Fix #315 - Allow declaring of custom types for specific profiles

examples/src/main/java/example/CustomObservation.java

@@ -0,0 +1,7 @@
+package example;
+
+import org.hl7.fhir.dstu3.model.Observation;
+
+public class CustomObservation extends Observation {
+
+}

examples/src/main/java/example/ExtensionsDstu2.java

@@ -12,7 +12,7 @@ import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.parser.DataFormatException;
 
-public class Extensions {
+public class ExtensionsDstu2 {
 
 @SuppressWarnings("unused")
 public static void main(String[] args) throws DataFormatException, IOException {

examples/src/main/java/example/ExtensionsDstu3.java

@@ -0,0 +1,140 @@
+package example;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.hl7.fhir.dstu3.model.DateTimeType;
+import org.hl7.fhir.dstu3.model.Extension;
+import org.hl7.fhir.dstu3.model.HumanName;
+import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.StringType;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.rest.client.IGenericClient;
+
+public class ExtensionsDstu3 {
+
+   public void customType() {
+
+IGenericClient client = FhirContext.forDstu3().newRestfulGenericClient("http://foo");
+
+//START SNIPPET: customTypeClientSimple
+// Create an example patient
+MyPatient custPatient = new MyPatient();
+custPatient.addName().addFamily("Smith").addGiven("John");
+custPatient.setPetName(new StringType("Rover")); // populate the extension
+
+// Create the resource like normal
+client.create().resource(custPatient).execute();
+
+// You can also read the resource back like normal
+custPatient = client.read().resource(MyPatient.class).withId("123").execute();
+//END SNIPPET: customTypeClientSimple
+
+      
+   }
+
+   public void customTypeDeclared() {
+
+
+//START SNIPPET: customTypeClientDeclared
+FhirContext ctx = FhirContext.forDstu3();
+
+// Instruct the context that if it receives a resource which
+// claims to conform to the given profile (by URL), it should
+// use the MyPatient type to parse this resource
+ctx.setDefaultTypeForProfile("http://example.com/StructureDefinition/mypatient", MyPatient.class);
+
+// You can declare as many default types as you like
+ctx.setDefaultTypeForProfile("http://foo.com/anotherProfile", CustomObservation.class);
+
+// Create a client
+IGenericClient client = ctx.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3");
+
+// You can also read the resource back like normal
+Patient patient = client.read().resource(Patient.class).withId("123").execute();
+if (patient instanceof MyPatient) {
+   // If the server supplied a resource which declared to conform
+   // to the given profile, MyPatient will have been returned so
+   // process it differently..
+}
+
+//END SNIPPET: customTypeClientDeclared
+
+      
+   }
+
+@SuppressWarnings("unused")
+public static void main(String[] args) throws DataFormatException, IOException {
+
+	
+// START SNIPPET: resourceExtension
+// Create an example patient
+Patient patient = new Patient();
+patient.addIdentifier().setUse(IdentifierUse.OFFICIAL).setSystem("urn:example").setValue("7000135");
+
+// Create an extension
+Extension ext = new Extension();
+ext.setUrl("http://example.com/extensions#someext");
+ext.setValue(new DateTimeType("2011-01-02T11:13:15"));
+
+// Add the extension to the resource
+patient.addExtension(ext);
+//END SNIPPET: resourceExtension
+
+
+//START SNIPPET: resourceStringExtension
+// Continuing the example from above, we will add a name to the patient, and then
+// add an extension to part of that name
+HumanName name = patient.addName();
+name.addFamily("Shmoe");
+
+// Add a new "given name", which is of type String 
+StringType given = name.addGivenElement();
+given.setValue("Joe");
+
+// Create an extension and add it to the String
+Extension givenExt = new Extension("http://examples.com#moreext", new StringType("Hello"));
+given.addExtension(givenExt);
+//END SNIPPET: resourceStringExtension
+
+FhirContext ctx = FhirContext.forDstu3();
+String output = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
+System.out.println(output);
+
+
+//START SNIPPET: parseExtension
+// Get all extensions (modifier or not) for a given URL
+List<Extension> resourceExts = patient.getExtensionsByUrl("http://fooextensions.com#exts");
+
+// Get all non-modifier extensions regardless of URL
+List<Extension> nonModExts = patient.getExtension();
+
+//Get all non-modifier extensions regardless of URL
+List<Extension> modExts = patient.getModifierExtension();
+//END SNIPPET: parseExtension
+
+}
+
+
+public void foo() {
+//START SNIPPET: subExtension
+Patient patient = new Patient();
+
+// Add an extension (initially with no contents) to the resource 
+Extension parent = new Extension("http://example.com#parent");
+patient.addExtension(parent);
+
+// Add two extensions as children to the parent extension
+Extension child1 = new Extension("http://example.com#childOne", new StringType("value1"));
+parent.addExtension(child1);
+
+Extension child2 = new Extension("http://example.com#chilwo", new StringType("value1"));
+parent.addExtension(child2);
+//END SNIPPET: subExtension
+	
+}
+
+}

examples/src/main/java/example/MyPatient.java

@@ -4,13 +4,14 @@ package example;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.hl7.fhir.dstu3.model.DateTimeType;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.StringType;
+
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.api.annotation.Extension;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.primitive.DateTimeDt;
-import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.util.ElementUtil;
 
 /**
@@ -25,6 +26,8 @@ import ca.uhn.fhir.util.ElementUtil;
 @ResourceDef(name="Patient", profile="http://example.com/StructureDefinition/mypatient")
 public class MyPatient extends Patient {
 
+   private static final long serialVersionUID = 1L;
+
    /**
 	 * Each extension is defined in a field. Any valid HAPI Data Type
 	 * can be used for the field type. Note that the [name=""] attribute
@@ -34,7 +37,7 @@ public class MyPatient extends Patient {
 	@Child(name="petName")	
 	@Extension(url="http://example.com/dontuse#petname", definedLocally=false, isModifier=false)
 	@Description(shortDefinition="The name of the patient's favourite pet")
-	private StringDt myPetName;
+	private StringType myPetName;
 
 	/**
 	 * The second example extension uses a List type to provide
@@ -46,7 +49,7 @@ public class MyPatient extends Patient {
 	@Child(name="importantDates", max=Child.MAX_UNLIMITED)	
 	@Extension(url="http://example.com/dontuse#importantDates", definedLocally=false, isModifier=true)
 	@Description(shortDefinition="Some dates of note for this patient")
-	private List<DateTimeDt> myImportantDates;
+	private List<DateTimeType> myImportantDates;
 
 	/**
 	 * It is important to override the isEmpty() method, adding a check for any
@@ -67,28 +70,28 @@ public class MyPatient extends Patient {
 	 ********/
 	
 	/** Getter for important dates */
-	public List<DateTimeDt> getImportantDates() {
+	public List<DateTimeType> getImportantDates() {
 		if (myImportantDates==null) {
-			myImportantDates = new ArrayList<DateTimeDt>();
+			myImportantDates = new ArrayList<DateTimeType>();
 		}
 		return myImportantDates;
 	}
 
 	/** Getter for pet name */
-	public StringDt getPetName() {
+	public StringType getPetName() {
 		if (myPetName == null) {
-			myPetName = new StringDt();
+			myPetName = new StringType();
 		}
 		return myPetName;
 	}
 
 	/** Setter for important dates */
-	public void setImportantDates(List<DateTimeDt> theImportantDates) {
+	public void setImportantDates(List<DateTimeType> theImportantDates) {
 		myImportantDates = theImportantDates;
 	}
 
 	/** Setter for pet name */
-	public void setPetName(StringDt thePetName) {
+	public void setPetName(StringType thePetName) {
 		myPetName = thePetName;
 	}
 

examples/src/main/java/example/MyPatientUse.java

@@ -18,7 +18,7 @@ import ca.uhn.fhir.parser.IParser;
 
 public class MyPatientUse {
 
-   @ResourceDef
+   @ResourceDef()
    public static class MyPatient extends Patient {
 
       @Child(name="petName")  

hapi-fhir-base-test-mindeps-server/.classpath

@@ -6,22 +6,16 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry combineaccessrules="false" kind="src" path="/hapi-fhir-base"/>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

hapi-fhir-base-test-mindeps-server/.project

@@ -5,6 +5,16 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.m2e.core.maven2Builder</name>
 			<arguments>
@@ -13,5 +23,7 @@
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
 	</natures>
 </projectDescription>

hapi-fhir-base-test-mindeps-server/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,7 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
+org.eclipse.jdt.core.compiler.compliance=1.7
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.7

hapi-fhir-base-test-mindeps-server/.settings/org.eclipse.wst.common.project.facet.core.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <installed facet="java" version="1.7"/>
+</faceted-project>

hapi-fhir-base-test-mindeps-server/src/test/java/ca/uhn/fhir/parser/MultiVersionJsonParserTest.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.parser;
 
+import static org.hamcrest.Matchers.stringContainsInOrder;
 import static org.junit.Assert.assertThat;
 
 import org.hamcrest.core.StringContains;
@@ -22,7 +23,10 @@ public class MultiVersionJsonParserTest {
 		String str = FhirContext.forDstu2().newJsonParser().encodeResourceToString(p);
 		ourLog.info(str);
 
-		assertThat(str, StringContains.containsString("{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://foo#ext\",\"valueQuantity\":{\"value\":2.2}}],\"identifier\":[{\"system\":\"urn:sys\",\"value\":\"001\"}]}"));
+		assertThat(str, stringContainsInOrder(
+			"{\"resourceType\":\"Patient\"",
+			"\"extension\":[{\"url\":\"http://foo#ext\",\"valueQuantity\":{\"value\":2.2}}]",
+			"\"identifier\":[{\"system\":\"urn:sys\",\"value\":\"001\"}]"));
 	}
 
 }

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

@@ -50,6 +50,7 @@ import ca.uhn.fhir.rest.client.IRestfulClientFactory;
 import ca.uhn.fhir.rest.client.apache.ApacheRestfulClientFactory;
 import ca.uhn.fhir.rest.client.api.IBasicClient;
 import ca.uhn.fhir.rest.client.api.IRestfulClient;
+import ca.uhn.fhir.rest.server.AddProfileTagEnum;
 import ca.uhn.fhir.rest.server.IVersionSpecificBundleFactory;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.VersionUtil;
@@ -77,7 +78,9 @@ public class FhirContext {
 
 	private static final List<Class<? extends IBaseResource>> EMPTY_LIST = Collections.emptyList();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirContext.class);
+	private AddProfileTagEnum myAddProfileTagWhenEncoding = AddProfileTagEnum.ONLY_FOR_CUSTOM;
 	private volatile Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinition = Collections.emptyMap();
+	private Map<String, Class<? extends IBaseResource>> myDefaultTypeForProfile = new HashMap<String, Class<? extends IBaseResource>>();
 	private volatile Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = Collections.emptyMap();
 	private HapiLocalizer myLocalizer = new HapiLocalizer();
 	private volatile Map<String, BaseRuntimeElementDefinition<?>> myNameToElementDefinition = Collections.emptyMap();
@@ -144,6 +147,26 @@ public class FhirContext {
 		return getLocalizer().getMessage(FhirContext.class, "unknownResourceName", theResourceName, theVersion);
 	}
 
+	/**
+	 * When encoding resources, this setting configures the parser to include
+	 * an entry in the resource's metadata section which indicates which profile(s) the
+	 * resource claims to conform to. The default is {@link AddProfileTagEnum#ONLY_FOR_CUSTOM}.
+	 * 
+	 * @see #setAddProfileTagWhenEncoding(AddProfileTagEnum) for more information
+	 */
+	public AddProfileTagEnum getAddProfileTagWhenEncoding() {
+		return myAddProfileTagWhenEncoding;
+	}
+
+	/**
+	 * Returns the default resource type for the given profile
+	 * 
+	 * @see #setDefaultTypeForProfile(String, Class)
+	 */
+	public Class<? extends IBaseResource> getDefaultTypeForProfile(String theProfile) {
+		return myDefaultTypeForProfile.get(theProfile);
+	}
+
 	/**
 	 * Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
 	 * for extending the core library.
@@ -298,14 +321,6 @@ public class FhirContext {
 		return myIdToResourceDefinition.values();
 	}
 
-	/**
-	 * Set the restful client factory
-	 * @param theRestfulClientFactory
-	 */
-	public void setRestfulClientFactory(IRestfulClientFactory theRestfulClientFactory) {
-		this.myRestfulClientFactory = theRestfulClientFactory;
-	}
-
 	/**
 	 * Get the restful client factory. If no factory has been set, this will be initialized with 
 	 * a new ApacheRestfulClientFactory.
@@ -326,6 +341,17 @@ public class FhirContext {
 		return myVersion;
 	}
 
+	/**
+	 * Returns <code>true</code> if any default types for specific profiles have been defined
+	 * within this context.
+	 * 
+	 * @see #setDefaultTypeForProfile(String, Class)
+	 * @see #getDefaultTypeForProfile(String)
+	 */
+	public boolean hasDefaultTypeForProfile() {
+		return !myDefaultTypeForProfile.isEmpty();
+	}
+
 	/**
 	 * This method should be considered experimental and will likely change in future releases
 	 * of HAPI. Use with caution!
@@ -473,6 +499,50 @@ public class FhirContext {
 		return classToElementDefinition;
 	}
 	
+	/**
+	 * When encoding resources, this setting configures the parser to include
+	 * an entry in the resource's metadata section which indicates which profile(s) the
+	 * resource claims to conform to. The default is {@link AddProfileTagEnum#ONLY_FOR_CUSTOM}.
+	 * <p>
+	 * This feature is intended for situations where custom resource types are being used,
+	 * avoiding the need to manually add profile declarations for these custom types.
+	 * </p>  
+	 * <p>
+	 * See <a href="http://jamesagnew.gihhub.io/hapi-fhir/doc_extensions.html">Profiling and Extensions</a>
+	 * for more information on using custom types.
+	 * </p>
+	 * <p>
+	 * Note that this feature automatically adds the profile, but leaves any profile tags
+	 * which have been manually added in place as well.
+	 * </p>
+	 * 
+	 * @param theAddProfileTagWhenEncoding
+	 *           The add profile mode (must not be <code>null</code>)
+	 */
+	public void setAddProfileTagWhenEncoding(AddProfileTagEnum theAddProfileTagWhenEncoding) {
+		Validate.notNull(theAddProfileTagWhenEncoding, "theAddProfileTagWhenEncoding must not be null");
+		myAddProfileTagWhenEncoding = theAddProfileTagWhenEncoding;
+	}
+
+	/**
+	 * Sets the default type which will be used when parsing a resource that is found to be
+	 * of the given profile. 
+	 * <p>
+	 * For example, this method is invoked with the profile string of
+	 * <code>"http://example.com/some_patient_profile"</code> and the type of <code>MyPatient.class</code>,
+	 * if the parser is parsing a resource and finds that it declares that it conforms to that profile,
+	 * the <code>MyPatient</code> type will be used unless otherwise specified.
+	 * </p>
+	 * 
+	 * @param theProfile The profile string, e.g. <code>"http://example.com/some_patient_profile"</code>. Must not be <code>null</code> or empty.
+	 * @param theClass The resource type. Must not be <code>null</code> or empty.
+	 */
+	public void setDefaultTypeForProfile(String theProfile, Class<? extends IBaseResource> theClass) {
+		Validate.notBlank(theProfile, "theProfile must not be null or empty");
+		Validate.notNull(theClass, "theProfile must not be null");
+		myDefaultTypeForProfile.put(theProfile, theClass);
+	}
+
 	/**
 	 * This feature is not yet in its final state and should be considered an internal part of HAPI for now - use with
 	 * caution
@@ -495,6 +565,14 @@ public class FhirContext {
 		myParserErrorHandler = theParserErrorHandler;
 	}
 
+	/**
+	 * Set the restful client factory
+	 * @param theRestfulClientFactory
+	 */
+	public void setRestfulClientFactory(IRestfulClientFactory theRestfulClientFactory) {
+		this.myRestfulClientFactory = theRestfulClientFactory;
+	}
+
 	@SuppressWarnings({ "cast" })
 	private List<Class<? extends IElement>> toElementList(Collection<Class<? extends IBaseResource>> theResourceTypes) {
 		if (theResourceTypes == null) {
@@ -508,21 +586,28 @@ public class FhirContext {
 	}
 
 	/**
-	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU1}
+	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU1 DSTU1}
 	 */
 	public static FhirContext forDstu1() {
 		return new FhirContext(FhirVersionEnum.DSTU1);
 	}
 
 	/**
-	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU 2}
+	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU2}
 	 */
 	public static FhirContext forDstu2() {
 		return new FhirContext(FhirVersionEnum.DSTU2);
 	}
 
 	/**
-	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU3 DSTU 3}
+	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2_HL7ORG DSTU2} (using the Reference Implementation Structures)
+	 */
+	public static FhirContext forDstu2Hl7Org() {
+		return new FhirContext(FhirVersionEnum.DSTU2_HL7ORG);
+	}
+
+	/**
+	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU3 DSTU3}
 	 * 
 	 * @since 1.4
 	 */
@@ -530,10 +615,6 @@ public class FhirContext {
 		return new FhirContext(FhirVersionEnum.DSTU3);
 	}
 
-	public static FhirContext forDstu2Hl7Org() {
-		return new FhirContext(FhirVersionEnum.DSTU2_HL7ORG);
-	}
-
 	private static Collection<Class<? extends IBaseResource>> toCollection(Class<? extends IBaseResource> theResourceType) {
 		ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<Class<? extends IBaseResource>>(1);
 		retVal.add(theResourceType);

