValue().indexOf(':');
+						String resType = nextInclude.getParamType();
-						if (colonIdx < 2) {
+						if (isBlank(resType)) {
 							continue;
 						}
-						String resType = nextInclude.getValue().substring(0, colonIdx);
 						RuntimeResourceDefinition def = myContext.getResourceDefinition(resType);
 						if (def == null) {
 							ourLog.warn("Unknown resource type in include/revinclude=" + nextInclude.getValue());
 							continue;
 						}
 
-						String paramName = nextInclude.getValue().substring(colonIdx + 1);
+						String paramName = nextInclude.getParamName();
-						RuntimeSearchParam param = def.getSearchParam(paramName);
+						RuntimeSearchParam param = isNotBlank(paramName) ? def.getSearchParam(paramName) : null;
 						if (param == null) {
 							ourLog.warn("Unknown param name in include/revinclude=" + nextInclude.getValue());
 							continue;
@@ -1399,11 +1400,20 @@ public class SearchBuilder {
 						paths = param.getPathsSplit();
 					}
 
+					String targetResourceType = defaultString(nextInclude.getParamTargetType(), null);
 					for (String nextPath : paths) {
-						String sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
+						String sql;
+						if (targetResourceType != null) {
+							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
+						} else {
+							sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
+						}
 						TypedQuery<ResourceLink> q = myEntityManager.createQuery(sql, ResourceLink.class);
 						q.setParameter("src_path", nextPath);
 						q.setParameter("target_pids", nextRoundMatches);
+						if (targetResourceType != null) {
+							q.setParameter("target_resource_type", targetResourceType);
+						}
 						List<ResourceLink> results = q.getResultList();
 						for (ResourceLink resourceLink : results) {
 							if (theReverseMode) {
@@ -1595,7 +1605,7 @@ public class SearchBuilder {
 		final Set<Long> revIncludedPids;
 		if (theParams.getEverythingMode() == null) {
 			if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
-				revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true, null, lu);
+				revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true, lu);
 			} else {
 				revIncludedPids = new HashSet<Long>();
 			}
@@ -1623,7 +1633,7 @@ public class SearchBuilder {
 
 						// Load includes
 						pidsSubList = new ArrayList<Long>(pidsSubList);
-						revIncludedPids.addAll(loadReverseIncludes(pidsSubList, theParams.getIncludes(), false, null, theParams.getLastUpdated()));
+						revIncludedPids.addAll(loadReverseIncludes(pidsSubList, theParams.getIncludes(), false, theParams.getLastUpdated()));
 
 						// Execute the query and make sure we return distinct results
 						List<IBaseResource> resources = new ArrayList<IBaseResource>();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceLink.java

@@ -36,6 +36,7 @@ import javax.persistence.Table;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.hibernate.annotations.ColumnDefault;
 import org.hibernate.search.annotations.Field;
 
 @Entity
@@ -64,6 +65,11 @@ public class ResourceLink implements Serializable {
 	@Column(name = "SRC_RESOURCE_ID", insertable = false, updatable = false, nullable = false)
 	private Long mySourceResourcePid;
 
+	@Column(name = "SOURCE_RESOURCE_TYPE", nullable=false, length=ResourceTable.RESTYPE_LEN)
+	@ColumnDefault("''") // TODO: remove this (it's only here for simplifying upgrades of 1.3 -> 1.4)
+	@Field()
+	private String mySourceResourceType;
+
 	@ManyToOne(optional = false, fetch=FetchType.LAZY)
 	@JoinColumn(name = "TARGET_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = false)
 	private ResourceTable myTargetResource;
@@ -71,18 +77,21 @@ public class ResourceLink implements Serializable {
 	@Column(name = "TARGET_RESOURCE_ID", insertable = false, updatable = false, nullable = false)
 	@Field()
 	private Long myTargetResourcePid;
-	
+
+	@Column(name = "TARGET_RESOURCE_TYPE", nullable=false, length=ResourceTable.RESTYPE_LEN)
+	@ColumnDefault("''") // TODO: remove this (it's only here for simplifying upgrades of 1.3 -> 1.4)
+	@Field()
+	private String myTargetResourceType;
+
 	public ResourceLink() {
 		super();
 	}
 
 	public ResourceLink(String theSourcePath, ResourceTable theSourceResource, ResourceTable theTargetResource) {
 		super();
-		mySourcePath = theSourcePath;
+		setSourcePath(theSourcePath);
-		mySourceResource = theSourceResource;
+		setSourceResource(theSourceResource);
-		mySourceResourcePid = theSourceResource.getId();
+		setTargetResource(theTargetResource);
-		myTargetResource = theTargetResource;
-		myTargetResourcePid = theTargetResource.getId();
 	}
 
 	@Override
@@ -140,12 +149,14 @@ public class ResourceLink implements Serializable {
 	public void setSourceResource(ResourceTable theSourceResource) {
 		mySourceResource = theSourceResource;
 		mySourceResourcePid = theSourceResource.getId();
+		mySourceResourceType = theSourceResource.getResourceType();
 	}
 
 	public void setTargetResource(ResourceTable theTargetResource) {
 		Validate.notNull(theTargetResource);
 		myTargetResource = theTargetResource;
 		myTargetResourcePid = theTargetResource.getId();
+		myTargetResourceType = theTargetResource.getResourceType();
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/ServletSubRequestDetails.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.provider;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * 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 java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchFtTest.java

@@ -4,7 +4,9 @@ import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertThat;
 import static org.mockito.Mockito.mock;
 
 import java.util.List;
@@ -14,9 +16,8 @@ import javax.servlet.http.HttpServletRequest;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Test;
 