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

@@ -683,6 +683,14 @@ class ModelScanner {
 			}
 		}
 
+		Class<? extends IBaseResource> builtInType = myNameToResourceType.get(resourceName.toLowerCase());
+		boolean standardType = builtInType != null && builtInType.equals(theClass) == true;
+		if (primaryNameProvider) {
+			if (builtInType != null && builtInType.equals(theClass) == false) {
+				primaryNameProvider = false;
+			}
+		}
+		
 		String resourceId = resourceDefinition.id();
 		if (!isBlank(resourceId)) {
 			if (myIdToResourceDefinition.containsKey(resourceId)) {
@@ -691,7 +699,7 @@ class ModelScanner {
 			}
 		}
 
-		RuntimeResourceDefinition resourceDef = new RuntimeResourceDefinition(myContext, resourceName, theClass, resourceDefinition, isStandardType(theClass));
+		RuntimeResourceDefinition resourceDef = new RuntimeResourceDefinition(myContext, resourceName, theClass, resourceDefinition, standardType);
 		myClassToElementDefinitions.put(theClass, resourceDef);
 		if (primaryNameProvider) {
 			if (resourceDef.getStructureVersion() == myVersion) {

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

@@ -155,10 +155,6 @@ public class RuntimeResourceDefinition extends BaseRuntimeElementCompositeDefini
 		return "Bundle".equals(getName());
 	}
 
-	public boolean isStandardProfile() {
-		return myResourceProfile.startsWith("http://hl7.org/fhir/profiles");
-	}
-
 	@Override
 	public void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
 		super.sealAndInitialize(theContext, theClassToElementDefinitions);

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

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.model.api;
 
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -62,6 +64,15 @@ public interface IResource extends ICompositeElement, org.hl7.fhir.instance.mode
 	 */
 	CodeDt getLanguage();
 
+	/**
+	 * Returns a view of the {@link #getResourceMetadata() resource metadata} map.
+	 * Note that getters from this map return immutable objects, but the <code>addFoo()</code>
+	 * and <code>setFoo()</code> methods may be used to modify metadata. 
+	 * 
+	 * @since 1.5
+	 */
+	IBaseMetaType getMeta();
+
 	/**
 	 * Returns the metadata map for this object, creating it if neccesary. Metadata entries are used to get/set feed bundle entries, such as the resource version, or the last updated timestamp.
 	 * <p>
@@ -72,10 +83,23 @@ public interface IResource extends ICompositeElement, org.hl7.fhir.instance.mode
 	 */
 	ResourceMetadataMap getResourceMetadata();
 
+	/**
+	 * Returns a String representing the name of this Resource. This return value is not used for anything by HAPI itself, but is provided as a convenience to developers using the API.
+	 * 
+	 * @return the name of this resource, e.g. "Patient", or "Observation"
+	 */
+	String getResourceName();
+
+	/**
+	 * Returns the FHIR version represented by this structure
+	 */
+	@Override
+	public ca.uhn.fhir.context.FhirVersionEnum getStructureFhirVersionEnum();
+
 	/**
 	 * Returns the narrative block for this resource
 	 */
-	BaseNarrativeDt getText();
+	BaseNarrativeDt<?> getText();
 
 	/**
 	 * Sets the ID of this resource. Note that this identifier is the URL (or a portion of the URL) used to access this resource, and is not the same thing as any business identifiers stored within the
@@ -99,16 +123,4 @@ public interface IResource extends ICompositeElement, org.hl7.fhir.instance.mode
 	 */
 	void setResourceMetadata(ResourceMetadataMap theMap);
 
-	/**
-	 * Returns a String representing the name of this Resource. This return value is not used for anything by HAPI itself, but is provided as a convenience to developers using the API.
-	 * 
-	 * @return the name of this resource, e.g. "Patient", or "Observation"
-	 */
-	String getResourceName();
-
-	/**
-	 * Returns the FHIR version represented by this structure
-	 */
-	public ca.uhn.fhir.context.FhirVersionEnum getStructureFhirVersionEnum();
-
 }

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

@@ -26,6 +26,7 @@ import java.net.URI;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
 
 /**
  * A single tag
@@ -34,7 +35,7 @@ import org.apache.commons.lang3.builder.ToStringStyle;
  * {@link #getScheme() scheme} and 
  * </p>
  */
-public class Tag extends BaseElement implements IElement {
+public class Tag extends BaseElement implements IElement, IBaseCoding {
 	
 	private static final long serialVersionUID = 1L;
 	
@@ -59,10 +60,6 @@ public class Tag extends BaseElement implements IElement {
 	private String myScheme;
 	private String myTerm;
 
-	/**
-	 * @deprecated Tags will become immutable in a future release, so this constructor should not be used.
-	 */
-	@Deprecated
 	public Tag() {
 	}
 
@@ -149,12 +146,7 @@ public class Tag extends BaseElement implements IElement {
 
 	/**
 	 * Sets the label and returns a reference to this tag
-	 * 
-	 * @deprecated Tags will become immutable in a future release of HAPI in order to facilitate
-	 * ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
-	 * tag object
 	 */
-	@Deprecated
 	public Tag setLabel(String theLabel) {
 		myLabel = theLabel;
 		return this;
@@ -162,12 +154,7 @@ public class Tag extends BaseElement implements IElement {
 
 	/**
 	 * Sets the scheme and returns a reference to this tag
-	 * 
-	 * @deprecated Tags will become immutable in a future release of HAPI in order to facilitate
-	 * ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
-	 * tag object
 	 */
-	@Deprecated
 	public Tag setScheme(String theScheme) {
 		myScheme = theScheme;
 		return this;
@@ -175,12 +162,7 @@ public class Tag extends BaseElement implements IElement {
 
 	/**
 	 * Sets the term and returns a reference to this tag
-	 * 
-	 * @deprecated Tags will become immutable in a future release of HAPI in order to facilitate
-	 * ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
-	 * tag object
 	 */
-	@Deprecated
 	public Tag setTerm(String theTerm) {
 		myTerm = theTerm;
 		return this;
@@ -207,4 +189,37 @@ public class Tag extends BaseElement implements IElement {
 		return b.toString();
 	}
 
+	@Override
+	public String getCode() {
+		return getTerm();
+	}
+
+	@Override
+	public String getDisplay() {
+		return getLabel();
+	}
+
+	@Override
+	public String getSystem() {
+		return getScheme();
+	}
+
+	@Override
+	public IBaseCoding setCode(String theTerm) {
+		setTerm(myTerm);
+		return this;
+	}
+
+	@Override
+	public IBaseCoding setDisplay(String theLabel) {
+		setLabel(theLabel);
+		return this;
+	}
+
+	@Override
+	public IBaseCoding setSystem(String theScheme) {
+		setScheme(theScheme);
+		return this;
+	}
+
 }

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

@@ -53,6 +53,10 @@ public @interface ResourceDef {
 	/**
 	 * The URL indicating the profile for this resource definition. If specified, this URL will be
 	 * automatically added to the meta tag when the resource is serialized.
+	 * <p>
+	 * This URL should be fully qualified to indicate the complete URL of
+	 * the profile being used, e.g. <code>http://example.com/fhir/StructureDefiniton/some_profile</code>
+	 * </p>
 	 */
 	String profile() default "";
 	

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

@@ -78,12 +78,14 @@ public abstract class BaseParser implements IParser {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
 
-	private IIdType myEncodeForceResourceId;
 	private ContainedResources myContainedResources;
 	private FhirContext myContext;
+	private Set<String> myDontEncodeElements;
+	private boolean myDontEncodeElementsIncludesStars;
 	private Set<String> myEncodeElements;
 	private Set<String> myEncodeElementsAppliesToResourceTypes;
 	private boolean myEncodeElementsIncludesStars;
+	private IIdType myEncodeForceResourceId;
 	private IParserErrorHandler myErrorHandler;
 	private boolean myOmitResourceId;
 	private String myServerBaseUrl;
@@ -91,10 +93,6 @@ public abstract class BaseParser implements IParser {
 	private boolean mySummaryMode;
 	private boolean mySuppressNarratives;
 
-	private Set<String> myDontEncodeElements;
-
-	private boolean myDontEncodeElementsIncludesStars;
-
 	/**
 	 * Constructor
 	 * 
@@ -439,6 +437,47 @@ public abstract class BaseParser implements IParser {
 		return tags;
 	}
 
+	@SuppressWarnings("deprecation")
+	protected <T extends IPrimitiveType<String>> List<T> getProfileTagsForEncoding(IBaseResource theResource, List<T> theProfiles) {
+		switch (myContext.getAddProfileTagWhenEncoding()) {
+		case NEVER:
+			return theProfiles;
+		case ONLY_FOR_CUSTOM:
+			RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
+			if (resDef.isStandardType()) {
+				return theProfiles;
+			}
+			break;
+		case ALWAYS:
+			break;
+		}
+
+		if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
+			RuntimeResourceDefinition nextDef = myContext.getResourceDefinition(theResource);
+			String profile = nextDef.getResourceProfile(myServerBaseUrl);
+			if (isNotBlank(profile)) {
+				for (T next : theProfiles) {
+					if (profile.equals(next.getValue())) {
+						return theProfiles;
+					}
+				}
+
+				List<T> newList = new ArrayList<T>();
+				newList.addAll(theProfiles);
+
+				BaseRuntimeElementDefinition<?> idElement = myContext.getElementDefinition("id");
+				@SuppressWarnings("unchecked")
+				T newId = (T) idElement.newInstance();
+				newId.setValue(profile);
+
+				newList.add(newId);
+				return newList;
+			}
+		}
+
+		return theProfiles;
+	}
+
 	/**
 	 * If set to <code>true</code> (default is <code>false</code>), narratives will not be included in the encoded
 	 * values.
@@ -595,6 +634,17 @@ public abstract class BaseParser implements IParser {
 				filterCodingsWithNoCodeOrSystem(metaValue.getTag());
 				filterCodingsWithNoCodeOrSystem(metaValue.getSecurity());
 
+				List<? extends IPrimitiveType<String>> newProfileList = getProfileTagsForEncoding(theResource, metaValue.getProfile());
+				List<? extends IPrimitiveType<String>> oldProfileList = metaValue.getProfile();
+				if (oldProfileList != newProfileList) {
+					oldProfileList.clear();
+					for (IPrimitiveType<String> next : newProfileList) {
+						if (isNotBlank(next.getValue())) {
+							metaValue.addProfile(next.getValue());
+						}
+					}
+				}
+
 				if (shouldAddSubsettedTag()) {
 					IBaseCoding coding = metaValue.addTag();
 					coding.setCode(Constants.TAG_SUBSETTED_CODE);
@@ -748,11 +798,11 @@ public abstract class BaseParser implements IParser {
 	}
 
 	protected static <T> List<T> extractMetadataListNotNull(IResource resource, ResourceMetadataKeyEnum<List<T>> key) {
-		List<T> securityLabels = key.get(resource);
+		List<? extends T> securityLabels = key.get(resource);
 		if (securityLabels == null) {
 			securityLabels = Collections.emptyList();
 		}
-		return securityLabels;
+		return new ArrayList<T>(securityLabels);
 	}
 
 	static boolean hasExtensions(IBase theElement) {

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

@@ -222,7 +222,8 @@ public interface IParser {
 	 * <li><b>Patient</b> - Don't encode patient and all its children</li>
 	 * <li><b>Patient.name</b> - Don't encode the patient's name</li>
 	 * <li><b>Patient.name.family</b> - Don't encode the patient's family name</li>
-	 * <li><b>*.text</b> - Don't encode the text element on any resource (only the very first position may contain a wildcard)</li>
+	 * <li><b>*.text</b> - Don't encode the text element on any resource (only the very first position may contain a
+	 * wildcard)</li>
 	 * </ul>
 	 * <p>
 	 * DSTU2 note: Note that values including meta, such as <code>Patient.meta</code>
@@ -244,7 +245,8 @@ public interface IParser {
 	 * <li><b>Patient</b> - Encode patient and all its children</li>
 	 * <li><b>Patient.name</b> - Encode only the patient's name</li>
 	 * <li><b>Patient.name.family</b> - Encode only the patient's family name</li>
-	 * <li><b>*.text</b> - Encode the text element on any resource (only the very first position may contain a wildcard)</li>
+	 * <li><b>*.text</b> - Encode the text element on any resource (only the very first position may contain a
+	 * wildcard)</li>
 	 * </ul>
 	 * 
 	 * @param theEncodeElements

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

@@ -838,7 +838,9 @@ public class JsonParser extends BaseParser implements IParser {
 			// Object securityLabelRawObj =
 
 			List<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
-			List<IdDt> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
+			List<? extends IIdType> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
+			profiles = super.getProfileTagsForEncoding(resource, profiles);
+			
 			TagList tags = getMetaTagsForEncoding(resource);
 			InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
 			IdDt resourceId = resource.getId();
@@ -854,7 +856,7 @@ public class JsonParser extends BaseParser implements IParser {
 
 				if (profiles != null && profiles.isEmpty() == false) {
 					theEventWriter.writeStartArray("profile");
-					for (IdDt profile : profiles) {
+					for (IIdType profile : profiles) {
 						if (profile != null && isNotBlank(profile.getValue())) {
 							theEventWriter.write(profile.getValue());
 						}

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

@@ -43,6 +43,7 @@ import org.hl7.fhir.instance.model.api.IBaseElement;
 import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
 import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IBaseXhtml;
@@ -1433,6 +1434,11 @@ class ParserState<T> {
 
 		}
 
+		@Override
+		protected void populateTarget() {
+			// nothing
+		}
+
 	}
 
 	private class ContainedResourcesStateHl7Org extends PreResourceState {
@@ -1464,6 +1470,11 @@ class ParserState<T> {
 			def.getChildByName("contained").getMutator().addValue(preResCurrentElement, res);
 		}
 
+		@Override
+		protected void populateTarget() {
+			// nothing
+		}
+
 	}
 
 	private class DeclaredExtensionState extends BaseState {
@@ -1969,6 +1980,8 @@ class ParserState<T> {
 			}
 		}
 
+		protected abstract void populateTarget();
+
 		public PreResourceState(PreResourceState thePreResourcesState, FhirVersionEnum theParentVersion) {
 			super(thePreResourcesState);
 			Validate.notNull(theParentVersion);
@@ -2045,6 +2058,40 @@ class ParserState<T> {
 		public void wereBack() {
 			final boolean bundle = "Bundle".equals(myContext.getResourceDefinition(myInstance).getName());
 
+			if (myContext.hasDefaultTypeForProfile()) {
+				IBaseMetaType meta = myInstance.getMeta();
+				Class<? extends IBaseResource> wantedProfileType = null;
+				String usedProfile = null;
+				for (IPrimitiveType<String> next : meta.getProfile()) {
+					if (isNotBlank(next.getValue())) {
+						wantedProfileType = myContext.getDefaultTypeForProfile(next.getValue());
+						if (wantedProfileType != null) {
+							usedProfile = next.getValue();
+							break;
+						}
+					}
+				}
+	
+				if (wantedProfileType != null && !wantedProfileType.equals(myInstance.getClass())) {
+					if (myResourceType == null || myResourceType.isAssignableFrom(wantedProfileType)) {
+						ourLog.debug("Converting resource of type {} to type defined for profile \"{}\": {}", new Object[] {myInstance.getClass().getName(), usedProfile, wantedProfileType});
+						
+						/*
+						 * This isn't the most efficient thing really.. If we want a specific
+						 * type we just re-parse into that type. The problem is that we don't know
+						 * until we've parsed the resource which type we want to use because the
+						 * profile declarations are in the text of the resource itself.
+						 * 
+						 * At some point it would be good to write code which can present a view
+						 * of one type backed by another type and use that.
+						 */
+						IParser parser = myContext.newJsonParser();
+						String asString = parser.encodeResourceToString(myInstance);
+						myInstance = parser.parseResource(wantedProfileType, asString);
+					}
+				}
+			}
+			
 			FhirTerser terser = myContext.newTerser();
 			terser.visit(myInstance, new IModelVisitor() {
 
@@ -2114,6 +2161,7 @@ class ParserState<T> {
 
 			}
 
+			populateTarget();
 		}
 
 	}
@@ -2141,14 +2189,19 @@ class ParserState<T> {
 			assert theResourceType == null || IResource.class.isAssignableFrom(theResourceType);
 		}
 
+//		@Override
+//		public void enteringNewElement(String theNamespaceUri, String theLocalPart) throws DataFormatException {
+//			super.enteringNewElement(theNamespaceUri, theLocalPart);
+//			populateTarget();
+//		}
+
 		@Override
-		public void enteringNewElement(String theNamespaceUri, String theLocalPart) throws DataFormatException {
+		protected void populateTarget() {
-			super.enteringNewElement(theNamespaceUri, theLocalPart);
 			if (myEntry != null) {
 				myEntry.setResource((IResource) getCurrentElement());
 			}
 			if (myMutator != null) {
-				myMutator.addValue(myTarget, getCurrentElement());
+				myMutator.setValue(myTarget, getCurrentElement());
 			}
 		}
 
@@ -2192,10 +2245,9 @@ class ParserState<T> {
 		}
 
 		@Override
-		public void enteringNewElement(String theNamespaceUri, String theLocalPart) throws DataFormatException {
+		protected void populateTarget() {
-			super.enteringNewElement(theNamespaceUri, theLocalPart);
 			if (myMutator != null) {
-				myMutator.addValue(myTarget, getCurrentElement());
+				myMutator.setValue(myTarget, getCurrentElement());
 			}
 		}
 

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

@@ -132,16 +132,6 @@ public class XmlParser extends BaseParser implements IParser {
 		} catch (XMLStreamException e1) {
 			throw new DataFormatException(e1);
 		}
-
-		// XMLEventReader streamReader;
-		// try {
-		// streamReader = myXmlInputFactory.createXMLEventReader(theReader);
-		// } catch (XMLStreamException e) {
-		// throw new DataFormatException(e);
-		// } catch (FactoryConfigurationError e) {
-		// throw new ConfigurationException("Failed to initialize STaX event factory", e);
-		// }
-		// return streamReader;
 	}
 
 	private XMLStreamWriter createXmlWriter(Writer theWriter) throws XMLStreamException {
@@ -433,8 +423,6 @@ public class XmlParser extends BaseParser implements IParser {
 			theEventWriter.writeEndElement();
 		}
 
-		String bundleBaseUrl = theBundle.getLinkBase().getValue();
-
 		writeOptionalTagWithValue(theEventWriter, "type", theBundle.getType().getValue());
 		writeOptionalTagWithValue(theEventWriter, "total", theBundle.getTotalResults().getValueAsString());
 
@@ -841,7 +829,9 @@ public class XmlParser extends BaseParser implements IParser {
 					versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
 				}
 				List<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
-				List<IdDt> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
+				List<? extends IIdType> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
+				profiles = super.getProfileTagsForEncoding(resource, profiles);
+				
 				TagList tags = getMetaTagsForEncoding((resource));
 
 				if (super.shouldEncodeResourceMeta(resource) && ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
@@ -851,7 +841,7 @@ public class XmlParser extends BaseParser implements IParser {
 						writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
 					}
 
-					for (IdDt profile : profiles) {
+					for (IIdType profile : profiles) {
 						theEventWriter.writeStartElement("profile");
 						theEventWriter.writeAttribute("value", profile.getValue());
 						theEventWriter.writeEndElement();

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

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.rest.server;
 
+import ca.uhn.fhir.context.FhirContext;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -21,9 +23,9 @@ package ca.uhn.fhir.rest.server;
  */
 
 /**
- * RESTful server behaviour for automatically adding profile tags
+ * RESTful server behaviour for automatically adding profile tags when serializing resources
  * 
- * @see RestfulServer#setAddProfileTag(AddProfileTagEnum)
+ * @see FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)
  */
 public enum AddProfileTagEnum {
 	/**
@@ -33,7 +35,13 @@ public enum AddProfileTagEnum {
 
 	/**
 	 * Add any profile tags that returned resources appear to conform to
+	 * 
+	 * @deprecated This mode causes even FHIR's default profiles to be exported in the
+	 * resource metadata section. This is not generally expected behaviour from other
+	 * systems and it offers no real benefit, so it will be removed at some point. This
+	 * option was deprecated in HAPI 1.5
 	 */
+	@Deprecated
 	ALWAYS,
 
 	/**

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

@@ -48,7 +48,9 @@ public interface IRestfulServerDefaults {
 
 	/**
 	 * @return Returns the setting for automatically adding profile tags
+	 * @deprecated As of HAPI FHIR 1.5, this property has been moved to {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
 	 */
+	@Deprecated
 	AddProfileTagEnum getAddProfileTag();
 
 	/**

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

@@ -40,7 +40,7 @@ public interface IVersionSpecificBundleFactory {
 
 	void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theCompleteUrl, Integer theTotalResults, BundleTypeEnum theBundleType, IPrimitiveType<Date> theLastUpdated);
 
-	void initializeBundleFromBundleProvider(IRestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl, boolean thePrettyPrint,
+	void initializeBundleFromBundleProvider(IRestfulServer<?> theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl, boolean thePrettyPrint,
 			int theOffset, Integer theCount, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes);
 
 	Bundle getDstu1Bundle();

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

@@ -74,6 +74,7 @@ import ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.ReflectionUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.util.VersionUtil;
@@ -93,7 +94,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	private static final ExceptionHandlingInterceptor DEFAULT_EXCEPTION_HANDLER = new ExceptionHandlingInterceptor();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestfulServer.class);
 	private static final long serialVersionUID = 1L;
-	private AddProfileTagEnum myAddProfileTag;
 	private BundleInclusionRule myBundleInclusionRule = BundleInclusionRule.BASED_ON_INCLUDES;
 	private boolean myDefaultPrettyPrint = false;
 	private EncodingEnum myDefaultResponseEncoding = EncodingEnum.XML;
@@ -369,11 +369,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		return count;
 	}
 
-	@Override
-	public AddProfileTagEnum getAddProfileTag() {
-		return myAddProfileTag;
-	}
-
 	@Override
 	public BundleInclusionRule getBundleInclusionRule() {
 		return myBundleInclusionRule;
@@ -1117,10 +1112,13 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 *
 	 * @param theAddProfileTag
 	 *           The behaviour enum (must not be null)
+	 * @deprecated As of HAPI FHIR 1.5, this property has been moved to {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
 	 */
+	@Deprecated
+	@CoverageIgnore
 	public void setAddProfileTag(AddProfileTagEnum theAddProfileTag) {
 		Validate.notNull(theAddProfileTag, "theAddProfileTag must not be null");
-		myAddProfileTag = theAddProfileTag;
+		myFhirContext.setAddProfileTagWhenEncoding(theAddProfileTag);
 	}
 
 	/**
@@ -1394,4 +1392,13 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		return nextString.length() > 0 && (nextString.charAt(0) == '_' || nextString.charAt(0) == '$' || nextString.equals(Constants.URL_TOKEN_METADATA));
 	}
 
+	/**
+	 * @deprecated As of HAPI FHIR 1.5, this property has been moved to {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
+	 */
+	@Override
+	@Deprecated
+	public AddProfileTagEnum getAddProfileTag() {
+		return myFhirContext.getAddProfileTagWhenEncoding();
+	}
+
 }

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

@@ -26,7 +26,6 @@ import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.io.Writer;
 import java.net.URLEncoder;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Date;
@@ -49,15 +48,12 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 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.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
-import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 import ca.uhn.fhir.parser.IParser;
@@ -77,36 +73,6 @@ public class RestfulServerUtils {
 
 	private static final HashSet<String> TEXT_ENCODE_ELEMENTS = new HashSet<String>(Arrays.asList("Bundle", "*.text"));
 
-	public static void addProfileToBundleEntry(FhirContext theContext, IBaseResource theResource, String theServerBase) {
-		if (theResource instanceof IResource) {
-			if (theContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
-				RuntimeResourceDefinition nextDef = theContext.getResourceDefinition(theResource);
-				String profile = nextDef.getResourceProfile(theServerBase);
-				if (isNotBlank(profile)) {
-					List<IdDt> newList = new ArrayList<IdDt>();
-					List<IdDt> existingList = ResourceMetadataKeyEnum.PROFILES.get((IResource) theResource);
-					if (existingList != null) {
-						newList.addAll(existingList);
-					}
-					newList.add(new IdDt(profile));
-					ResourceMetadataKeyEnum.PROFILES.put((IResource) theResource, newList);
-				}
-			} else {
-				TagList tl = ResourceMetadataKeyEnum.TAG_LIST.get((IResource) theResource);
-				if (tl == null) {
-					tl = new TagList();
-					ResourceMetadataKeyEnum.TAG_LIST.put((IResource) theResource, tl);
-				}
-
-				RuntimeResourceDefinition nextDef = theContext.getResourceDefinition(theResource);
-				String profile = nextDef.getResourceProfile(theServerBase);
-				if (isNotBlank(profile)) {
-					tl.add(new Tag(Tag.HL7_ORG_PROFILE_TAG, profile, null));
-				}
-			}
-		}
-	}
-
 	public static void configureResponseParser(RequestDetails theRequestDetails, IParser parser) {
 		// Pretty print
 		boolean prettyPrint = RestfulServerUtils.prettyPrintResponse(theRequestDetails.getServer(), theRequestDetails);
@@ -608,13 +574,6 @@ public class RestfulServerUtils {
 			}
 		}
 
-		if (theServer.getAddProfileTag() != AddProfileTagEnum.NEVER) {
-			RuntimeResourceDefinition def = theServer.getFhirContext().getResourceDefinition(theResource);
-			if (theServer.getAddProfileTag() == AddProfileTagEnum.ALWAYS || !def.isStandardProfile()) {
-				addProfileToBundleEntry(theServer.getFhirContext(), theResource, serverBase);
-			}
-		}
-
 		String contentType;
 		if (theResource instanceof IBaseBinary && responseEncoding == null) {
 			IBaseBinary bin = (IBaseBinary) theResource;

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

@@ -55,8 +55,6 @@ public interface IAnyResource extends IBaseResource {
 
 	IPrimitiveType<String> getLanguageElement();
 
-	IBaseMetaType getMeta();
-
 	public Object getUserData(String name);
 
 	@Override

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

@@ -39,6 +39,8 @@ import ca.uhn.fhir.model.api.Include;
  */
 public interface IBaseResource extends IBase, IElement {
 
+	IBaseMetaType getMeta();
+
 	/**
 	 * Include constant for <code>*</code> (return all includes)
 	 */

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

@@ -32,7 +32,7 @@ package org.hl7.fhir.instance.model.api;
  * which version of the strctures your application is using.   
  * </p>
  */
-public interface IIdType extends IBase {
+public interface IIdType extends IPrimitiveType<String> {
 
 	void applyTo(IBaseResource theResource);
 

hapi-fhir-structures-dstu/.classpath

@@ -36,5 +36,5 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

hapi-fhir-structures-dstu/src/main/java/ca/uhn/fhir/model/dstu/resource/BaseResource.java

@@ -1,5 +1,10 @@
 package ca.uhn.fhir.model.dstu.resource;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Date;
+import java.util.List;
+
 /*
  * #%L
  * HAPI FHIR Structures - DSTU1 (FHIR v0.80)
@@ -23,35 +28,31 @@ package ca.uhn.fhir.model.dstu.resource;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.model.api.BaseElement;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.SearchParamDefinition;
+import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.resource.ResourceMetadataMap;
+import ca.uhn.fhir.model.dstu.composite.CodingDt;
 import ca.uhn.fhir.model.dstu.composite.ContainedDt;
 import ca.uhn.fhir.model.dstu.composite.NarrativeDt;
 import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.gclient.StringClientParam;
 import ca.uhn.fhir.util.ElementUtil;
 
 public abstract class BaseResource extends BaseElement implements IResource {
 
-	/**
-	 * Search parameter constant for <b>_language</b>
-	 */
-	@SearchParamDefinition(name="_language", path="", description="The language of the resource", type="string"  )
-	public static final String SP_RES_LANGUAGE = "_language";
-
-
-	/**
-	 * Search parameter constant for <b>_id</b>
-	 */
-	@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="string"  )
-	public static final String SP_RES_ID = "_id";
-
 	/**
 	 * <b>Fluent Client</b> search parameter constant for <b>_id</b>
 	 * <p>
@@ -63,9 +64,24 @@ public abstract class BaseResource extends BaseElement implements IResource {
 	public static final StringClientParam RES_ID = new StringClientParam(BaseResource.SP_RES_ID);
 
 
+	/**
+	 * Search parameter constant for <b>_id</b>
+	 */
+	@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="string"  )
+	public static final String SP_RES_ID = "_id";
+
+	/**
+	 * Search parameter constant for <b>_language</b>
+	 */
+	@SearchParamDefinition(name="_language", path="", description="The language of the resource", type="string"  )
+	public static final String SP_RES_LANGUAGE = "_language";
+	
+
+	
 	@Child(name = "contained", order = 2, min = 0, max = 1)
 	private ContainedDt myContained;
 
+
 	private IdDt myId;
 
 	@Child(name = "language", order = 0, min = 0, max = Child.MAX_UNLIMITED)
@@ -104,6 +120,216 @@ public abstract class BaseResource extends BaseElement implements IResource {
 		return myLanguage;
 	}
 
+	@Override
+	public IBaseMetaType getMeta() {
+		return new IBaseMetaType() {
+			
+			private static final long serialVersionUID = 1L;
+
+			@Override
+			public IBaseMetaType addProfile(String theProfile) {
+				ArrayList<IdDt> newTagList = new ArrayList<IdDt>();
+				List<IdDt> existingTagList = ResourceMetadataKeyEnum.PROFILES.get(BaseResource.this);
+				if (existingTagList != null) {
+					newTagList.addAll(existingTagList);
+				}
+				ResourceMetadataKeyEnum.PROFILES.put(BaseResource.this, newTagList);
+				
+				IdDt tag = new IdDt(theProfile);
+				newTagList.add(tag);
+				return this;
+			}
+			
+			@Override
+			public IBaseCoding addSecurity() {
+				List<BaseCodingDt> tagList = ResourceMetadataKeyEnum.SECURITY_LABELS.get(BaseResource.this);
+				if (tagList == null) {
+					tagList = new ArrayList<BaseCodingDt>();
+					ResourceMetadataKeyEnum.SECURITY_LABELS.put(BaseResource.this, tagList);
+				}
+				CodingDt tag = new CodingDt();
+				tagList.add(tag);
+				return asBaseCoding(tag);
+			}
+			
+			@Override
+			public IBaseCoding addTag() {
+				TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(BaseResource.this);
+				if (tagList == null) {
+					tagList = new TagList();
+					ResourceMetadataKeyEnum.TAG_LIST.put(BaseResource.this, tagList);
+				}
+				Tag tag = new Tag();
+				tagList.add(tag);
+				return tag;
+			}
+			
+			/**
+			 * This view is used because the old DSTU1 BaseCodingDt can't implements IBaseCoding
+			 */
+			private IBaseCoding asBaseCoding(final BaseCodingDt theCoding) {
+				return new IBaseCoding() {
+					private static final long serialVersionUID = 1L;
+
+					@Override
+					public String getCode() {
+						return theCoding.getCodeElement().getValue();
+					}
+					
+					@Override
+					public String getDisplay() {
+						return theCoding.getDisplayElement().getValue();
+					}
+					
+					@Override
+					public List<String> getFormatCommentsPost() {
+						return Collections.emptyList();
+					}
+					
+					@Override
+					public List<String> getFormatCommentsPre() {
+						return Collections.emptyList();
+					}
+					
+					@Override
+					public String getSystem() {
+						return theCoding.getSystemElement().getValue();
+					}
+					
+					@Override
+					public boolean hasFormatComment() {
+						return false;
+					}
+					
+					@Override
+					public boolean isEmpty() {
+						return ElementUtil.isEmpty(getSystem(), getCode(), getDisplay());
+					}
+					
+					@Override
+					public IBaseCoding setCode(String theTerm) {
+						theCoding.setCode(theTerm);
+						return this;
+					}
+					
+					@Override
+					public IBaseCoding setDisplay(String theLabel) {
+						theCoding.setDisplay(theLabel);
+						return this;
+					}
+					
+					@Override
+					public IBaseCoding setSystem(String theScheme) {
+						theCoding.setSystem(theScheme);
+						return this;
+					}
+				};
+			}
+			
+			@Override
+			public List<String> getFormatCommentsPost() {
+				return Collections.emptyList();
+			}
+			
+			@Override
+			public List<String> getFormatCommentsPre() {
+				return Collections.emptyList();
+			}
+			
+			@Override
+			public Date getLastUpdated() {
+				InstantDt lu = ResourceMetadataKeyEnum.UPDATED.get(BaseResource.this);
+				if (lu != null) {
+					return lu.getValue();
+				}
+				return null;
+			}
+			
+			@Override
+			public List<? extends IPrimitiveType<String>> getProfile() {
+				ArrayList<IPrimitiveType<String>> retVal = new ArrayList<IPrimitiveType<String>>();
+				List<IdDt> profilesList = ResourceMetadataKeyEnum.PROFILES.get(BaseResource.this);
+				if (profilesList == null) {
+					return Collections.emptyList();
+				}
+				for (IdDt next : profilesList) {
+					retVal.add(next);
+				}
+				return Collections.unmodifiableList(retVal);
+			}
+
+			@Override
+			public List<? extends IBaseCoding> getSecurity() {
+				ArrayList<IBaseCoding> retVal = new ArrayList<IBaseCoding>();
+				List<BaseCodingDt> labelsList = ResourceMetadataKeyEnum.SECURITY_LABELS.get(BaseResource.this);
+				if (labelsList == null) {
+					return Collections.emptyList();
+				}
+				for (BaseCodingDt next : labelsList) {
+					retVal.add(asBaseCoding(next));
+				}
+				return Collections.unmodifiableList(retVal);
+			}
+			
+			@Override
+			public IBaseCoding getSecurity(String theSystem, String theCode) {
+				for (BaseCodingDt next : ResourceMetadataKeyEnum.SECURITY_LABELS.get(BaseResource.this)) {
+					if (theSystem.equals(next.getSystemElement().getValue()) && theCode.equals(next.getCodeElement().getValue())) {
+						return asBaseCoding(next);
+					}
+				}
+				return null;
+			}
+			
+			@Override
+			public List<? extends IBaseCoding> getTag() {
+				ArrayList<IBaseCoding> retVal = new ArrayList<IBaseCoding>();
+				for (Tag next : ResourceMetadataKeyEnum.TAG_LIST.get(BaseResource.this)) {
+					retVal.add(next);
+				}
+				return Collections.unmodifiableList(retVal);
+			}
+			
+			@Override
+			public IBaseCoding getTag(String theSystem, final String theCode) {
+				for (final Tag next : ResourceMetadataKeyEnum.TAG_LIST.get(BaseResource.this)) {
+					if (next.getScheme().equals(theSystem) && next.getTerm().equals(theCode)) {
+						return next;
+					}
+				}
+				return null;
+			}
+			
+			@Override
+			public String getVersionId() {
+				return getId().getVersionIdPart();
+			}
+			
+			@Override
+			public boolean hasFormatComment() {
+				return false;
+			}
+			
+			@Override
+			public boolean isEmpty() {
+				return getResourceMetadata().isEmpty();
+			}
+			
+			@Override
+			public IBaseMetaType setLastUpdated(Date theHeaderDateValue) {
+				ResourceMetadataKeyEnum.UPDATED.put(BaseResource.this, new InstantDt(theHeaderDateValue));
+				return this;
+			}
+			
+
+			@Override
+			public IBaseMetaType setVersionId(String theVersionId) {
+				setId(getId().withVersion(theVersionId));
+				return this;
+			}
+		};
+	}
+
 	@Override
 	public ResourceMetadataMap getResourceMetadata() {
 		if (myResourceMetadata == null) {
@@ -120,10 +346,23 @@ public abstract class BaseResource extends BaseElement implements IResource {
 		return myText;
 	}
 