-import ca.uhn.fhir.jpa.dao.FhirSearchDao;
-import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.model.dstu2.resource.Device;
 import ca.uhn.fhir.model.dstu2.resource.Media;
 import ca.uhn.fhir.model.dstu2.resource.Observation;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -1430,27 +1430,45 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 		{
 			Organization org = new Organization();
 			org.getNameElement().setValue(methodName + "_O1Parent");
-			parentOrgId = myOrganizationDao.create(org).getId();
+			parentOrgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
 		}
+		IIdType orgId;
+		IIdType patientId;
 		{
 			Organization org = new Organization();
 			org.getNameElement().setValue(methodName + "_O1");
 			org.setPartOf(new ResourceReferenceDt(parentOrgId));
-			IIdType orgId = myOrganizationDao.create(org).getId();
+			orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
 
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("Tester_" + methodName + "_P1").addGiven("Joe");
 			patient.getManagingOrganization().setReference(orgId);
-			myPatientDao.create(patient);
+			patient.addCareProvider().setReference(orgId);
+			patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
 		}
+		IIdType practId2;
+		{
+			Practitioner pract = new Practitioner();
+			pract.getName().addFamily(methodName + "_PRACT1");
+			practId2 = myPractitionerDao.create(pract).getId().toUnqualifiedVersionless();
+		}
+		IIdType patientId2;
 		{
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("002");
 			patient.addName().addFamily("Tester_" + methodName + "_P2").addGiven("John");
-			myPatientDao.create(patient);
+			patient.addCareProvider().setReference(practId2);
+			patientId2 = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
 		}
 
+		{
+			// Typed include
+			SearchParameterMap params = new SearchParameterMap();
+			params.addInclude(Patient.INCLUDE_CAREPROVIDER.withType("Practitioner"));
+			List<IIdType> ids = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(ids, containsInAnyOrder(patientId, patientId2, practId2));
+		}
 		{
 			// No includes
 			SearchParameterMap params = new SearchParameterMap();
@@ -1527,6 +1545,13 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 			assertEquals(1, patients.size());
 			assertEquals(Patient.class, patients.get(0).getClass());
 		}
+		{
+			// Untyped include
+			SearchParameterMap params = new SearchParameterMap();
+			params.addInclude(Patient.INCLUDE_CAREPROVIDER);
+			List<IIdType> ids = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(ids, containsInAnyOrder(orgId, patientId, patientId2, practId2));
+		}
 	}
 
 	@SuppressWarnings("unused")

hapi-fhir-structures-dstu/src/main/java/ca/uhn/fhir/rest/server/provider/ServerConformanceProvider.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.server.provider;
 
+/*
+ * #%L
+ * HAPI FHIR Structures - DSTU1 (FHIR v0.80)
+ * %%
+ * 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 java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/model/primitive/BaseDateTimeDtTest.java

@@ -65,7 +65,7 @@ public class BaseDateTimeDtTest {
 		DateTimeDt dt = DateTimeDt.withCurrentTime();
 		String str = dt.getValueAsString();
 		char offset = str.charAt(19);
-		if (offset != '+' && offset != '-') {
+		if (offset != '+' && offset != '-' && offset != 'Z') {
 			fail("No timezone provided: " + str);
 		}
 	}
@@ -75,7 +75,7 @@ public class BaseDateTimeDtTest {
 		InstantDt dt = InstantDt.withCurrentTime();
 		String str = dt.getValueAsString();
 		char offset = str.charAt(23);
-		if (offset != '+' && offset != '-') {
+		if (offset != '+' && offset != '-' && offset != 'Z') {
 			fail("No timezone provided: " + str);
 		}
 	}

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

@@ -20,9 +20,6 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
-import net.sf.json.JSON;
-import net.sf.json.JSONSerializer;
-
 import org.apache.commons.io.IOUtils;
 import org.hamcrest.core.IsNot;
 import org.hamcrest.core.StringContains;
@@ -30,7 +27,6 @@ import org.hamcrest.text.StringContainsInOrder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.junit.Before;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.ConfigurationException;
@@ -68,6 +64,7 @@ import ca.uhn.fhir.model.dstu.resource.ValueSet.DefineConcept;
 import ca.uhn.fhir.model.dstu.valueset.AddressUseEnum;
 import ca.uhn.fhir.model.dstu.valueset.IdentifierUseEnum;
 import ca.uhn.fhir.model.dstu.valueset.NarrativeStatusEnum;
+import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.DecimalDt;
@@ -76,6 +73,8 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
+import net.sf.json.JSON;
+import net.sf.json.JSONSerializer;
 
 public class JsonParserTest {
 	private static FhirContext ourCtx;
@@ -1318,11 +1317,14 @@ public class JsonParserTest {
 	public void testSimpleResourceEncode() throws IOException {
 
 		String xmlString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.xml"), Charset.forName("UTF-8"));
-		Patient obs = ourCtx.newXmlParser().parseResource(Patient.class, xmlString);
+		IParser parser = ourCtx.newXmlParser();
+		parser.setParserErrorHandler(new StrictErrorHandler());
+		Patient obs = parser.parseResource(Patient.class, xmlString);
 
 		List<ExtensionDt> undeclaredExtensions = obs.getContact().get(0).getName().getFamily().get(0).getUndeclaredExtensions();
 		ExtensionDt undeclaredExtension = undeclaredExtensions.get(0);
 		assertEquals("http://hl7.org/fhir/Profile/iso-21090#qualifier", undeclaredExtension.getUrl());
+		assertEquals("VV", ((CodeDt)undeclaredExtension.getValue()).getValue());
 
 		ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToWriter(obs, new OutputStreamWriter(System.out));
 
@@ -1341,7 +1343,7 @@ public class JsonParserTest {
 
 		ourLog.info("Expected: {}", exp);
 		ourLog.info("Actual  : {}", act);
-		assertEquals(exp, act);
+		assertEquals("\nExpected: " + exp + "\nActual  : " + act, exp, act);
 
 	}
 
@@ -1376,8 +1378,7 @@ public class JsonParserTest {
 
 		ourLog.info("Expected: {}", exp);
 		ourLog.info("Actual  : {}", act);
-		assertEquals(exp, act);
+		assertEquals("\nExpected: " + exp + "\nActual  : " + act, exp, act);
-
 	}
 
 	@Test

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

@@ -1,7 +1,10 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -51,56 +54,21 @@ import ca.uhn.fhir.util.PortUtil;
 public class IncludeTest {
 
 	private static CloseableHttpClient ourClient;
+	private static FhirContext ourCtx;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(IncludeTest.class);
 	private static int ourPort;
 	private static Server ourServer;
-	private static FhirContext ourCtx;
 
 	@Test
-	public void testNoIncludes() throws Exception {
+	public void testBadInclude() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello");
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo&_include=baz");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
-		assertEquals(1, bundle.size());
-
-		Patient p = bundle.getResources(Patient.class).get(0);
-		assertEquals(0, p.getName().size());
-		assertEquals("Hello", p.getId().getIdPart());
-	}
-
-	@Test
-	public void testOneInclude() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo");
-		HttpResponse status = ourClient.execute(httpGet);
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
-		assertEquals(1, bundle.size());
-
-		Patient p = bundle.getResources(Patient.class).get(0);
-		assertEquals(1, p.getName().size());
-		assertEquals("Hello", p.getId().getIdPart());
-		assertEquals("foo", p.getName().get(0).getFamilyFirstRep().getValue());
-	}
-
-	// @Test
-	public void testMixedContainedAndNonContained() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/DiagnosticReport?_query=stitchedInclude&_pretty=true");
 		HttpResponse status = ourClient.execute(httpGet);
+		assertEquals(400, status.getStatusLine().getStatusCode());
 		String responseContent = IOUtils.toString(status.getEntity().getContent());
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		ourLog.info(responseContent);
-
+		assertThat(responseContent, containsString("Invalid _include parameter value"));
-		assertEquals(200, status.getStatusLine().getStatusCode());
-		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
-		assertEquals(4, bundle.size());
 	}
 
 	@Test
@@ -128,6 +96,32 @@ public class IncludeTest {
 
 	}
 
+	@Test
+	public void testIIncludedResourcesNonContainedInDeclaredExtension() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=declaredExtInclude&_pretty=true");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
+
+		ourLog.info(responseContent);
+
+		assertEquals(4, bundle.size());
+		assertEquals(new IdDt("Patient/p1"), bundle.toListOfResources().get(0).getId().toUnqualifiedVersionless());
+		assertEquals(new IdDt("Patient/p2"), bundle.toListOfResources().get(1).getId().toUnqualifiedVersionless());
+		assertEquals(new IdDt("Organization/o1"), bundle.toListOfResources().get(2).getId().toUnqualifiedVersionless());
+		assertEquals(new IdDt("Organization/o2"), bundle.toListOfResources().get(3).getId().toUnqualifiedVersionless());
+
+		Patient p1 = (Patient) bundle.toListOfResources().get(0);
+		assertEquals(0, p1.getContained().getContainedResources().size());
+
+		Patient p2 = (Patient) bundle.toListOfResources().get(1);
+		assertEquals(0, p2.getContained().getContainedResources().size());
+
+	}
+
 	@Test
 	public void testIIncludedResourcesNonContainedInExtension() throws Exception {
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=extInclude&_pretty=true");
@@ -179,29 +173,81 @@ public class IncludeTest {
 	}
 
 	@Test
-	public void testIIncludedResourcesNonContainedInDeclaredExtension() throws Exception {
+	public void testIncludeWithType() {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=declaredExtInclude&_pretty=true");
+		assertEquals("Patient:careProvider:Practitioner", new Include("Patient:careProvider", true).withType("Practitioner").getValue());
+		assertEquals(true, new Include("Patient:careProvider", true).withType("Practitioner").isRecurse());
+		assertEquals(false, new Include("Patient:careProvider:Organization", true).withType("Practitioner").isLocked());
+		assertEquals("Practitioner", new Include("Patient:careProvider", true).withType("Practitioner").getParamTargetType());
+		assertEquals(null, new Include("Patient:careProvider", true).getParamTargetType());
+
+		assertEquals("Patient:careProvider:Practitioner", new Include("Patient:careProvider:Organization", true).withType("Practitioner").getValue());
+		assertEquals(true, new Include("Patient:careProvider:Organization", true).toLocked().withType("Practitioner").isLocked());
+
+		try {
+			new Include("").withType("Patient");
+			fail();
+		} catch (IllegalStateException e) {
+			// good
+		}
+		try {
+			new Include("Patient").withType("Patient");
+			fail();
+		} catch (IllegalStateException e) {
+			// good
+		}
+		try {
+			new Include("Patient:").withType("Patient");
+			fail();
+		} catch (IllegalStateException e) {
+			// good
+		}
+	}
+
+	// @Test
+	public void testMixedContainedAndNonContained() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/DiagnosticReport?_query=stitchedInclude&_pretty=true");
+		HttpResponse status = ourClient.execute(httpGet);
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		ourLog.info(responseContent);
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
+		assertEquals(4, bundle.size());
+	}
+
+	@Test
+	public void testNoIncludes() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello");
 		HttpResponse status = ourClient.execute(httpGet);
 		String responseContent = IOUtils.toString(status.getEntity().getContent());
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		assertEquals(200, status.getStatusLine().getStatusCode());
 		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
+		assertEquals(1, bundle.size());
 