+	/**
+	 * Intended to be called by extending classes {@link #isEmpty()} implementations, returns <code>true</code> if all
+	 * content in this superclass instance is empty per the semantics of {@link #isEmpty()}.
+	 */
+	@Override
+	protected boolean isBaseEmpty() {
+		return super.isBaseEmpty() && ElementUtil.isEmpty(myLanguage, myText, myId);
+	}
+
 	public void setContained(ContainedDt theContained) {
 		myContained = theContained;
 	}
 
+	public void setId(IdDt theId) {
+		myId = theId;
+	}
+
 	public BaseResource setId(IIdType theId) {
 		if (theId instanceof IdDt) {
 			myId = (IdDt) theId;
@@ -133,10 +372,6 @@ public abstract class BaseResource extends BaseElement implements IResource {
 		return this;
 	}
 
-	public void setId(IdDt theId) {
-		myId = theId;
-	}
-
 	public BaseResource setId(String theId) {
 		if (theId == null) {
 			myId = null;
@@ -168,13 +403,4 @@ public abstract class BaseResource extends BaseElement implements IResource {
 		return b.toString();
 	}
 
-	/**
-	 * Intended to be called by extending classes {@link #isEmpty()} implementations, returns <code>true</code> if all
-	 * content in this superclass instance is empty per the semantics of {@link #isEmpty()}.
-	 */
-	@Override
-	protected boolean isBaseEmpty() {
-		return super.isBaseEmpty() && ElementUtil.isEmpty(myLanguage, myText, myId);
-	}
-
 }

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

@@ -19,8 +19,7 @@ package ca.uhn.fhir.rest.server;
  * limitations under the License.
  * #L%
  */
-
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import static org.apache.commons.lang3.StringUtils.*;
 
 import java.util.ArrayList;
 import java.util.Date;
@@ -29,7 +28,6 @@ import java.util.List;
 import java.util.Set;
 import java.util.UUID;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -43,6 +41,8 @@ import ca.uhn.fhir.model.api.BundleEntry;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
 import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -53,7 +53,6 @@ import ca.uhn.fhir.util.ResourceReferenceInfo;
 
 public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu1BundleFactory.class);
 	private Bundle myBundle;
 	private FhirContext myContext;
 
@@ -186,7 +185,7 @@ public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 	}
 
 	@Override
-	public void initializeBundleFromBundleProvider(IRestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
+	public void initializeBundleFromBundleProvider(IRestfulServer<?> 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;
@@ -224,16 +223,11 @@ public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 					throw new InternalErrorException("Server method returned resource of type[" + next.getClass().getSimpleName() + "] with no ID specified (IResource#setId(IdDt) must be called)");
 				}
 			}
+			if (theServer.getAddProfileTag() != AddProfileTagEnum.NEVER) {
+				addProfileIfNeeded(theServer, theServerBase, next);
+			}
 		}
 
-		if (theServer.getAddProfileTag() != AddProfileTagEnum.NEVER) {
-			for (IBaseResource nextRes : resourceList) {
-				RuntimeResourceDefinition def = theServer.getFhirContext().getResourceDefinition(nextRes);
-				if (theServer.getAddProfileTag() == AddProfileTagEnum.ALWAYS || !def.isStandardProfile()) {
-					RestfulServerUtils.addProfileToBundleEntry(theServer.getFhirContext(), nextRes, theServerBase);
-				}
-			}
-		}
 
 		addResourcesToBundle(new ArrayList<IBaseResource>(resourceList), theBundleType, theServerBase, theServer.getBundleInclusionRule(), theIncludes);
 		addRootPropertiesToBundle(null, theServerBase, theCompleteUrl, theResult.size(), theBundleType, theResult.getPublished());
@@ -256,6 +250,23 @@ public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 		}
 	}
 
+	private void addProfileIfNeeded(IRestfulServer<?> theServer, String theServerBase, IBaseResource nextRes) {
+		RuntimeResourceDefinition def = theServer.getFhirContext().getResourceDefinition(nextRes);
+		if (theServer.getAddProfileTag() == AddProfileTagEnum.ALWAYS || !def.isStandardType()) {
+			TagList tl = ResourceMetadataKeyEnum.TAG_LIST.get((IResource) nextRes);
+			if (tl == null) {
+				tl = new TagList();
+				ResourceMetadataKeyEnum.TAG_LIST.put((IResource) nextRes, tl);
+			}
+
+			RuntimeResourceDefinition nextDef = myContext.getResourceDefinition(nextRes);
+			String profile = nextDef.getResourceProfile(theServerBase);
+			if (isNotBlank(profile)) {
+				tl.add(new Tag(Tag.HL7_ORG_PROFILE_TAG, profile, null));
+			}
+		}
+	}
+
 	@Override
 	public void initializeBundleFromResourceList(String theAuthor, List<? extends IBaseResource> theResult, String theServerBase, String theCompleteUrl, int theTotalResults,
 			BundleTypeEnum theBundleType) {

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

@@ -214,9 +214,6 @@ public class CustomTypeTest {
 	
 	private static boolean ourReturnExtended = false;
 	
-	/**
-	 * Created by dsotnikov on 2/25/2014.
-	 */
 	public static class DummyPatientResourceProvider implements IResourceProvider {
 		
 		@Search

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

@@ -7,6 +7,7 @@ import java.util.List;
 import javax.servlet.ServletException;
 
 import org.hamcrest.core.StringContains;
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Test;
@@ -299,6 +300,12 @@ public class ServerInvalidDefinitionTest {
 				public List<String> getFormatCommentsPost() {
 					return null;
 				}
+
+				@Override
+				public IBaseMetaType getMeta() {
+					// TODO Auto-generated method stub
+					return null;
+				}
 			}.getClass();
 		}
 

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

@@ -1,5 +1,10 @@
 package ca.uhn.fhir.model.dstu2.resource;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Date;
+import java.util.List;
+
 /*
  * #%L
  * HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
@@ -23,35 +28,31 @@ package ca.uhn.fhir.model.dstu2.resource;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.model.api.BaseElement;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.Tag;
+import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.SearchParamDefinition;
+import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.resource.ResourceMetadataMap;
+import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.composite.ContainedDt;
 import ca.uhn.fhir.model.dstu2.composite.NarrativeDt;
 import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.gclient.StringClientParam;
 import ca.uhn.fhir.util.ElementUtil;
 
 public abstract class BaseResource extends BaseElement implements IResource {
 
-	/**
-	 * Search parameter constant for <b>_language</b>
-	 */
-	@SearchParamDefinition(name="_language", path="", description="The language of the resource", type="string"  )
-	public static final String SP_RES_LANGUAGE = "_language";
-
-
-	/**
-	 * Search parameter constant for <b>_id</b>
-	 */
-	@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="string"  )
-	public static final String SP_RES_ID = "_id";
-
 	/**
 	 * <b>Fluent Client</b> search parameter constant for <b>_id</b>
 	 * <p>
@@ -62,10 +63,23 @@ public abstract class BaseResource extends BaseElement implements IResource {
 	 */
 	public static final StringClientParam RES_ID = new StringClientParam(BaseResource.SP_RES_ID);
 	
+	/**
+	 * Search parameter constant for <b>_id</b>
+	 */
+	@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="string"  )
+	public static final String SP_RES_ID = "_id";
+
+
+	/**
+	 * Search parameter constant for <b>_language</b>
+	 */
+	@SearchParamDefinition(name="_language", path="", description="The language of the resource", type="string"  )
+	public static final String SP_RES_LANGUAGE = "_language";
 
 	@Child(name = "contained", order = 2, min = 0, max = 1)
 	private ContainedDt myContained;
 
+
 	private IdDt myId;
 
 	@Child(name = "language", order = 0, min = 0, max = Child.MAX_UNLIMITED)
@@ -104,6 +118,157 @@ public abstract class BaseResource extends BaseElement implements IResource {
 		return myLanguage;
 	}
 
+	@Override
+	public IBaseMetaType getMeta() {
+		return new IBaseMetaType() {
+			
+			private static final long serialVersionUID = 1L;
+
+			@Override
+			public IBaseMetaType addProfile(String theProfile) {
+				ArrayList<IdDt> newTagList = new ArrayList<IdDt>();
+				List<IdDt> existingTagList = ResourceMetadataKeyEnum.PROFILES.get(BaseResource.this);
+				if (existingTagList != null) {
+					newTagList.addAll(existingTagList);
+				}
+				ResourceMetadataKeyEnum.PROFILES.put(BaseResource.this, newTagList);
+				
+				IdDt tag = new IdDt(theProfile);
+				newTagList.add(tag);
+				return this;
+			}
+			
+			@Override
+			public IBaseCoding addSecurity() {
+				List<BaseCodingDt> tagList = ResourceMetadataKeyEnum.SECURITY_LABELS.get(BaseResource.this);
+				if (tagList == null) {
+					tagList = new ArrayList<BaseCodingDt>();
+					ResourceMetadataKeyEnum.SECURITY_LABELS.put(BaseResource.this, tagList);
+				}
+				CodingDt tag = new CodingDt();
+				tagList.add(tag);
+				return tag;
+			}
+			
+			@Override
+			public IBaseCoding addTag() {
+				TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(BaseResource.this);
+				if (tagList == null) {
+					tagList = new TagList();
+					ResourceMetadataKeyEnum.TAG_LIST.put(BaseResource.this, tagList);
+				}
+				Tag tag = new Tag();
+				tagList.add(tag);
+				return tag;
+			}
+			
+			@Override
+			public List<String> getFormatCommentsPost() {
+				return Collections.emptyList();
+			}
+			
+			@Override
+			public List<String> getFormatCommentsPre() {
+				return Collections.emptyList();
+			}
+			
+			@Override
+			public Date getLastUpdated() {
+				InstantDt lu = ResourceMetadataKeyEnum.UPDATED.get(BaseResource.this);
+				if (lu != null) {
+					return lu.getValue();
+				}
+				return null;
+			}
+			
+			@Override
+			public List<? extends IPrimitiveType<String>> getProfile() {
+				ArrayList<IPrimitiveType<String>> retVal = new ArrayList<IPrimitiveType<String>>();
+				List<IdDt> profilesList = ResourceMetadataKeyEnum.PROFILES.get(BaseResource.this);
+				if (profilesList == null) {
+					return Collections.emptyList();
+				}
+				for (IdDt next : profilesList) {
+					retVal.add(next);
+				}
+				return Collections.unmodifiableList(retVal);
+			}
+			
+			@Override
+			public List<? extends IBaseCoding> getSecurity() {
+				ArrayList<CodingDt> retVal = new ArrayList<CodingDt>();
+				List<BaseCodingDt> labelsList = ResourceMetadataKeyEnum.SECURITY_LABELS.get(BaseResource.this);
+				if (labelsList == null) {
+					return Collections.emptyList();
+				}
+				for (BaseCodingDt next : labelsList) {
+					retVal.add(new CodingDt(next.getSystemElement().getValue(), next.getCodeElement().getValue()).setDisplay(next.getDisplayElement().getValue()));
+				}
+				return Collections.unmodifiableList(retVal);
+			}
+			
+			@Override
+			public IBaseCoding getSecurity(String theSystem, String theCode) {
+				for (IBaseCoding next : getSecurity()) {
+					if (theSystem.equals(next.getSystem()) && theCode.equals(next.getCode())) {
+						return next;
+					}
+				}
+				return null;
+			}
+			
+			@Override
+			public List<? extends IBaseCoding> getTag() {
+				ArrayList<IBaseCoding> retVal = new ArrayList<IBaseCoding>();
+				TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(BaseResource.this);
+				if (tagList == null) {
+					return Collections.emptyList();
+				}
+				for (Tag next : tagList) {
+					retVal.add(next);
+				}
+				return Collections.unmodifiableList(retVal);
+			}
+			
+			@Override
+			public IBaseCoding getTag(String theSystem, String theCode) {
+				for (IBaseCoding next : getTag()) {
+					if (next.getSystem().equals(theSystem) && next.getCode().equals(theCode)) {
+						return next;
+					}
+				}
+				return null;
+			}
+			
+			@Override
+			public String getVersionId() {
+				return getId().getVersionIdPart();
+			}
+			
+			@Override
+			public boolean hasFormatComment() {
+				return false;
+			}
+			
+			@Override
+			public boolean isEmpty() {
+				return getResourceMetadata().isEmpty();
+			}
+			
+			@Override
+			public IBaseMetaType setLastUpdated(Date theHeaderDateValue) {
+				ResourceMetadataKeyEnum.UPDATED.put(BaseResource.this, new InstantDt(theHeaderDateValue));
+				return this;
+			}
+			
+			@Override
+			public IBaseMetaType setVersionId(String theVersionId) {
+				setId(getId().withVersion(theVersionId));
+				return this;
+			}
+		};
+	}
+
 	@Override
 	public ResourceMetadataMap getResourceMetadata() {
 		if (myResourceMetadata == null) {
@@ -120,6 +285,15 @@ public abstract class BaseResource extends BaseElement implements IResource {
 		return myText;
 	}
 
+	/**
+	 * Intended to be called by extending classes {@link #isEmpty()} implementations, returns <code>true</code> if all
+	 * content in this superclass instance is empty per the semantics of {@link #isEmpty()}.
+	 */
+	@Override
+	protected boolean isBaseEmpty() {
+		return super.isBaseEmpty() && ElementUtil.isEmpty(myLanguage, myText, myId);
+	}
+
 	public void setContained(ContainedDt theContained) {
 		myContained = theContained;
 	}
@@ -168,13 +342,4 @@ public abstract class BaseResource extends BaseElement implements IResource {
 		return b.toString();
 	}
 
-	/**
-	 * Intended to be called by extending classes {@link #isEmpty()} implementations, returns <code>true</code> if all
-	 * content in this superclass instance is empty per the semantics of {@link #isEmpty()}.
-	 */
-	@Override
-	protected boolean isBaseEmpty() {
-		return super.isBaseEmpty() && ElementUtil.isEmpty(myLanguage, myText, myId);
-	}
-
 }

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/Dstu2BundleFactory.java

@@ -35,7 +35,6 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@@ -51,7 +50,6 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
 import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
-import ca.uhn.fhir.rest.server.AddProfileTagEnum;
 import ca.uhn.fhir.rest.server.BundleInclusionRule;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.EncodingEnum;
@@ -65,7 +63,6 @@ import ca.uhn.fhir.util.ResourceReferenceInfo;
 
 public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu2BundleFactory.class);
 	private Bundle myBundle;
 	private FhirContext myContext;
 	private String myBase;
@@ -302,7 +299,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 	}
 
 	@Override
-	public void initializeBundleFromBundleProvider(IRestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
+	public void initializeBundleFromBundleProvider(IRestfulServer<?> theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
 			boolean thePrettyPrint, int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
 		myBase = theServerBase;
 		
@@ -352,15 +349,6 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 			}
 		}
 
-		if (theServer.getAddProfileTag() != AddProfileTagEnum.NEVER) {
-			for (IBaseResource nextRes : resourceList) {
-				RuntimeResourceDefinition def = theServer.getFhirContext().getResourceDefinition(nextRes);
-				if (theServer.getAddProfileTag() == AddProfileTagEnum.ALWAYS || !def.isStandardProfile()) {
-					RestfulServerUtils.addProfileToBundleEntry(theServer.getFhirContext(), nextRes, theServerBase);
-				}
-			}
-		}
-
 		addResourcesToBundle(new ArrayList<IBaseResource>(resourceList), theBundleType, theServerBase, theServer.getBundleInclusionRule(), theIncludes);
 		addRootPropertiesToBundle(null, theServerBase, theCompleteUrl, theResult.size(), theBundleType, theResult.getPublished());
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/CustomTypeDstu2Test.java