-		ourLog.info(responseContent);
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(0, p.getName().size());
+		assertEquals("Hello", p.getId().getIdPart());
+	}
 
-		assertEquals(4, bundle.size());
+	@Test
-		assertEquals(new IdDt("Patient/p1"), bundle.toListOfResources().get(0).getId().toUnqualifiedVersionless());
+	public void testOneInclude() throws Exception {
-		assertEquals(new IdDt("Patient/p2"), bundle.toListOfResources().get(1).getId().toUnqualifiedVersionless());
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo");
-		assertEquals(new IdDt("Organization/o1"), bundle.toListOfResources().get(2).getId().toUnqualifiedVersionless());
+		HttpResponse status = ourClient.execute(httpGet);
-		assertEquals(new IdDt("Organization/o2"), bundle.toListOfResources().get(3).getId().toUnqualifiedVersionless());
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
 
-		Patient p1 = (Patient) bundle.toListOfResources().get(0);
+		assertEquals(200, status.getStatusLine().getStatusCode());
-		assertEquals(0, p1.getContained().getContainedResources().size());
+		Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
-
+		assertEquals(1, bundle.size());
-		Patient p2 = (Patient) bundle.toListOfResources().get(1);
-		assertEquals(0, p2.getContained().getContainedResources().size());
 
+		Patient p = bundle.getResources(Patient.class).get(0);
+		assertEquals(1, p.getName().size());
+		assertEquals("Hello", p.getId().getIdPart());
+		assertEquals("foo", p.getName().get(0).getFamilyFirstRep().getValue());
 	}
 
 	@Test
@@ -226,18 +272,6 @@ public class IncludeTest {
 
 	}
 
-	@Test
-	public void testBadInclude() throws Exception {
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo&_include=baz");
-		HttpResponse status = ourClient.execute(httpGet);
-		assertEquals(400, status.getStatusLine().getStatusCode());
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		ourLog.info(responseContent);
-		assertThat(responseContent, containsString("Invalid _include parameter value"));
-	}
-
 	@AfterClass
 	public static void afterClass() throws Exception {
 		ourServer.stop();
@@ -268,27 +302,20 @@ public class IncludeTest {
 
 	}
 
-	@ResourceDef(name = "Patient")
+	public static void main(String[] args) {
-	public static class ExtPatient extends Patient {
-		@Child(name = "secondOrg")
-		@Extension(url = "http://foo#secondOrg", definedLocally = false, isModifier = false)
-		private ResourceReferenceDt mySecondOrg;
 
-		@Override
+		Organization org = new Organization();
-		public boolean isEmpty() {
+		org.setId("Organization/65546");
-			return super.isEmpty() && ElementUtil.isEmpty(mySecondOrg);
+		org.getName().setValue("Contained Test Organization");
-		}
 
-		public ResourceReferenceDt getSecondOrg() {
+		Patient patient = new Patient();
-			if (mySecondOrg == null) {
+		patient.setId("Patient/1333");
-				mySecondOrg = new ResourceReferenceDt();
+		patient.addIdentifier("urn:mrns", "253345");
-			}
+		patient.getManagingOrganization().setResource(patient);
-			return mySecondOrg;
-		}
 
-		public void setSecondOrg(ResourceReferenceDt theSecondOrg) {
+		System.out.println(FhirContext.forDstu1().newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
-			mySecondOrg = theSecondOrg;
+
-		}
+		patient.getManagingOrganization().getReference();
 
 	}
 
@@ -345,11 +372,10 @@ public class IncludeTest {
 	 */
 	public static class DummyPatientResourceProvider implements IResourceProvider {
 
-		@Search(queryName = "normalInclude")
+		@Search(queryName = "containedInclude")
-		public List<Patient> normalInclude() {
+		public List<Patient> containedInclude() {
 			Organization o1 = new Organization();
 			o1.getName().setValue("o1");
-			o1.setId("o1");
 
 			Patient p1 = new Patient();
 			p1.setId("p1");
@@ -364,25 +390,6 @@ public class IncludeTest {
 			return Arrays.asList(p1, p2);
 		}
 
-		@Search(queryName = "extInclude")
-		public List<Patient> extInclude() {
-			Organization o1 = new Organization();
-			o1.getName().setValue("o1");
-			o1.setId("o1");
-
-			Patient p1 = new Patient();
-			p1.setId("p1");
-			p1.addIdentifier().setLabel("p1");
-			p1.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
-
-			Patient p2 = new Patient();
-			p2.setId("p2");
-			p2.addIdentifier().setLabel("p2");
-			p2.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
-
-			return Arrays.asList(p1, p2);
-		}
-
 		@Search(queryName = "declaredExtInclude")
 		public List<ExtPatient> declaredExtInclude() {
 			Organization o1 = new Organization();
@@ -407,20 +414,21 @@ public class IncludeTest {
 			return Arrays.asList(p1, p2);
 		}
 
-		@Search(queryName = "containedInclude")
+		@Search(queryName = "extInclude")
-		public List<Patient> containedInclude() {
+		public List<Patient> extInclude() {
 			Organization o1 = new Organization();
 			o1.getName().setValue("o1");
+			o1.setId("o1");
 
 			Patient p1 = new Patient();
 			p1.setId("p1");
 			p1.addIdentifier().setLabel("p1");
-			p1.getManagingOrganization().setResource(o1);
+			p1.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
 