@@ -0,0 +1,510 @@
+package ca.uhn.fhir.parser;
+
+import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.nullValue;
+import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.primitive.DateTimeDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.server.AddProfileTagEnum;
+import ca.uhn.fhir.util.ElementUtil;
+
+public class CustomTypeDstu2Test {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CustomTypeDstu2Test.class);
+	private static final FhirContext ourCtx = FhirContext.forDstu2();
+
+	@Test
+	public void testAccessEmptyMetaLists() {
+		Patient p = new Patient();
+		assertThat(p.getMeta().getProfile(), empty());
+		assertThat(p.getMeta().getFormatCommentsPost(), empty());
+		assertThat(p.getMeta().getFormatCommentsPre(), empty());
+		assertThat(p.getMeta().getLastUpdated(), nullValue());
+		assertThat(p.getMeta().getSecurity(), empty());
+		assertThat(p.getMeta().getSecurity("foo", "bar"), nullValue());
+		assertThat(p.getMeta().getTag(), empty());
+		assertThat(p.getMeta().getTag("foo", "bar"), nullValue());
+		assertThat(p.getMeta().getVersionId(), nullValue());
+		
+	}
+	
+	
+	@Test
+	public void testEncodeCompleteMetaLists() {
+		Patient p = new Patient();
+		p.getMeta().addProfile("http://foo/profile1");
+		p.getMeta().addProfile("http://foo/profile2");
+		p.getMeta().addSecurity().setSystem("SEC_S1").setCode("SEC_C1").setDisplay("SED_D1");
+		p.getMeta().addSecurity().setSystem("SEC_S2").setCode("SEC_C2").setDisplay("SED_D2");
+		p.getMeta().addTag().setSystem("TAG_S1").setCode("TAG_C1").setDisplay("TAG_D1");
+		p.getMeta().addTag().setSystem("TAG_S2").setCode("TAG_C2").setDisplay("TAG_D2");
+		
+		String out = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(out);
+		
+		//@formatter:off
+		assertThat(out, stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://foo/profile1\"/>", 
+			"<profile value=\"http://foo/profile2\"/>", 
+			"<security>", 
+			"<system value=\"SEC_S1\"/>", 
+			"<code value=\"SEC_C1\"/>", 
+			"<display value=\"SED_D1\"/>", 
+			"</security>", 
+			"<security>", 
+			"<system value=\"SEC_S2\"/>", 
+			"<code value=\"SEC_C2\"/>", 
+			"<display value=\"SED_D2\"/>", 
+			"</security>", 
+			"<tag>", 
+			"<system value=\"TAG_S1\"/>", 
+			"<display value=\"TAG_D1\"/>", 
+			"</tag>", 
+			"<tag>", 
+			"<system value=\"TAG_S2\"/>", 
+			"<display value=\"TAG_D2\"/>", 
+			"</tag>", 
+			"</meta>"));
+		//@formatter:on
+		
+	}
+
+	@Before
+	public void before() {
+		ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.ONLY_FOR_CUSTOM);
+	}
+	
+	@Test
+	public void testEncodeWithCustomType() {
+
+		MyCustomPatient patient = new MyCustomPatient();
+
+		patient.addIdentifier().setSystem("urn:system").setValue("1234");
+		patient.addName().addFamily("Rossi").addGiven("Mario");
+		patient.setInsulinLevel(new QuantityDt());
+		patient.setGlucoseLevel(new QuantityDt());
+		patient.setHbA1c(new QuantityDt());
+		patient.setBloodPressure(new QuantityDt());
+		patient.setCholesterol(new QuantityDt());
+		patient.setWeight(new StringDt("80 kg"));
+		patient.setWeight(new StringDt("185 cm"));
+		patient.setCheckDates(new ArrayList<DateTimeDt>());
+		patient.getCheckDates().add(new DateTimeDt("2014-01-26T11:11:11"));
+
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String messageString = p.encodeResourceToString(patient);
+
+		ourLog.info(messageString);
+		
+		//@formatter:off
+		assertThat(messageString, stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://example.com/foo\"/>", 
+			"</meta>"));
+		//@formatter:on
+
+		//@formatter:off
+		assertThat(messageString, not(stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://example.com/foo\"", "/>", 
+			"<profile value=\"http://example.com/foo\"/>", 
+			"</meta>")));
+		//@formatter:on
+	}
+
+	@Test
+	public void testEncodeWithCustomTypeAndAutoInsertedProfile() {
+
+		MyCustomPatient patient = new MyCustomPatient();
+
+		patient.getMeta().addProfile("http://example.com/foo");
+		patient.getMeta().addProfile("http://example.com/bar");
+		
+		patient.addIdentifier().setSystem("urn:system").setValue("1234");
+		patient.addName().addFamily("Rossi").addGiven("Mario");
+		patient.setInsulinLevel(new QuantityDt());
+		patient.setGlucoseLevel(new QuantityDt());
+		patient.setHbA1c(new QuantityDt());
+		patient.setBloodPressure(new QuantityDt());
+		patient.setCholesterol(new QuantityDt());
+		patient.setWeight(new StringDt("80 kg"));
+		patient.setWeight(new StringDt("185 cm"));
+		patient.setCheckDates(new ArrayList<DateTimeDt>());
+		patient.getCheckDates().add(new DateTimeDt("2014-01-26T11:11:11"));
+
+		ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.ONLY_FOR_CUSTOM);
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String messageString = p.encodeResourceToString(patient);
+
+		ourLog.info(messageString);
+		
+		//@formatter:off
+		assertThat(messageString, stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://example.com/foo\"/>", 
+			"<profile value=\"http://example.com/bar\"/>", 
+			"</meta>"));
+		//@formatter:on
+
+		//@formatter:off
+		assertThat(messageString, not(stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://example.com/foo\"", "/>", 
+			"<profile value=\"http://example.com/foo\"/>", 
+			"</meta>")));
+		//@formatter:on
+	}
+
+	@Test
+	public void testEncodeNormalType() {
+
+		Patient patient = new Patient();
+
+		patient.addIdentifier().setSystem("urn:system").setValue("1234");
+		patient.addName().addFamily("Rossi").addGiven("Mario");
+
+		ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.ONLY_FOR_CUSTOM);
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String messageString = p.encodeResourceToString(patient);
+		ourLog.info(messageString);
+
+		assertThat(messageString, not(containsString("<profile")));
+	}
+
+	@Test
+	public void parseResourceWithNoDirective() {
+		String input = createResource(true);
+		
+		FhirContext ctx = FhirContext.forDstu2();
+		Patient parsed = (Patient) ctx.newXmlParser().parseResource(input);
+		assertEquals(1, parsed.getMeta().getProfile().size());
+		assertEquals("http://example.com/foo", parsed.getMeta().getProfile().get(0).getValue());
+		
+		List<ExtensionDt> exts = parsed.getUndeclaredExtensionsByUrl("http://example.com/Weight");
+		assertEquals(1, exts.size());
+		assertEquals("185 cm", ((StringDt)exts.get(0).getValueAsPrimitive()).getValue());
+	}
+
+	@Test
+	public void parseResourceWithDirective() {
+		String input = createResource(true);
+		
+		FhirContext ctx = FhirContext.forDstu2();
+		ctx.setDefaultTypeForProfile("http://example.com/foo", MyCustomPatient.class);
+		
+		MyCustomPatient parsed = (MyCustomPatient) ctx.newXmlParser().parseResource(input);
+		assertEquals(1, parsed.getMeta().getProfile().size());
+		assertEquals("http://example.com/foo", parsed.getMeta().getProfile().get(0).getValue());
+		
+		List<ExtensionDt> exts = parsed.getUndeclaredExtensionsByUrl("http://example.com/Weight");
+		assertEquals(0, exts.size());
+		
+		assertEquals("185 cm", parsed.getWeight().getValue());
+	}
+
+	@Test
+	public void parseBundleWithResourceDirective() {
+		
+		String input = createBundle(createResource(false), createResource(true));
+		
+		FhirContext ctx = FhirContext.forDstu2();
+		ctx.setDefaultTypeForProfile("http://example.com/foo", MyCustomPatient.class);
+		
+		Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, input);
+		
+		Patient res0 = (Patient) bundle.getEntry().get(0).getResource();
+		assertEquals(0, res0.getMeta().getProfile().size());
+		List<ExtensionDt> exts = res0.getUndeclaredExtensionsByUrl("http://example.com/Weight");
+		assertEquals(1, exts.size());
+		assertEquals("185 cm", ((StringDt)exts.get(0).getValueAsPrimitive()).getValue());
+
+		MyCustomPatient res1 = (MyCustomPatient) bundle.getEntry().get(1).getResource();
+		assertEquals(1, res1.getMeta().getProfile().size());
+		assertEquals("http://example.com/foo", res1.getMeta().getProfile().get(0).getValue());
+		exts = res1.getUndeclaredExtensionsByUrl("http://example.com/Weight");
+		assertEquals(0, exts.size());
+		assertEquals("185 cm", res1.getWeight().getValue());
+	}
+
+	private String createBundle(String... theResources) {
+		StringBuilder b = new StringBuilder();
+		b.append("<Bundle xmlns=\"http://hl7.org/fhir\">\n");
+		for (String next : theResources) {
+			b.append("	<entry>\n");
+			b.append("		<resource>\n");
+			b.append(next);
+			b.append("		</resource>\n");
+			b.append("	</entry>\n");
+		}
+		b.append("</Bundle>");
+		return b.toString();
+	}
+
+	private String createResource(boolean theWithProfile) {
+		StringBuilder b = new StringBuilder();
+		b.append("<Patient xmlns=\"http://hl7.org/fhir\">\n");
+		if (theWithProfile) {
+			b.append("   <meta>\n");
+			b.append("      <profile value=\"http://example.com/foo\"/>\n");
+			b.append("   </meta>\n");
+		}
+		b.append("   <extension url=\"http://example.com/BloodPressure\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"110\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"mmHg\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <modifierExtension url=\"http://example.com/diabetes2\">\n");
+		b.append("      <valueDateTime value=\"2010-01-02\"/>\n");
+		b.append("   </modifierExtension>\n");
+		b.append("   <modifierExtension url=\"http://example.com/diabetes2\">\n");
+		b.append("      <valueDateTime value=\"2014-01-26T11:11:11\"/>\n");
+		b.append("   </modifierExtension>\n");
+		b.append("   <extension url=\"http://example.com/Cholesterol\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"2\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"mmol/l\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <extension url=\"http://example.com/Glucose\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"95\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"mg/dl\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <extension url=\"http://example.com/HbA1c\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"48\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"mmol/mol\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <extension url=\"http://example.com/Insuline\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"125\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"pmol/l\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <extension url=\"http://example.com/Weight\">\n");
+		b.append("      <valueString value=\"185 cm\"/>\n");
+		b.append("   </extension>\n");
+		b.append("   <identifier>\n");
+		b.append("      <system value=\"urn:system\"/>\n");
+		b.append("      <value value=\"1234\"/>\n");
+		b.append("   </identifier>\n");
+		b.append("   <name>\n");
+		b.append("      <family value=\"Rossi\"/>\n");
+		b.append("      <given value=\"Mario\"/>\n");
+		b.append("   </name>\n");
+		b.append("</Patient>");
+		String input =
+			b.toString();
+		return input;
+	}
+	
+	
+	@ResourceDef(name = "Patient", profile = "http://example.com/foo")
+	public static class MyCustomPatient extends Patient {
+
+		private static final long serialVersionUID = 1L;
+
+		@Child(name = "bloodPressure") // once every 3 month. The average target is 130/80 mmHg or less
+		@Extension(url = "http://example.com/BloodPressure", definedLocally = false, isModifier = false)
+		@Description(shortDefinition = "The value of the patient's blood pressure")
+		private QuantityDt myBloodPressure;
+
+		// Dates of periodic tests
+		@Child(name = "CheckDates", max = Child.MAX_UNLIMITED)
+		@Extension(url = "http://example.com/diabetes2", definedLocally = false, isModifier = true)
+		@Description(shortDefinition = "Dates of periodic tests")
+		private List<DateTimeDt> myCheckDates;
+
+		@Child(name = "cholesterol") // once a year. The target is triglycerides =< 2 mmol/l e cholesterol =< 4 mmol/l
+		@Extension(url = "http://example.com/Cholesterol", definedLocally = false, isModifier = false)
+		@Description(shortDefinition = "The value of the patient's cholesterol")
+		private QuantityDt myCholesterol;
+
+		@Child(name = "glucoseLevel") // fingerprick test
+		@Extension(url = "http://example.com/Glucose", definedLocally = false, isModifier = false)
+		@Description(shortDefinition = "The value of the patient's blood glucose")
+		private QuantityDt myGlucoseLevel;
+
+		// Periodic Tests
+		@Child(name = "hbA1c") // once every 6 month. The average target is 53 mmol/mol (or 7%) or less.
+		@Extension(url = "http://example.com/HbA1c", definedLocally = false, isModifier = false)
+		@Description(shortDefinition = "The value of the patient's glucose")
+		private QuantityDt myHbA1c;
+
+		@Child(name = "Height")
+		@Extension(url = "http://example.com/Height", definedLocally = false, isModifier = false)
+		@Description(shortDefinition = "The patient's height in cm")
+		private StringDt myHeight;
+
+		@Child(name = "insulinLevel") // Normal range is [43,208] pmol/l
+		@Extension(url = "http://example.com/Insuline", definedLocally = false, isModifier = false)
+		@Description(shortDefinition = "The value of the patient's insulin")
+		private QuantityDt myInsulinLevel;
+
+		// Other parameters
+		@Child(name = "weight")
+		@Extension(url = "http://example.com/Weight", definedLocally = false, isModifier = false)
+		@Description(shortDefinition = "The patient's weight in Kg")
+		private StringDt myWeight;
+
+		public QuantityDt Cholesterol() {
+			if (myCholesterol == null) {
+				myCholesterol = new QuantityDt();
+			}
+			myCholesterol.getValue();
+			myCholesterol.getSystem();
+			myCholesterol.getCode();
+
+			return myCholesterol;
+		}
+
+		public QuantityDt getBloodPressure() {
+			if (myBloodPressure == null) {
+				myBloodPressure = new QuantityDt();
+			}
+			myBloodPressure.getValue();
+			myBloodPressure.getSystem();
+			myBloodPressure.getCode();
+
+			return myBloodPressure;
+		}
+
+		public List<DateTimeDt> getCheckDates() {
+			if (myCheckDates == null) {
+				myCheckDates = new ArrayList<DateTimeDt>();
+			}
+			return myCheckDates;
+		}
+
+		public QuantityDt getGlucoseLevel() {
+			if (myGlucoseLevel == null) {
+				myGlucoseLevel = new QuantityDt();
+			}
+			myGlucoseLevel.getValue();
+			myGlucoseLevel.getSystem();
+			myGlucoseLevel.getCode();
+
+			return myGlucoseLevel;
+		}
+
+		public QuantityDt getHbA1c() {
+			if (myHbA1c == null) {
+				myHbA1c = new QuantityDt();
+			}
+			myHbA1c.getValue();
+			myHbA1c.getSystem();
+			myHbA1c.getCode();
+
+			return myHbA1c;
+		}
+
+		public StringDt getHeight() {
+			if (myHeight == null) {
+				myHeight = new StringDt();
+			}
+			return myHeight;
+		}
+
+		public QuantityDt getInsulinLevel() {
+			if (myInsulinLevel == null) {
+				myInsulinLevel = new QuantityDt();
+			}
+			myInsulinLevel.getValue();
+			myInsulinLevel.getSystem();
+			myInsulinLevel.getCode();
+
+			return myInsulinLevel;
+		}
+
+		public StringDt getWeight() {
+			if (myWeight == null) {
+				myWeight = new StringDt();
+			}
+			return myWeight;
+		}
+
+		@Override
+		public boolean isEmpty() {
+			return super.isEmpty() && ElementUtil.isEmpty(myInsulinLevel, myGlucoseLevel, myHbA1c, myBloodPressure, myCholesterol, myWeight, myHeight, myCheckDates);
+		}
+
+		public void setBloodPressure(QuantityDt bloodPressure) {
+			myBloodPressure = bloodPressure;
+			myBloodPressure.setValue(110);
+			myBloodPressure.setSystem("http://unitsofmeasure.org");
+			myBloodPressure.setCode("mmHg");
+		}
+
+		public void setCheckDates(List<DateTimeDt> theCheckDates) {
+			myCheckDates = theCheckDates;
+			myCheckDates.add(new DateTimeDt("2010-01-02"));
+		}
+
+		public void setCholesterol(QuantityDt cholesterol) {
+			myCholesterol = cholesterol;
+			myCholesterol.setValue(2);
+			myCholesterol.setSystem("http://unitsofmeasure.org");
+			myCholesterol.setCode("mmol/l");
+		}
+
+		public void setGlucoseLevel(QuantityDt glucoseLevel) {
+			myGlucoseLevel = glucoseLevel;
+			myGlucoseLevel.setValue(95);
+			myGlucoseLevel.setSystem("http://unitsofmeasure.org");
+			myGlucoseLevel.setCode("mg/dl");
+		}
+
+		public void setHbA1c(QuantityDt hba1c) {
+			myHbA1c = hba1c;
+			myHbA1c.setValue(48);
+			myHbA1c.setSystem("http://unitsofmeasure.org");
+			myHbA1c.setCode("mmol/mol");
+		}
+
+		public void setHeight(StringDt height) {
+			myHeight = height;
+		}
+
+		// Setter/Getter methods
+		public void setInsulinLevel(QuantityDt insulinLevel) {
+			myInsulinLevel = insulinLevel;
+			myInsulinLevel.setValue(125);
+			myInsulinLevel.setSystem("http://unitsofmeasure.org");
+			myInsulinLevel.setCode("pmol/l");
+		}
+
+		public void setWeight(StringDt weight) {
+			myWeight = weight;
+		}
+
+	}
+}