 			Patient p2 = new Patient();
 			p2.setId("p2");
 			p2.addIdentifier().setLabel("p2");
-			p2.getManagingOrganization().setResource(o1);
+			p2.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
 
 			return Arrays.asList(p1, p2);
 		}
@@ -449,22 +457,48 @@ public class IncludeTest {
 			return Patient.class;
 		}
 
+		@Search(queryName = "normalInclude")
+		public List<Patient> normalInclude() {
+			Organization o1 = new Organization();
+			o1.getName().setValue("o1");
+			o1.setId("o1");
+
+			Patient p1 = new Patient();
+			p1.setId("p1");
+			p1.addIdentifier().setLabel("p1");
+			p1.getManagingOrganization().setResource(o1);
+
+			Patient p2 = new Patient();
+			p2.setId("p2");
+			p2.addIdentifier().setLabel("p2");
+			p2.getManagingOrganization().setResource(o1);
+
+			return Arrays.asList(p1, p2);
+		}
+
 	}
 
-	public static void main(String[] args) {
+	@ResourceDef(name = "Patient")
+	public static class ExtPatient extends Patient {
+		@Child(name = "secondOrg")
+		@Extension(url = "http://foo#secondOrg", definedLocally = false, isModifier = false)
+		private ResourceReferenceDt mySecondOrg;
 
-		Organization org = new Organization();
+		public ResourceReferenceDt getSecondOrg() {
-		org.setId("Organization/65546");
+			if (mySecondOrg == null) {
-		org.getName().setValue("Contained Test Organization");
+				mySecondOrg = new ResourceReferenceDt();
+			}
+			return mySecondOrg;
+		}
 
-		Patient patient = new Patient();
+		@Override
-		patient.setId("Patient/1333");
+		public boolean isEmpty() {
-		patient.addIdentifier("urn:mrns", "253345");
+			return super.isEmpty() && ElementUtil.isEmpty(mySecondOrg);
-		patient.getManagingOrganization().setResource(patient);
+		}
 
-		System.out.println(FhirContext.forDstu1().newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
+		public void setSecondOrg(ResourceReferenceDt theSecondOrg) {
-
+			mySecondOrg = theSecondOrg;
-		patient.getManagingOrganization().getReference();
+		}
 
 	}
 

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/FhirDstu21.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.model.dstu21;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/AgeDt.java

@@ -6,7 +6,7 @@ import ca.uhn.fhir.model.primitive.IntegerDt;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/BoundCodeableConceptDt.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.model.dstu21.composite;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/ContainedDt.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.model.dstu21.composite;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/CountDt.java

@@ -5,7 +5,7 @@ import ca.uhn.fhir.model.dstu21.composite.QuantityDt;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/DistanceDt.java

@@ -6,7 +6,7 @@ import ca.uhn.fhir.model.primitive.IntegerDt;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/DurationDt.java

@@ -5,7 +5,7 @@ import ca.uhn.fhir.model.dstu21.composite.QuantityDt;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/MoneyDt.java

@@ -5,7 +5,7 @@ import ca.uhn.fhir.model.dstu21.composite.QuantityDt;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/NarrativeDt.java

@@ -18,7 +18,7 @@ package ca.uhn.fhir.model.dstu21.composite;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/ResourceReferenceDt.java

@@ -18,7 +18,7 @@ package ca.uhn.fhir.model.dstu21.composite;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/composite/SimpleQuantityDt.java

@@ -7,7 +7,7 @@ import ca.uhn.fhir.model.dstu21.valueset.QuantityComparatorEnum;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/model/dstu21/resource/BaseResource.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.model.dstu21.resource;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/rest/server/provider/dstu21/Dstu21BundleFactory.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.rest.server.provider.dstu21;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/rest/server/provider/dstu21/ServerConformanceProvider.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.rest.server.provider.dstu21;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/main/java/ca/uhn/fhir/rest/server/provider/dstu21/ServerProfileProvider.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.rest.server.provider.dstu21;
 
 /*
  * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
+ * HAPI FHIR Structures - DSTU2.1 (FHIR v1.1.x)
  * %%
  * Copyright (C) 2014 - 2015 University Health Network
  * %%

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/XmlParserDstu21Test.java

@@ -125,7 +125,7 @@ public class XmlParserDstu21Test {
 		assertArrayEquals(new byte[] { 1, 2, 3, 4 }, bin.getContent());
 
 	}
-	
+
 	@Test
 	public void testEncodeEmptyBinary() {
 		String output = ourCtx.newXmlParser().encodeResourceToString(new Binary());
@@ -142,18 +142,16 @@ public class XmlParserDstu21Test {
 		ourCtx.newJsonParser().parseResource(encoded);
 	}
 
-	
 	@Test
 	public void testEncodeDoesntIncludeUuidId() {
 		Patient p = new Patient();
 		p.setId(new IdDt("urn:uuid:42795ed8-041f-4ebf-b6f4-78ef6f64c2f2"));
 		p.addIdentifier().setSystem("ACME");
-		
+
 		String actual = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
 		assertThat(actual, not(containsString("78ef6f64c2f2")));
 	}
-	
+
-	
 	@Test
 	public void testContainedResourceInExtensionUndeclared() {
 		Patient p = new Patient();
@@ -341,11 +339,9 @@ public class XmlParserDstu21Test {
 		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
 		assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
 		assertThat(enc, containsString("<modifierExtension url=\"http://example.com/extensions#modext\"><valueDate value=\"1995-01-02\"/></modifierExtension>"));
-		assertThat(enc, containsString(
+		assertThat(enc, containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
-				"<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
 		assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
-		assertThat(enc, containsString(
+		assertThat(enc, containsString("<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
-				"<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
 