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

@@ -1,228 +0,0 @@
-package ca.uhn.fhir.parser;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.Test;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.annotation.Child;
-import ca.uhn.fhir.model.api.annotation.Description;
-import ca.uhn.fhir.model.api.annotation.Extension;
-import ca.uhn.fhir.model.api.annotation.ResourceDef;
-import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.primitive.DateTimeDt;
-import ca.uhn.fhir.model.primitive.StringDt;
-import ca.uhn.fhir.util.ElementUtil;
-
-public class CustomTypeTest {
-
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CustomTypeTest.class);
-
-	@Test
-	public void testEncode() {
-
-		FhirContext ctx = FhirContext.forDstu2();
-
-		MyCustomPatient patient = new MyCustomPatient();
-
-		patient.addIdentifier().setSystem("urn:system").setValue("1234");
-		patient.addName().addFamily("Rossi").addGiven("Mario");
-		patient.setInsulinLevel(new QuantityDt());
-		patient.setGlucoseLevel(new QuantityDt());
-		patient.setHbA1c(new QuantityDt());
-		patient.setBloodPressure(new QuantityDt());
-		patient.setCholesterol(new QuantityDt());
-		patient.setWeight(new StringDt("80 kg"));
-		patient.setWeight(new StringDt("185 cm"));
-		patient.setCheckDates(new ArrayList<DateTimeDt>());
-		patient.getCheckDates().add(new DateTimeDt("2014-01-26T11:11:11"));
-
-		IParser p = ctx.newXmlParser().setPrettyPrint(true);
-		String messageString = p.encodeResourceToString(patient);
-
-		ourLog.info(messageString);
-
-	}
-
-	@ResourceDef(name = "Patient")
-	public static class MyCustomPatient extends Patient {
-
-		private static final long serialVersionUID = 1L;
-
-		@Child(name = "bloodPressure") // once every 3 month. The average target is 130/80 mmHg or less
-		@Extension(url = "http://example.com/BloodPressure", definedLocally = false, isModifier = false)
-		@Description(shortDefinition = "The value of the patient's blood pressure")
-		private QuantityDt myBloodPressure;
-
-		// Dates of periodic tests
-		@Child(name = "CheckDates", max = Child.MAX_UNLIMITED)
-		@Extension(url = "http://example.com/diabetes2", definedLocally = false, isModifier = true)
-		@Description(shortDefinition = "Dates of periodic tests")
-		private List<DateTimeDt> myCheckDates;
-
-		@Child(name = "cholesterol") // once a year. The target is triglycerides =< 2 mmol/l e cholesterol =< 4 mmol/l
-		@Extension(url = "http://example.com/Cholesterol", definedLocally = false, isModifier = false)
-		@Description(shortDefinition = "The value of the patient's cholesterol")
-		private QuantityDt myCholesterol;
-
-		@Child(name = "glucoseLevel") // fingerprick test
-		@Extension(url = "http://example.com/Glucose", definedLocally = false, isModifier = false)
-		@Description(shortDefinition = "The value of the patient's blood glucose")
-		private QuantityDt myGlucoseLevel;
-
-		// Periodic Tests
-		@Child(name = "hbA1c") // once every 6 month. The average target is 53 mmol/mol (or 7%) or less.
-		@Extension(url = "http://example.com/HbA1c", definedLocally = false, isModifier = false)
-		@Description(shortDefinition = "The value of the patient's glucose")
-		private QuantityDt myHbA1c;
-
-		@Child(name = "Height")
-		@Extension(url = "http://example.com/Height", definedLocally = false, isModifier = false)
-		@Description(shortDefinition = "The patient's height in cm")
-		private StringDt myHeight;
-
-		@Child(name = "insulinLevel") // Normal range is [43,208] pmol/l
-		@Extension(url = "http://example.com/Insuline", definedLocally = false, isModifier = false)
-		@Description(shortDefinition = "The value of the patient's insulin")
-		private QuantityDt myInsulinLevel;
-
-		// Other parameters
-		@Child(name = "weight")
-		@Extension(url = "http://example.com/Weight", definedLocally = false, isModifier = false)
-		@Description(shortDefinition = "The patient's weight in Kg")
-		private StringDt myWeight;
-
-		public QuantityDt Cholesterol() {
-			if (myCholesterol == null) {
-				myCholesterol = new QuantityDt();
-			}
-			myCholesterol.getValue();
-			myCholesterol.getSystem();
-			myCholesterol.getCode();
-
-			return myCholesterol;
-		}
-
-		public QuantityDt getBloodPressure() {
-			if (myBloodPressure == null) {
-				myBloodPressure = new QuantityDt();
-			}
-			myBloodPressure.getValue();
-			myBloodPressure.getSystem();
-			myBloodPressure.getCode();
-
-			return myBloodPressure;
-		}
-
-		public List<DateTimeDt> getCheckDates() {
-			if (myCheckDates == null) {
-				myCheckDates = new ArrayList<DateTimeDt>();
-			}
-			return myCheckDates;
-		}
-
-		public QuantityDt getGlucoseLevel() {
-			if (myGlucoseLevel == null) {
-				myGlucoseLevel = new QuantityDt();
-			}
-			myGlucoseLevel.getValue();
-			myGlucoseLevel.getSystem();
-			myGlucoseLevel.getCode();
-
-			return myGlucoseLevel;
-		}
-
-		public QuantityDt getHbA1c() {
-			if (myHbA1c == null) {
-				myHbA1c = new QuantityDt();
-			}
-			myHbA1c.getValue();
-			myHbA1c.getSystem();
-			myHbA1c.getCode();
-
-			return myHbA1c;
-		}
-
-		public StringDt getHeight() {
-			if (myHeight == null) {
-				myHeight = new StringDt();
-			}
-			return myHeight;
-		}
-
-		public QuantityDt getInsulinLevel() {
-			if (myInsulinLevel == null) {
-				myInsulinLevel = new QuantityDt();
-			}
-			myInsulinLevel.getValue();
-			myInsulinLevel.getSystem();
-			myInsulinLevel.getCode();
-
-			return myInsulinLevel;
-		}
-
-		public StringDt getWeight() {
-			if (myWeight == null) {
-				myWeight = new StringDt();
-			}
-			return myWeight;
-		}
-
-		@Override
-		public boolean isEmpty() {
-			return super.isEmpty() && ElementUtil.isEmpty(myInsulinLevel, myGlucoseLevel, myHbA1c, myBloodPressure, myCholesterol, myWeight, myHeight, myCheckDates);
-		}
-
-		public void setBloodPressure(QuantityDt bloodPressure) {
-			myBloodPressure = bloodPressure;
-			myBloodPressure.setValue(110);
-			myBloodPressure.setSystem("http://unitsofmeasure.org");
-			myBloodPressure.setCode("mmHg");
-		}
-
-		public void setCheckDates(List<DateTimeDt> theCheckDates) {
-			myCheckDates = theCheckDates;
-			myCheckDates.add(new DateTimeDt("2010-01-02"));
-		}
-
-		public void setCholesterol(QuantityDt cholesterol) {
-			myCholesterol = cholesterol;
-			myCholesterol.setValue(2);
-			myCholesterol.setSystem("http://unitsofmeasure.org");
-			myCholesterol.setCode("mmol/l");
-		}
-
-		public void setGlucoseLevel(QuantityDt glucoseLevel) {
-			myGlucoseLevel = glucoseLevel;
-			myGlucoseLevel.setValue(95);
-			myGlucoseLevel.setSystem("http://unitsofmeasure.org");
-			myGlucoseLevel.setCode("mg/dl");
-		}
-
-		public void setHbA1c(QuantityDt hba1c) {
-			myHbA1c = hba1c;
-			myHbA1c.setValue(48);
-			myHbA1c.setSystem("http://unitsofmeasure.org");
-			myHbA1c.setCode("mmol/mol");
-		}
-
-		public void setHeight(StringDt height) {
-			myHeight = height;
-		}
-
-		// Setter/Getter methods
-		public void setInsulinLevel(QuantityDt insulinLevel) {
-			myInsulinLevel = insulinLevel;
-			myInsulinLevel.setValue(125);
-			myInsulinLevel.setSystem("http://unitsofmeasure.org");
-			myInsulinLevel.setCode("pmol/l");
-		}
-
-		public void setWeight(StringDt weight) {
-			myWeight = weight;
-		}
-
-	}
-}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java

@@ -94,6 +94,24 @@ public class JsonParserDstu2Test {
 		assertEquals(true, obs.getReadOnly().getValue().booleanValue());
 	}
 
+	
+	@Test
+	public void testParseBundleWithCustomObservationType() {
+		ReportObservation obs = new ReportObservation();
+		obs.setReadOnly(true);
+
+		IParser p = ourCtx.newJsonParser();
+//		p.set
+		p.setParserErrorHandler(mock(IParserErrorHandler.class, new ThrowsException(new IllegalStateException())));
+
+		String encoded = p.encodeResourceToString(obs);
+		ourLog.info(encoded);
+
+		obs = p.parseResource(ReportObservation.class, encoded);
+		assertEquals(true, obs.getReadOnly().getValue().booleanValue());
+	}
+
+	
 	@Test
 	public void testEncodeAndParseExtensions() throws Exception {
 

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

@@ -9,7 +9,7 @@ import ca.uhn.fhir.model.primitive.BooleanDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.util.ElementUtil;
 
-@ResourceDef(name = "Observation", id = "reportobservation")
+@ResourceDef(name = "Observation", id = "http://example.com/reportobservation")
 public class ReportObservation extends Observation {
 
 	private static final long serialVersionUID = 1L;

hapi-fhir-structures-dstu2/src/test/resources/bundle_orion.xml

@@ -1,5 +1,4 @@
-<Bundle 
+<Bundle xmlns="http://hl7.org/fhir">
-    xmlns="http://hl7.org/fhir">
 	<id value="487d3669-0e1c-4867-b124-400d1849548d"></id>
 	<type value="searchset"></type>
 	<base value="http://localhost:19080/fhir/dstu1"></base>
@@ -17,8 +16,7 @@
 			<url value="Observation"></url>
 		</link>
 		<resource>
-            <Observation 
+			<Observation xmlns="http://hl7.org/fhir">
-                xmlns="http://hl7.org/fhir">
 				<id value="0d87f02c-da2c-4551-9ead-2956f0165a4f"></id>
 				<extension url="http://orionhealth.com/fhir/extensions#created-by"></extension>
 				<extension url="http://orionhealth.com/fhir/extensions#last-modified-by"></extension>
@@ -46,8 +44,7 @@
 			<url value="Observation"></url>
 		</link>
 		<resource>
-            <Observation 
+			<Observation xmlns="http://hl7.org/fhir">
-                xmlns="http://hl7.org/fhir">
 				<id value="c54ac0cc-a99f-40aa-9541-c5aa853a2e88"></id>
 				<extension url="http://orionhealth.com/fhir/extensions#created-by"></extension>
 				<extension url="http://orionhealth.com/fhir/extensions#last-modified-by"></extension>

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/rest/server/Dstu3BundleFactory.java

@@ -31,27 +31,24 @@ import java.util.UUID;
 
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.dstu3.model.Bundle;
-import org.hl7.fhir.dstu3.model.DomainResource;
-import org.hl7.fhir.dstu3.model.IdType;
-import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Bundle.BundleLinkComponent;
 import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
 import org.hl7.fhir.dstu3.model.Bundle.SearchEntryMode;
+import org.hl7.fhir.dstu3.model.DomainResource;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
 import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
-import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
-import ca.uhn.fhir.rest.server.AddProfileTagEnum;
 import ca.uhn.fhir.rest.server.BundleInclusionRule;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.EncodingEnum;
@@ -65,7 +62,6 @@ import ca.uhn.fhir.util.ResourceReferenceInfo;
 
 public class Dstu3BundleFactory implements IVersionSpecificBundleFactory {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu3BundleFactory.class);
 	private Bundle myBundle;
 	private FhirContext myContext;
 	private String myBase;
@@ -308,7 +304,7 @@ public class Dstu3BundleFactory implements IVersionSpecificBundleFactory {
 	}
 
 	@Override
-	public void initializeBundleFromBundleProvider(IRestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
+	public void initializeBundleFromBundleProvider(IRestfulServer<?> theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
 			boolean thePrettyPrint, int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
 		myBase = theServerBase;
 		
@@ -358,15 +354,6 @@ public class Dstu3BundleFactory implements IVersionSpecificBundleFactory {
 			}
 		}
 
-		if (theServer.getAddProfileTag() != AddProfileTagEnum.NEVER) {
-			for (IBaseResource nextRes : resourceList) {
-				RuntimeResourceDefinition def = theServer.getFhirContext().getResourceDefinition(nextRes);
-				if (theServer.getAddProfileTag() == AddProfileTagEnum.ALWAYS || !def.isStandardProfile()) {
-					RestfulServerUtils.addProfileToBundleEntry(theServer.getFhirContext(), nextRes, theServerBase);
-				}
-			}
-		}
-
 		addResourcesToBundle(new ArrayList<IBaseResource>(resourceList), theBundleType, theServerBase, theServer.getBundleInclusionRule(), theIncludes);
 		addRootPropertiesToBundle(null, theServerBase, theCompleteUrl, theResult.size(), theBundleType, theResult.getPublished());
 

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/context/FhirContextDstu3Test.java

@@ -9,12 +9,24 @@ import org.junit.Test;
 import ca.uhn.fhir.context.BaseRuntimeChildDatatypeDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.rest.client.MyPatientWithExtensions;
 
 public class FhirContextDstu3Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirContextDstu3Test.class);
 
 	private FhirContext ourCtx = FhirContext.forDstu3();
 	
+	@Test
+	public void testCustomTypeDoesntBecomeDefault() {
+		FhirContext ctx = FhirContext.forDstu3();
+		
+		MyPatientWithExtensions pt = new MyPatientWithExtensions();
+		pt.addName().addGiven("FOO");
+		ctx.newXmlParser().encodeResourceToString(pt);
+		
+		assertEquals(Patient.class, ctx.getResourceDefinition("Patient").getImplementingClass());
+	}
+	
 	@Test
 	public void testQueryBoundCode() {
 		RuntimeResourceDefinition patientType = ourCtx.getResourceDefinition(Patient.class);

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/CustomTypeDstu3Test.java

@@ -1,11 +1,20 @@
 package ca.uhn.fhir.parser;
 
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.nullValue;
+import static org.hamcrest.Matchers.stringContainsInOrder;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import org.hl7.fhir.dstu3.model.DateTimeType;
+import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Quantity;
+import org.hl7.fhir.dstu3.model.StringType;
+import org.junit.Before;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -13,17 +22,215 @@ import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.api.annotation.Extension;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.server.AddProfileTagEnum;
 import ca.uhn.fhir.util.ElementUtil;
 
 public class CustomTypeDstu3Test {
 
+	private static final FhirContext ourCtx = FhirContext.forDstu3();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CustomTypeDstu3Test.class);
 
+	@Before
+	public void before() {
+		ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.ONLY_FOR_CUSTOM);
+	}
+	
+	
+	private String createBundle(String... theResources) {
+		StringBuilder b = new StringBuilder();
+		b.append("<Bundle xmlns=\"http://hl7.org/fhir\">\n");
+		for (String next : theResources) {
+			b.append("	<entry>\n");
+			b.append("		<resource>\n");
+			b.append(next);
+			b.append("		</resource>\n");
+			b.append("	</entry>\n");
+		}
+		b.append("</Bundle>");
+		return b.toString();
+	}
+	
+	private String createResource(boolean theWithProfile) {
+		StringBuilder b = new StringBuilder();
+		b.append("<Patient xmlns=\"http://hl7.org/fhir\">\n");
+		if (theWithProfile) {
+			b.append("   <meta>\n");
+			b.append("      <profile value=\"http://example.com/foo\"/>\n");
+			b.append("   </meta>\n");
+		}
+		b.append("   <extension url=\"http://example.com/BloodPressure\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"110\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"mmHg\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <modifierExtension url=\"http://example.com/diabetes2\">\n");
+		b.append("      <valueDateTime value=\"2010-01-02\"/>\n");
+		b.append("   </modifierExtension>\n");
+		b.append("   <modifierExtension url=\"http://example.com/diabetes2\">\n");
+		b.append("      <valueDateTime value=\"2014-01-26T11:11:11\"/>\n");
+		b.append("   </modifierExtension>\n");
+		b.append("   <extension url=\"http://example.com/Cholesterol\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"2\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"mmol/l\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <extension url=\"http://example.com/Glucose\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"95\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"mg/dl\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <extension url=\"http://example.com/HbA1c\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"48\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"mmol/mol\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <extension url=\"http://example.com/Insuline\">\n");
+		b.append("      <valueQuantity>\n");
+		b.append("         <value value=\"125\"/>\n");
+		b.append("         <system value=\"http://unitsofmeasure.org\"/>\n");
+		b.append("         <code value=\"pmol/l\"/>\n");
+		b.append("      </valueQuantity>\n");
+		b.append("   </extension>\n");
+		b.append("   <extension url=\"http://example.com/Weight\">\n");
+		b.append("      <valueString value=\"185 cm\"/>\n");
+		b.append("   </extension>\n");
+		b.append("   <identifier>\n");
+		b.append("      <system value=\"urn:system\"/>\n");
+		b.append("      <value value=\"1234\"/>\n");
+		b.append("   </identifier>\n");
+		b.append("   <name>\n");
+		b.append("      <family value=\"Rossi\"/>\n");
+		b.append("      <given value=\"Mario\"/>\n");
+		b.append("   </name>\n");
+		b.append("</Patient>");
+		String input =
+			b.toString();
+		return input;
+	}
+
 	@Test
-	public void testEncode() {
+	public void parseBundleWithResourceDirective() {
+		
+		String input = createBundle(createResource(false), createResource(true));
 		
 		FhirContext ctx = FhirContext.forDstu3();
+		ctx.setDefaultTypeForProfile("http://example.com/foo", MyCustomPatient.class);
+		
+		Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, input);
+		
+		Patient res0 = (Patient) bundle.getEntry().get(0).getResource();
+		assertEquals(0, res0.getMeta().getProfile().size());
+		List<org.hl7.fhir.dstu3.model.Extension> exts = res0.getExtensionsByUrl("http://example.com/Weight");
+		assertEquals(1, exts.size());
+		assertEquals("185 cm", ((StringType)exts.get(0).getValue()).getValue());
+
+		MyCustomPatient res1 = (MyCustomPatient) bundle.getEntry().get(1).getResource();
+		assertEquals(1, res1.getMeta().getProfile().size());
+		assertEquals("http://example.com/foo", res1.getMeta().getProfile().get(0).getValue());
+		exts = res1.getExtensionsByUrl("http://example.com/Weight");
+		assertEquals(0, exts.size());
+		assertEquals("185 cm", res1.getWeight().getValue());
+	}
+	
+	@Test
+	public void parseResourceWithDirective() {
+		String input = createResource(true);
+		
+		FhirContext ctx = FhirContext.forDstu3();
+		ctx.setDefaultTypeForProfile("http://example.com/foo", MyCustomPatient.class);
+		
+		MyCustomPatient parsed = (MyCustomPatient) ctx.newXmlParser().parseResource(input);
+		assertEquals(1, parsed.getMeta().getProfile().size());
+		assertEquals("http://example.com/foo", parsed.getMeta().getProfile().get(0).getValue());
+		
+		List<org.hl7.fhir.dstu3.model.Extension> exts = parsed.getExtensionsByUrl("http://example.com/Weight");
+		assertEquals(0, exts.size());
+		
+		assertEquals("185 cm", parsed.getWeight().getValue());
+	}
+
+	@Test
+	public void parseResourceWithNoDirective() {
+		String input = createResource(true);
+		
+		FhirContext ctx = FhirContext.forDstu3();
+		Patient parsed = (Patient) ctx.newXmlParser().parseResource(input);
+		assertEquals(1, parsed.getMeta().getProfile().size());
+		assertEquals("http://example.com/foo", parsed.getMeta().getProfile().get(0).getValue());
+		
+		List<org.hl7.fhir.dstu3.model.Extension> exts = parsed.getExtensionsByUrl("http://example.com/Weight");
+		assertEquals(1, exts.size());
+		assertEquals("185 cm", ((StringType)exts.get(0).getValue()).getValue());
+	}
+
+	@Test
+	public void testAccessEmptyMetaLists() {
+		Patient p = new Patient();
+		assertThat(p.getMeta().getProfile(), empty());
+		assertThat(p.getMeta().getFormatCommentsPost(), empty());
+		assertThat(p.getMeta().getFormatCommentsPre(), empty());
+		assertThat(p.getMeta().getLastUpdated(), nullValue());
+		assertThat(p.getMeta().getSecurity(), empty());
+		assertThat(p.getMeta().getSecurity("foo", "bar"), nullValue());
+		assertThat(p.getMeta().getTag(), empty());
+		assertThat(p.getMeta().getTag("foo", "bar"), nullValue());
+		assertThat(p.getMeta().getVersionId(), nullValue());
+		
+	}
+
+	@Test
+	public void testEncodeCompleteMetaLists() {
+		Patient p = new Patient();
+		p.getMeta().addProfile("http://foo/profile1");
+		p.getMeta().addProfile("http://foo/profile2");
+		p.getMeta().addSecurity().setSystem("SEC_S1").setCode("SEC_C1").setDisplay("SED_D1");
+		p.getMeta().addSecurity().setSystem("SEC_S2").setCode("SEC_C2").setDisplay("SED_D2");
+		p.getMeta().addTag().setSystem("TAG_S1").setCode("TAG_C1").setDisplay("TAG_D1");
+		p.getMeta().addTag().setSystem("TAG_S2").setCode("TAG_C2").setDisplay("TAG_D2");
+		
+		String out = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
+		ourLog.info(out);
+		
+		//@formatter:off
+		assertThat(out, stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://foo/profile1\"/>", 
+			"<profile value=\"http://foo/profile2\"/>", 
+			"<security>", 
+			"<system value=\"SEC_S1\"/>", 
+			"<code value=\"SEC_C1\"/>", 
+			"<display value=\"SED_D1\"/>", 
+			"</security>", 
+			"<security>", 
+			"<system value=\"SEC_S2\"/>", 
+			"<code value=\"SEC_C2\"/>", 
+			"<display value=\"SED_D2\"/>", 
+			"</security>", 
+			"<tag>", 
+			"<system value=\"TAG_S1\"/>", 
+			"<display value=\"TAG_D1\"/>", 
+			"</tag>", 
+			"<tag>", 
+			"<system value=\"TAG_S2\"/>", 
+			"<display value=\"TAG_D2\"/>", 
+			"</tag>", 
+			"</meta>"));
+		//@formatter:on
+		
+	}
+
+	@Test
+	public void testEncodeWithCustomType() {
 
 		MyCustomPatient patient = new MyCustomPatient();
 
@@ -36,17 +243,76 @@ public class CustomTypeDstu3Test {
 		patient.setCholesterol(new Quantity());
 		patient.setWeight(new StringDt("80 kg"));
 		patient.setWeight(new StringDt("185 cm"));
-		patient.setCheckDates(new ArrayList<DateTimeType>());
+		patient.setCheckDates(new ArrayList<DateTimeDt>());
-		patient.getCheckDates().add(new DateTimeType("2014-01-26T11:11:11"));
+		patient.getCheckDates().add(new DateTimeDt("2014-01-26T11:11:11"));
 
-		IParser p = ctx.newXmlParser().setPrettyPrint(true);
+		ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.ONLY_FOR_CUSTOM);
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
 		String messageString = p.encodeResourceToString(patient);
 
 		ourLog.info(messageString);
 		
+		//@formatter:off
+		assertThat(messageString, stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://example.com/foo\"/>", 
+			"</meta>"));
+		//@formatter:on
+
+		//@formatter:off
+		assertThat(messageString, not(stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://example.com/foo\"", "/>", 
+			"<profile value=\"http://example.com/foo\"/>", 
+			"</meta>")));
+		//@formatter:on
 	}
 
-	@ResourceDef(name = "Patient")
+	@Test
+	public void testEncodeWithCustomTypeAndAutoInsertedProfile() {
+
+		MyCustomPatient patient = new MyCustomPatient();
+
+		patient.getMeta().addProfile("http://example.com/foo");
+		patient.getMeta().addProfile("http://example.com/bar");
+		
+		patient.addIdentifier().setSystem("urn:system").setValue("1234");
+		patient.addName().addFamily("Rossi").addGiven("Mario");
+		patient.setInsulinLevel(new Quantity());
+		patient.setGlucoseLevel(new Quantity());
+		patient.setHbA1c(new Quantity());
+		patient.setBloodPressure(new Quantity());
+		patient.setCholesterol(new Quantity());
+		patient.setWeight(new StringDt("80 kg"));
+		patient.setWeight(new StringDt("185 cm"));
+		patient.setCheckDates(new ArrayList<DateTimeDt>());
+		patient.getCheckDates().add(new DateTimeDt("2014-01-26T11:11:11"));
+
+		ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.ONLY_FOR_CUSTOM);
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String messageString = p.encodeResourceToString(patient);
+
+		ourLog.info(messageString);
+		
+		//@formatter:off
+		assertThat(messageString, stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://example.com/foo\"/>", 
+			"<profile value=\"http://example.com/bar\"/>", 
+			"</meta>"));
+		//@formatter:on
+
+		//@formatter:off
+		assertThat(messageString, not(stringContainsInOrder(
+			"<meta>", 
+			"<profile value=\"http://example.com/foo\"", "/>", 
+			"<profile value=\"http://example.com/foo\"/>", 
+			"</meta>")));
+		//@formatter:on
+	}
+	
+	
+	@ResourceDef(name = "Patient", profile = "http://example.com/foo")
 	public static class MyCustomPatient extends Patient {
 
 		private static final long serialVersionUID = 1L;
@@ -60,7 +326,7 @@ public class CustomTypeDstu3Test {
 		@Child(name = "CheckDates", max = Child.MAX_UNLIMITED)
 		@Extension(url = "http://example.com/diabetes2", definedLocally = false, isModifier = true)
 		@Description(shortDefinition = "Dates of periodic tests")
-		private List<DateTimeType> myCheckDates;
+		private List<DateTimeDt> myCheckDates;
 
 		@Child(name = "cholesterol") // once a year. The target is triglycerides =< 2 mmol/l e cholesterol =< 4 mmol/l
 		@Extension(url = "http://example.com/Cholesterol", definedLocally = false, isModifier = false)
@@ -116,9 +382,9 @@ public class CustomTypeDstu3Test {
 			return myBloodPressure;
 		}
 
-		public List<DateTimeType> getCheckDates() {
+		public List<DateTimeDt> getCheckDates() {
 			if (myCheckDates == null) {
-				myCheckDates = new ArrayList<DateTimeType>();
+				myCheckDates = new ArrayList<DateTimeDt>();
 			}
 			return myCheckDates;
 		}
@@ -182,9 +448,9 @@ public class CustomTypeDstu3Test {
 			myBloodPressure.setCode("mmHg");
 		}
 
-		public void setCheckDates(List<DateTimeType> theCheckDates) {
+		public void setCheckDates(List<DateTimeDt> theCheckDates) {
 			myCheckDates = theCheckDates;
-			myCheckDates.add(new DateTimeType("2010-01-02"));
+			myCheckDates.add(new DateTimeDt("2010-01-02"));
 		}
 
 		public void setCholesterol(Quantity cholesterol) {

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/ClientWithCustomTypeDstu3Test.java

@@ -0,0 +1,116 @@
+package ca.uhn.fhir.rest.client;
+
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.nio.charset.Charset;
+import java.util.Arrays;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.input.ReaderInputStream;
+import org.apache.http.HttpResponse;
+import org.apache.http.ProtocolVersion;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpEntityEnclosingRequestBase;
+import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.message.BasicHeader;
+import org.apache.http.message.BasicStatusLine;
+import org.hl7.fhir.dstu3.model.Binary;
+import org.hl7.fhir.dstu3.model.Conformance;
+import org.hl7.fhir.dstu3.model.OperationOutcome;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.util.VersionUtil;
+
+public class ClientWithCustomTypeDstu3Test {
+	private static FhirContext ourCtx;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ClientWithCustomTypeDstu3Test.class);
+	private HttpClient myHttpClient;
+	private HttpResponse myHttpResponse;
+
+	@Before
+	public void before() {
+		myHttpClient = mock(HttpClient.class, new ReturnsDeepStubs());
+		ourCtx.getRestfulClientFactory().setHttpClient(myHttpClient);
+		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+		myHttpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
+	}
+
+	private byte[] extractBodyAsByteArray(ArgumentCaptor<HttpUriRequest> capt) throws IOException {
+		byte[] body = IOUtils.toByteArray(((HttpEntityEnclosingRequestBase) capt.getAllValues().get(0)).getEntity().getContent());
+		return body;
+	}
+
+	private String extractBodyAsString(ArgumentCaptor<HttpUriRequest> capt) throws IOException {
+		String body = IOUtils.toString(((HttpEntityEnclosingRequestBase) capt.getAllValues().get(0)).getEntity().getContent(), "UTF-8");
+		return body;
+	}
+
+
+	@Test
+	public void testReadCustomType() throws Exception {
+		IParser p = ourCtx.newXmlParser();
+
+		MyPatientWithExtensions response = new MyPatientWithExtensions();
+		response.addName().addFamily("FAMILY");
+		response.getStringExt().setValue("STRINGVAL");
+		response.getDateExt().setValueAsString("2011-01-02");
+		final String respString = p.encodeResourceToString(response);
+		
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
+			@Override
+			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
+			}
+		});
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		//@formatter:off
+		MyPatientWithExtensions value = client
+			.read()
+			.resource(MyPatientWithExtensions.class)
+			.withId("123")
+			.execute();
+		//@formatter:on
+
+		HttpUriRequest request = capt.getAllValues().get(0);
+
+		assertEquals("http://example.com/fhir/Patient/123", request.getURI().toASCIIString());
+		assertEquals("GET", request.getMethod());
+
+		assertEquals(1, value.getName().size());
+		assertEquals("FAMILY", value.getName().get(0).getFamilyAsSingleString());
+		assertEquals("STRINGVAL", value.getStringExt().getValue());
+		assertEquals("2011-01-02", value.getDateExt().getValueAsString());
+		
+	}
+
+
+
+	@BeforeClass
+	public static void beforeClass() {
+		ourCtx = FhirContext.forDstu3();
+	}
+
+}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/MyPatientWithExtensions.java

@@ -0,0 +1,94 @@
+package ca.uhn.fhir.rest.client;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.hl7.fhir.dstu3.model.BaseResource;
+import org.hl7.fhir.dstu3.model.DateType;
+import org.hl7.fhir.dstu3.model.DomainResource;
+import org.hl7.fhir.dstu3.model.HumanName;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.ResourceType;
+import org.hl7.fhir.dstu3.model.StringType;
+
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.util.ElementUtil;
+
+
+@ResourceDef(name="Patient", profile="http://example.com/StructureDefinition/patient_with_extensions")
+public class MyPatientWithExtensions extends DomainResource {
+	
+	private static final long serialVersionUID = 1L;
+
+	@Extension(url = "http://example.com/ext/date", definedLocally = false, isModifier = true)
+	@Child(name = "modExt")
+	private DateType myDateExt;
+
+	@Extension(url = "http://example.com/ext/string", definedLocally = false, isModifier = false)
+	@Child(name = "extAtt")
+	private StringType myStringExt;
+
+   @Child(name = "name", type = {HumanName.class}, min=0, max=Child.MAX_UNLIMITED, modifier=false, summary=true)
+   @Description(shortDefinition="A name associated with the patient", formalDefinition="A name associated with the individual." )
+	private List<HumanName> myName;
+	
+	
+	public List<HumanName> getName() {
+		if (myName == null) {
+			myName = new ArrayList<HumanName>();
+		}
+		return myName;
+	}
+
+	public void setName(List<HumanName> theName) {
+		myName = theName;
+	}
+
+	public DateType getDateExt() {
+		if (myDateExt == null) {
+			myDateExt = new DateType();
+		}
+		return myDateExt;
+	}
+
+	public StringType getStringExt() {
+		if (myStringExt == null) {
+			myStringExt = new StringType();
+		}
+		return myStringExt;
+	}
+
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && ElementUtil.isEmpty(myStringExt, myDateExt);
+	}
+
+	public void setDateExt(DateType theDateExt) {
+		myDateExt = theDateExt;
+	}
+
+	public void setStringExt(StringType theStringExt) {
+		myStringExt = theStringExt;
+	}
+
+	@Override
+	public DomainResource copy() {
+		return null;
+	}
+
+	@Override
+	public ResourceType getResourceType() {
+		return ResourceType.Patient;
+	}
+
+	public HumanName addName() {
+		HumanName retVal = new HumanName();
+		getName().add(retVal);
+		return retVal;
+	}
+
+
+}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/CreateDstu3Test.java

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.rest.server;
 
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.not;
+import static org.hamcrest.Matchers.stringContainsInOrder;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 
@@ -10,120 +12,88 @@ import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpResponse;
-import org.apache.http.client.methods.HttpPost;
+import org.apache.http.client.methods.HttpGet;
-import org.apache.http.entity.ContentType;
-import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.dstu3.model.DateType;
 import org.hl7.fhir.dstu3.model.IdType;
-import org.hl7.fhir.dstu3.model.OperationOutcome;
 import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.junit.AfterClass;
-import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.primitive.StringDt;
-import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
-import ca.uhn.fhir.rest.annotation.Create;
 import ca.uhn.fhir.rest.annotation.IdParam;
-import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.Read;
-import ca.uhn.fhir.rest.annotation.ResourceParam;
 import ca.uhn.fhir.rest.annotation.Search;
-import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.client.MyPatientWithExtensions;
 import ca.uhn.fhir.util.PortUtil;
 
 public class CreateDstu3Test {
 	private static CloseableHttpClient ourClient;
 
-	private static String ourLastConditionalUrl;
+	private static FhirContext ourCtx = FhirContext.forDstu3();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CreateDstu3Test.class);
 	private static int ourPort;
 	private static Server ourServer;
-	private static IdType ourLastId;
-	private static IdType ourLastIdParam;
-	private static boolean ourLastRequestWasSearch;
-	private static FhirContext ourCtx = FhirContext.forDstu3();
-
-	@Before
-	public void before() {
-		ourLastId = null;
-		ourLastConditionalUrl = null;
-		ourLastIdParam = null;
-		ourLastRequestWasSearch = false;
-	}
 
 	@Test
-	public void testCreateWithIdInBody() throws Exception {
+	public void testRead() throws Exception {
 