 		/*
 		 * Now parse this back
@@ -524,8 +520,11 @@ public class XmlParserDstu21Test {
 
 	/**
 	 * Test for #233
+	 * 
+	 * This was rolled back after a conversation with grahame
 	 */
 	@Test
+	@Ignore
 	public void testEncodeAndParseProfiledDatatype() {
 		MedicationOrder mo = new MedicationOrder();
 		mo.addDosageInstruction().getTiming().getRepeat().setBounds(new DurationDt().setCode("code"));
@@ -541,7 +540,8 @@ public class XmlParserDstu21Test {
 	/**
 	 * See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
 	 */
-	@Test @Ignore
+	@Test
+	@Ignore
 	public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
 		IParser xmlParser = ourCtx.newXmlParser();
 
@@ -751,10 +751,8 @@ public class XmlParserDstu21Test {
 		ourLog.info(encoded);
 
 		// @formatter:on
-		assertThat(encoded,
+		assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
-				stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
+				"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
-						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
-						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
 		//@formatter:off
 
 	}
@@ -786,10 +784,8 @@ public class XmlParserDstu21Test {
 		ourLog.info(encoded);
 		
 		//@formatter:on
-		assertThat(encoded,
+		assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
-				stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>",
+				"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
-						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>",
-						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
 		//@formatter:off
 	}
 
@@ -824,10 +820,8 @@ public class XmlParserDstu21Test {
 		ourLog.info(encoded);
 		
 		//@formatter:on
-		assertThat(encoded,
+		assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
-				stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
+				"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
-						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
-						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
 		//@formatter:off
 
 	}
@@ -1630,7 +1624,8 @@ public class XmlParserDstu21Test {
 	/**
 	 * See #191
 	 */
-	@Test @Ignore
+	@Test
+	@Ignore
 	public void testParseBundleWithLinksOfUnknownRelation() throws Exception {
 		String input = IOUtils.toString(XmlParserDstu21Test.class.getResourceAsStream("/bundle_orion.xml"));
 		ca.uhn.fhir.model.dstu21.resource.Bundle parsed = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu21.resource.Bundle.class, input);
@@ -1664,7 +1659,8 @@ public class XmlParserDstu21Test {
 	/**
 	 * see #144 and #146
 	 */
-	@Test @Ignore
+	@Test
+	@Ignore
 	public void testParseContained() {
 
 		FhirContext c = FhirContext.forDstu2();

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/narrative/DefaultThymeleafNarrativeGeneratorTestDstu2.java

@@ -9,6 +9,7 @@ import java.util.Date;
 
 import org.hamcrest.core.StringContains;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -195,6 +196,7 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 	}
 
 	@Test
+	@Ignore
 	public void testGenerateMedicationPrescription() {
 		MedicationOrder mp = new MedicationOrder();
 		mp.setId("12345");

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

@@ -32,6 +32,7 @@ import org.hamcrest.core.StringContains;
 import org.hamcrest.text.StringContainsInOrder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.junit.BeforeClass;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
 
@@ -68,6 +69,7 @@ import ca.uhn.fhir.model.dstu2.resource.MedicationOrder;
 import ca.uhn.fhir.model.dstu2.resource.MedicationStatement;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
+import ca.uhn.fhir.model.dstu2.resource.Parameters;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.dstu2.valueset.AddressUseEnum;
 import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
@@ -84,6 +86,7 @@ import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.primitive.MarkdownDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.parser.IParserErrorHandler.IParseLocation;
 import ca.uhn.fhir.rest.client.IGenericClient;
@@ -93,6 +96,46 @@ public class XmlParserDstu2Test {
 	private static final FhirContext ourCtx = FhirContext.forDstu2();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu2Test.class);
 
+	@Test
+	public void testChoiceTypeWithProfiledType() {
+		//@formatter:off
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
+			"        <extension url=\"http://example.com\">\n" + 
+			"          <valueMarkdown value=\"THIS IS MARKDOWN\"/>\n" + 
+			"        </extension>\n" + 
+			"</Patient>";
+		//@formatter:on
+		
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, input);
+		assertEquals(1, parsed.getUndeclaredExtensions().size());
+		ExtensionDt ext = parsed.getUndeclaredExtensions().get(0);
+		assertEquals("http://example.com", ext.getUrl());
+		assertEquals("THIS IS MARKDOWN", ((MarkdownDt)ext.getValue()).getValue());
+		
+		String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parsed);
+		assertThat(encoded, containsString("<valueMarkdown value=\"THIS IS MARKDOWN\"/>"));
+	}
+	
+	
+	@Test
+	public void testChoiceTypeWithProfiledType2() {
+		Parameters par = new Parameters();
+		par.addParameter().setValue((StringDt)new StringDt().setValue("ST"));
+		par.addParameter().setValue((MarkdownDt)new MarkdownDt().setValue("MD"));
+		
+		String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(par);
+		ourLog.info(str);
+		
+		assertThat(str, stringContainsInOrder("<valueString value=\"ST\"/>", "<valueMarkdown value=\"MD\"/>"));
+		
+		par = ourCtx.newXmlParser().parseResource(Parameters.class, str);
+		assertEquals(2, par.getParameter().size());
+		assertEquals(StringDt.class, par.getParameter().get(0).getValue().getClass());
+		assertEquals(MarkdownDt.class, par.getParameter().get(1).getValue().getClass());
+	}
+	
+	
+	
 	@Test
 	public void testBundleWithBinary() {
 		//@formatter:off
@@ -522,7 +565,7 @@ public class XmlParserDstu2Test {
 	}
 
 	/**
-	 * Test for #233
+	 * Test for #233 - This was reversed after a conversation with Grahame
 	 */
 	@Test
 	public void testEncodeAndParseProfiledDatatype() {
@@ -530,7 +573,7 @@ public class XmlParserDstu2Test {
 		mo.addDosageInstruction().getTiming().getRepeat().setBounds(new DurationDt().setCode("code"));
 		String out = ourCtx.newXmlParser().encodeResourceToString(mo);
 		ourLog.info(out);
-		assertThat(out, containsString("</boundsQuantity>"));
+		assertThat(out, containsString("</boundsDuration>"));
 
 		mo = ourCtx.newXmlParser().parseResource(MedicationOrder.class, out);
 		DurationDt duration = (DurationDt) mo.getDosageInstruction().get(0).getTiming().getRepeat().getBounds();
@@ -539,8 +582,11 @@ public class XmlParserDstu2Test {
 
 	/**
 	 * See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
+	 * 
+	 * Disabled because we reverted this change after a conversation with Grahame
 	 */
 	@Test
+	@Ignore
 	public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
 		IParser xmlParser = ourCtx.newXmlParser();
 
@@ -550,7 +596,7 @@ public class XmlParserDstu2Test {
 		assertEquals("1", q.getValueElement().getValueAsString());
 
 		String output = xmlParser.encodeResourceToString(ms);
-		assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
+		assertThat(output, containsString("<quantitySimpleQuantity><value value=\"1\"/></quantitySimpleQuantity>"));
 	}
 
 	@Test

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu2Test.java

@@ -1143,7 +1143,7 @@ public class GenericClientDstu2Test {
 		
 		assertEquals("http://example.com/fhir/Patient/1/$validate-code", capt.getAllValues().get(idx).getURI().toASCIIString());
 		ourLog.info(extractBody(capt, idx));
-		assertEquals("<Parameters xmlns=\"http://hl7.org/fhir\"><parameter><name value=\"code\"/><valueString value=\"8495-4\"/></parameter><parameter><name value=\"system\"/><valueUri value=\"http://loinc.org\"/></parameter></Parameters>",extractBody(capt, idx));
+		assertEquals("<Parameters xmlns=\"http://hl7.org/fhir\"><parameter><name value=\"code\"/><valueCode value=\"8495-4\"/></parameter><parameter><name value=\"system\"/><valueUri value=\"http://loinc.org\"/></parameter></Parameters>",extractBody(capt, idx));
 
 	}
 

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -182,7 +182,7 @@
 				<artifactId>maven-surefire-plugin</artifactId>
 				<version>2.19</version>
 				<configuration>
-					<redirectTestOutputToFile>false</redirectTestOutputToFile>
+					<redirectTestOutputToFile>true</redirectTestOutputToFile>
 					<runOrder>random</runOrder>
 					<argLine>-Dfile.encoding=UTF-8</argLine>
 					<reuseForks>false</reuseForks>

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

@@ -26,7 +26,6 @@ import org.hamcrest.core.IsNot;
 import org.hamcrest.core.StringContains;
 import org.hamcrest.text.StringContainsInOrder;
 import org.hl7.fhir.instance.model.Address;
-import org.hl7.fhir.instance.model.Attachment;
 import org.hl7.fhir.instance.model.Address.AddressUse;
 import org.hl7.fhir.instance.model.Address.AddressUseEnumFactory;
 import org.hl7.fhir.instance.model.Binary;
@@ -49,7 +48,6 @@ import org.hl7.fhir.instance.model.Identifier.IdentifierUse;
 import org.hl7.fhir.instance.model.InstantType;
 import org.hl7.fhir.instance.model.MedicationStatement;
 import org.hl7.fhir.instance.model.Narrative.NarrativeStatus;
-import org.hl7.fhir.instance.model.annotations.Child;
 import org.hl7.fhir.instance.model.Observation;
 import org.hl7.fhir.instance.model.Organization;
 import org.hl7.fhir.instance.model.Patient;
@@ -62,6 +60,7 @@ import org.hl7.fhir.instance.model.StringType;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.junit.BeforeClass;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.xml.sax.SAXException;
 
@@ -91,8 +90,11 @@ public class XmlParserHl7OrgDstu2Test {
 
 	 /**
    * See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
+   * 
+   * Disabled after conversation with Grahame 
    */
   @Test
+  @Ignore
   public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
     IParser xmlParser = ourCtx.newXmlParser();
 

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/parser/DatatypeGeneratorUsingSpreadsheet.java

@@ -68,7 +68,9 @@ public class DatatypeGeneratorUsingSpreadsheet extends BaseStructureSpreadsheetP
 			for (ClassInfo classInfo : tlc) {
 				DatatypeDef def = Class.forName(classInfo.getName()).getAnnotation(DatatypeDef.class);
 				if (def != null) {
-					getNameToDatatypeClass().put(def.name(), classInfo.getName());
+					if (classInfo.getName().contains("Bound") == false) {
+						getNameToDatatypeClass().put(def.name(), classInfo.getName());
+					}
 				}
 			}
 		} catch (IOException e) {
@@ -82,7 +84,9 @@ public class DatatypeGeneratorUsingSpreadsheet extends BaseStructureSpreadsheetP
 			for (ClassInfo classInfo : tlc) {
 				DatatypeDef def = Class.forName(classInfo.getName()).getAnnotation(DatatypeDef.class);
 				if (def != null) {
-					getNameToDatatypeClass().put(def.name(), classInfo.getName());
+					if (classInfo.getName().contains("Bound") == false) {
+						getNameToDatatypeClass().put(def.name(), classInfo.getName());
+					}
 				}
 			}
 		} catch (IOException e) {

pom.xml

@@ -240,7 +240,7 @@
 		<jetty_version>9.2.14.v20151106</jetty_version> 
 		<!-- Note on Hibernate versions: Hibernate 4.3+ uses JPA 2.1, which is too new for a number of platforms including JBoss EAP 6.x and Glassfish 3.0. Upgrade this version with caution! Also note that if 
 			you change this, you may get a failure in hibernate4-maven-plugin. See the note in hapi-fhir-jpaserver-base/pom.xml's configuration for that plugin... -->
-		<hibernate_version>5.0.3.Final</hibernate_version>
+		<hibernate_version>5.0.5.Final</hibernate_version>
 		<hibernate_validator_version>5.2.2.Final</hibernate_validator_version>
 		<maven_assembly_plugin_version>2.5.3</maven_assembly_plugin_version>
 		<maven_failsafe_plugin_version>2.18.1</maven_failsafe_plugin_version>
@@ -251,7 +251,7 @@
 		<mitreid-connect-version>1.1.8</mitreid-connect-version>
 		<phloc_schematron_version>2.7.1</phloc_schematron_version>
 		<phloc_commons_version>4.3.6</phloc_commons_version>
-		<spring_version>4.2.2.RELEASE</spring_version>
+		<spring_version>4.2.3.RELEASE</spring_version>
 		<thymeleaf-version>2.1.4.RELEASE</thymeleaf-version>
 		<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
 		<xmlunit_version>1.6</xmlunit_version>
@@ -277,7 +277,7 @@
 			<dependency>
 				<groupId>com.google.guava</groupId>
 				<artifactId>guava</artifactId>
-				<version>18.0</version>
+				<version>19.0</version>
 			</dependency>
 			<dependency>
 				<groupId>com.phloc</groupId>
@@ -392,12 +392,12 @@
 			<dependency>
 				<groupId>org.apache.lucene</groupId>
 				<artifactId>lucene-highlighter</artifactId>
-				<version>5.3.0</version>
+				<version>5.3.1</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.lucene</groupId>
 				<artifactId>lucene-analyzers-phonetic</artifactId>
-				<version>5.3.0</version>
+				<version>5.3.1</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.doxia</groupId>
@@ -407,17 +407,17 @@
 			<dependency>
 				<groupId>org.apache.maven.scm</groupId>
 				<artifactId>maven-scm-api</artifactId>
-				<version>1.9</version>
+				<version>1.9.4</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.scm</groupId>
 				<artifactId>maven-scm-manager-plexus</artifactId>
-				<version>1.9</version>
+				<version>1.9.4</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.scm</groupId>
 				<artifactId>maven-scm-provider-gitexe</artifactId>
-				<version>1.9</version>
+				<version>1.9.4</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.wagon</groupId>
@@ -552,7 +552,7 @@
 			<dependency>
 				<groupId>org.hibernate</groupId>
 				<artifactId>hibernate-search-orm</artifactId>
-				<version>5.5.0.Final</version>
+				<version>5.5.1.Final</version>
 			</dependency>
 			<dependency>
 				<groupId>org.javassist</groupId>
@@ -562,17 +562,17 @@
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>slf4j-android</artifactId>
-				<version>1.7.12</version>
+				<version>1.7.13</version>
 			</dependency>
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>slf4j-api</artifactId>
-				<version>1.7.12</version>
+				<version>1.7.13</version>
 			</dependency>
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>jcl-over-slf4j</artifactId>
-				<version>1.7.12</version>
+				<version>1.7.13</version>
 			</dependency>
 			<dependency>
 				<groupId>org.springframework</groupId>
@@ -663,7 +663,7 @@
 				<plugin>
 					<groupId>org.apache.felix</groupId>
 					<artifactId>maven-bundle-plugin</artifactId>
-					<version>3.0.0</version>
+					<version>3.0.1</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -931,12 +931,12 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-checkstyle-plugin</artifactId>
-					<version>2.15</version>
+					<version>2.17</version>
 					<dependencies>
 						<dependency>
 							<groupId>com.puppycrawl.tools</groupId>
 							<artifactId>checkstyle</artifactId>
-							<version>6.11.2</version>
+							<version>6.13</version>
 						</dependency>
 					</dependencies>
 					<configuration>

src/changes/changes.xml

@@ -7,6 +7,16 @@
 	</properties>
 	<body>
 		<release version="1.4" date="TBD">
+			<action type="add">
+            Bump the version of a few dependencies to the
+            latest versions (dependent HAPI modules listed in brackets):
+            <![CDATA[
+               <ul>
+                  <li>Hibernate (JPA, Web Tester): 5.0.3 -&gt; 5.0.5</li>
+                  <li>Springframework (JPA, Web Tester): 4.2.2 -&gt; 4.2.3</li>
+               </ul>
+            ]]>
+			</action>
 			<action type="fix">
 				Remove a dependency on a Java 1.7 class 
 				(ReflectiveOperationException) in several spots in the 
@@ -55,6 +65,17 @@
 				remains committed to supporting JDK 6+ in the compiled library, but these
 				days it can only be built using JDK 8. Thanks to joelsch for the PR!
 			</action>
+			<action type="fix">
+				When serializing a value[x] field, if the value type was a profiled type (e.g. markdown is a 
+				profile of string) HAPI 1.3 would use the base type in the element name, e.g.
+				valueString instead of valueMarkdown. After discussion with Grahame, this appears to
+				be incorrect behaviour so it has been fixed.
+			</action>
+			<action type="add" issue="240">
+				Support target parameter type in _include / _revinclude values, e.g.
+				_include=Patient:careProvider:Organization. Thanks to Joe Portner
+				for reporting!
+			<action>
 		</release>
 		<release version="1.3" date="2015-11-14">
 			<action type="add">