-		Patient patient = new Patient();
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/2?_format=xml&_pretty=true");
-		patient.setId("2");
+		HttpResponse status = ourClient.execute(httpGet);
-		patient.addIdentifier().setValue("002");
-
-		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient");
-//		httpPost.addHeader(Constants.HEADER_IF_NONE_EXIST, "Patient?identifier=system%7C001");
-		httpPost.setEntity(new StringEntity(ourCtx.newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
-
-		HttpResponse status = ourClient.execute(httpPost);
 
 		String responseContent = IOUtils.toString(status.getEntity().getContent());
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		ourLog.info("Response was:\n{}", responseContent);
 
-		assertEquals(400, status.getStatusLine().getStatusCode());
+		assertEquals(200, status.getStatusLine().getStatusCode());
-		OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, responseContent);
+		
-		assertEquals("Can not create resource with ID \"2\", an ID element must not be supplied in the resource body on a create (POST) operation", oo.getIssue().get(0).getDiagnostics());
+		//@formatter:off
+		assertThat(responseContent, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">", 
+				"<id value=\"2\"/>", 
+				"<modifierExtension url=\"http://example.com/ext/date\">", 
+				"<valueDate value=\"2011-01-01\"/>", 
+				"</modifierExtension>", 
+				"<meta>", 
+				"<profile value=\"http://example.com/StructureDefinition/patient_with_extensions\"/>", 
+				"</meta>", 
+				"</Patient>"));
+		//@formatter:on
 	}
 
 	@Test
-	public void testCreateWithIdInUrl() throws Exception {
+	public void testSearch() throws Exception {
 
-		Patient patient = new Patient();
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=xml&_pretty=true");
-		patient.addIdentifier().setValue("002");
+		HttpResponse status = ourClient.execute(httpGet);
-
-		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/2");
-//		httpPost.addHeader(Constants.HEADER_IF_NONE_EXIST, "Patient?identifier=system%7C001");
-		httpPost.setEntity(new StringEntity(ourCtx.newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
-
-		HttpResponse status = ourClient.execute(httpPost);
 
 		String responseContent = IOUtils.toString(status.getEntity().getContent());
 		IOUtils.closeQuietly(status.getEntity().getContent());
 
 		ourLog.info("Response was:\n{}", responseContent);
 
-		assertEquals(400, status.getStatusLine().getStatusCode());
+		assertEquals(200, status.getStatusLine().getStatusCode());
-		OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, responseContent);
-		assertEquals("Can not create resource with ID \"2\", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)", oo.getIssue().get(0).getDiagnostics());
-	}
 		
-	@Test
+		//@formatter:off
-	public void testCreateWithIdInUrlForConditional() throws Exception {
+		assertThat(responseContent, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">", 
+				"<id value=\"0\"/>", 
+				"<modifierExtension url=\"http://example.com/ext/date\">", 
+				"<valueDate value=\"2011-01-01\"/>", 
+				"</modifierExtension>", 
+				"<meta>", 
+				"<profile value=\"http://example.com/StructureDefinition/patient_with_extensions\"/>", 
+				"</meta>", 
+				"</Patient>"));
+		//@formatter:on
 		
-		Patient patient = new Patient();
+		assertThat(responseContent, not(containsString("http://hl7.org/fhir/")));
-		patient.addIdentifier().setValue("002");
-
-		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/2");
-		httpPost.addHeader(Constants.HEADER_IF_NONE_EXIST, "Patient?identifier=system%7C001");
-		httpPost.setEntity(new StringEntity(ourCtx.newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
-
-		HttpResponse status = ourClient.execute(httpPost);
-
-		String responseContent = IOUtils.toString(status.getEntity().getContent());
-		IOUtils.closeQuietly(status.getEntity().getContent());
-
-		ourLog.info("Response was:\n{}", responseContent);
-
-		assertEquals(400, status.getStatusLine().getStatusCode());
-		OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, responseContent);
-		assertEquals("Can not create resource with ID \"2\", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)", oo.getIssue().get(0).getDiagnostics());
 	}
 
 	@AfterClass
@@ -140,6 +110,7 @@ public class CreateDstu3Test {
 
 		ServletHandler proxyHandler = new ServletHandler();
 		RestfulServer servlet = new RestfulServer(ourCtx);
+
 		servlet.setResourceProviders(patientProvider);
 		ServletHolder servletHolder = new ServletHolder(servlet);
 		proxyHandler.addServletWithMapping(servletHolder, "/*");
@@ -160,18 +131,29 @@ public class CreateDstu3Test {
 			return Patient.class;
 		}
 
-		@Search
+		@Read()
-		public List<IResource> search(@OptionalParam(name = "foo") StringDt theString) {
+		public MyPatientWithExtensions read(@IdParam IdType theIdParam) {
-			ourLastRequestWasSearch = true;
+			MyPatientWithExtensions p0 = new MyPatientWithExtensions();
-			return new ArrayList<IResource>();
+			p0.setId(theIdParam);
+			p0.setDateExt(new DateType("2011-01-01"));
+			return p0;
 		}
 
-		@Create()
+		@Search
-		public MethodOutcome createPatient(@ResourceParam Patient thePatient, @ConditionalUrlParam String theConditional, @IdParam IdType theIdParam) {
+		public List<IBaseResource> search() {
-			ourLastConditionalUrl = theConditional;
+			ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
-			ourLastId = thePatient.getIdElement();
+
-			ourLastIdParam = theIdParam;
+			MyPatientWithExtensions p0 = new MyPatientWithExtensions();
-			return new MethodOutcome(new IdType("Patient/001/_history/002"));
+			p0.setId(new IdType("Patient/0"));
+			p0.setDateExt(new DateType("2011-01-01"));
+			retVal.add(p0);
+
+			Patient p1 = new Patient();
+			p1.setId(new IdType("Patient/1"));
+			p1.addName().addFamily("The Family");
+			retVal.add(p1);
+
+			return retVal;
 		}
 
 	}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/CustomTypeServerDstu3.java

@@ -0,0 +1,179 @@
+package ca.uhn.fhir.rest.server;
+
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.OperationOutcome;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
+import ca.uhn.fhir.rest.annotation.Create;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.util.PortUtil;
+
+public class CustomTypeServerDstu3 {
+	private static CloseableHttpClient ourClient;
+
+	private static String ourLastConditionalUrl;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CustomTypeServerDstu3.class);
+	private static int ourPort;
+	private static Server ourServer;
+	private static IdType ourLastId;
+	private static IdType ourLastIdParam;
+	private static boolean ourLastRequestWasSearch;
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+
+	@Before
+	public void before() {
+		ourLastId = null;
+		ourLastConditionalUrl = null;
+		ourLastIdParam = null;
+		ourLastRequestWasSearch = false;
+	}
+
+	@Test
+	public void testCreateWithIdInBody() throws Exception {
+
+		Patient patient = new Patient();
+		patient.setId("2");
+		patient.addIdentifier().setValue("002");
+
+		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient");
+//		httpPost.addHeader(Constants.HEADER_IF_NONE_EXIST, "Patient?identifier=system%7C001");
+		httpPost.setEntity(new StringEntity(ourCtx.newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+
+		HttpResponse status = ourClient.execute(httpPost);
+
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		ourLog.info("Response was:\n{}", responseContent);
+
+		assertEquals(400, status.getStatusLine().getStatusCode());
+		OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, responseContent);
+		assertEquals("Can not create resource with ID \"2\", an ID element must not be supplied in the resource body on a create (POST) operation", oo.getIssue().get(0).getDiagnostics());
+	}
+
+	@Test
+	public void testCreateWithIdInUrl() throws Exception {
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setValue("002");
+
+		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/2");
+//		httpPost.addHeader(Constants.HEADER_IF_NONE_EXIST, "Patient?identifier=system%7C001");
+		httpPost.setEntity(new StringEntity(ourCtx.newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+
+		HttpResponse status = ourClient.execute(httpPost);
+
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		ourLog.info("Response was:\n{}", responseContent);
+
+		assertEquals(400, status.getStatusLine().getStatusCode());
+		OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, responseContent);
+		assertEquals("Can not create resource with ID \"2\", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)", oo.getIssue().get(0).getDiagnostics());
+	}
+
+	@Test
+	public void testCreateWithIdInUrlForConditional() throws Exception {
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setValue("002");
+
+		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/2");
+		httpPost.addHeader(Constants.HEADER_IF_NONE_EXIST, "Patient?identifier=system%7C001");
+		httpPost.setEntity(new StringEntity(ourCtx.newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+
+		HttpResponse status = ourClient.execute(httpPost);
+
+		String responseContent = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		ourLog.info("Response was:\n{}", responseContent);
+
+		assertEquals(400, status.getStatusLine().getStatusCode());
+		OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, responseContent);
+		assertEquals("Can not create resource with ID \"2\", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)", oo.getIssue().get(0).getDiagnostics());
+	}
+
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		PatientProvider patientProvider = new PatientProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(ourCtx);
+		servlet.setResourceProviders(patientProvider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
+	public static class PatientProvider implements IResourceProvider {
+
+		@Override
+		public Class<Patient> getResourceType() {
+			return Patient.class;
+		}
+
+		@Search
+		public List<IResource> search(@OptionalParam(name = "foo") StringDt theString) {
+			ourLastRequestWasSearch = true;
+			return new ArrayList<IResource>();
+		}
+
+		@Create()
+		public MethodOutcome createPatient(@ResourceParam Patient thePatient, @ConditionalUrlParam String theConditional, @IdParam IdType theIdParam) {
+			ourLastConditionalUrl = theConditional;
+			ourLastId = thePatient.getIdElement();
+			ourLastIdParam = theIdParam;
+			return new MethodOutcome(new IdType("Patient/001/_history/002"));
+		}
+
+	}
+
+}

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

@@ -48,10 +48,8 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
-import ca.uhn.fhir.rest.server.AddProfileTagEnum;
 import ca.uhn.fhir.rest.server.BundleInclusionRule;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.EncodingEnum;
@@ -59,7 +57,6 @@ import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.IPagingProvider;
 import ca.uhn.fhir.rest.server.IRestfulServer;
 import ca.uhn.fhir.rest.server.IVersionSpecificBundleFactory;
-import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.RestfulServerUtils;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
@@ -298,7 +295,7 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
   }
 
   @Override
-  public void initializeBundleFromBundleProvider(IRestfulServer theServer, IBundleProvider theResult,
+  public void initializeBundleFromBundleProvider(IRestfulServer<?> theServer, IBundleProvider theResult,
       EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl, boolean thePrettyPrint,
       int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
     myBase = theServerBase;
@@ -344,15 +341,6 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
       }
     }
 
-    if (theServer.getAddProfileTag() != AddProfileTagEnum.NEVER) {
-      for (IBaseResource nextRes : resourceList) {
-        RuntimeResourceDefinition def = theServer.getFhirContext().getResourceDefinition(nextRes);
-        if (theServer.getAddProfileTag() == AddProfileTagEnum.ALWAYS || !def.isStandardProfile()) {
-          RestfulServerUtils.addProfileToBundleEntry(theServer.getFhirContext(), nextRes, theServerBase);
-        }
-      }
-    }
-
     addResourcesToBundle(resourceList, theBundleType, theServerBase, theServer.getBundleInclusionRule(), theIncludes);
     addRootPropertiesToBundle(null, theServerBase, theCompleteUrl, theResult.size(), theBundleType,
         theResult.getPublished());

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

@@ -60,6 +60,7 @@ import org.hl7.fhir.instance.model.StringType;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.INarrative;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.junit.After;
 import org.junit.BeforeClass;
 import org.junit.Ignore;
 import org.junit.Test;
@@ -67,11 +68,11 @@ import org.xml.sax.SAXException;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.base.composite.BaseNarrativeDt;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.parser.JsonParserHl7OrgTest.MyPatientWithOneDeclaredAddressExtension;
 import ca.uhn.fhir.parser.JsonParserHl7OrgTest.MyPatientWithOneDeclaredEnumerationExtension;
 import ca.uhn.fhir.parser.JsonParserHl7OrgTest.MyPatientWithOneDeclaredExtension;
+import ca.uhn.fhir.rest.server.AddProfileTagEnum;
 import ca.uhn.fhir.rest.server.Constants;
 import net.sf.json.JSON;
 import net.sf.json.JSONSerializer;
@@ -81,6 +82,11 @@ public class XmlParserHl7OrgDstu2Test {
 	private static FhirContext ourCtx;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserHl7OrgDstu2Test.class);
 
+	@After
+	public void after() {
+	   ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.ONLY_FOR_CUSTOM);
+	}
+
 	private String fixDivNodeText(String htmlNoNs) {
 		return htmlNoNs.replace("<div>", "<div xmlns=\"http://www.w3.org/1999/xhtml\">");
 	}
@@ -89,25 +95,6 @@ public class XmlParserHl7OrgDstu2Test {
 		return htmlNoNs.replace("<div>", "<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">");
 	}
 
-	 /**
-   * 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();
-
-    String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
-    MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
-    SimpleQuantity q = (SimpleQuantity) ms.getDosage().get(0).getQuantity();
-    assertEquals("1", q.getValueElement().getValueAsString());
-    
-    String output = xmlParser.encodeResourceToString(ms);
-    assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
-  }
-
 	
 	@Test
 	public void testComposition() {
@@ -575,6 +562,26 @@ 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();
+
+    String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
+    MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
+    SimpleQuantity q = (SimpleQuantity) ms.getDosage().get(0).getQuantity();
+    assertEquals("1", q.getValueElement().getValueAsString());
+    
+    String output = xmlParser.encodeResourceToString(ms);
+    assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
+  }
+
+	
 	@Test
 	public void testEncodeBinaryResource() {
 
@@ -587,7 +594,6 @@ public class XmlParserHl7OrgDstu2Test {
 
 	}
 
-	
 	@Test
 	public void testEncodeBinaryWithNoContentType() {
 		Binary b = new Binary();
@@ -613,7 +619,6 @@ public class XmlParserHl7OrgDstu2Test {
 		assertThat(val, containsString("home"));
 		assertThat(val, containsString("male"));
 	}
-
 	@Test
 	public void testEncodeBundle() throws InterruptedException {
 		Bundle b = new Bundle();
@@ -650,6 +655,7 @@ public class XmlParserHl7OrgDstu2Test {
 				
 		assertThat(bundleString, StringContainsInOrder.stringContainsInOrder(strings));
 	}
+	
 	@Test
 	public void testEncodeBundleCategory() {
 
@@ -718,6 +724,7 @@ public class XmlParserHl7OrgDstu2Test {
 
 	}
 
+	
 	@Test
 	public void testEncodeContainedWithNarrativeIsSuppresed() throws Exception {
 		IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
@@ -745,7 +752,6 @@ public class XmlParserHl7OrgDstu2Test {
 
 	}
 
-	
 	@Test
 	public void testEncodeDeclaredExtensionWithAddressContent() {
 		IParser parser = ourCtx.newXmlParser();
@@ -1110,6 +1116,7 @@ public class XmlParserHl7OrgDstu2Test {
 
 	}
 
+	
 	@Test
 	public void testExtensionOnComposite() throws Exception {
 
@@ -1133,7 +1140,6 @@ public class XmlParserHl7OrgDstu2Test {
 
 	}
 
-	
 	@Test
 	public void testExtensionOnPrimitive() throws Exception {
 
@@ -1219,6 +1225,7 @@ public class XmlParserHl7OrgDstu2Test {
 	@Test
 	public void testLoadAndEncodeDeclaredExtensions() throws ConfigurationException, DataFormatException, SAXException, IOException {
 		IParser p = ourCtx.newXmlParser();
+		ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.NEVER);
 
 		//@formatter:off
 		String msg = "<ResourceWithExtensionsA xmlns=\"http://hl7.org/fhir\">\n" + 

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/rest/server/BundleTypeInResponseHl7OrgTest.java

@@ -26,9 +26,6 @@ import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.util.PortUtil;
 
-/**
- * Created by dsotnikov on 2/25/2014.
- */
 public class BundleTypeInResponseHl7OrgTest {
 
 	private static CloseableHttpClient ourClient;

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

@@ -1,180 +0,0 @@
-package ca.uhn.fhir.model.dstu2.resource;
-
-/*
- * #%L
- * HAPI FHIR Structures - DSTU2 (FHIR v0.4.0)
- * %%
- * Copyright (C) 2014 - 2015 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import org.apache.commons.lang3.Validate;
-import org.apache.commons.lang3.builder.ToStringBuilder;
-import org.apache.commons.lang3.builder.ToStringStyle;
-import org.hl7.fhir.instance.model.api.IIdType;
-
-import ca.uhn.fhir.model.api.BaseElement;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.annotation.Child;
-import ca.uhn.fhir.model.api.annotation.SearchParamDefinition;
-import ca.uhn.fhir.model.base.resource.ResourceMetadataMap;
-import ca.uhn.fhir.model.dstu2.composite.ContainedDt;
-import ca.uhn.fhir.model.dstu2.composite.NarrativeDt;
-import ca.uhn.fhir.model.primitive.CodeDt;
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.gclient.StringClientParam;
-import ca.uhn.fhir.util.ElementUtil;
-
-public abstract class BaseResource extends BaseElement implements IResource {
-
-	/**
-	 * Search parameter constant for <b>_language</b>
-	 */
-	@SearchParamDefinition(name="_language", path="", description="The language of the resource", type="string"  )
-	public static final String SP_RES_LANGUAGE = "_language";
-
-
-	/**
-	 * Search parameter constant for <b>_id</b>
-	 */
-	@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="string"  )
-	public static final String SP_RES_ID = "_id";
-
-	/**
-	 * <b>Fluent Client</b> search parameter constant for <b>_id</b>
-	 * <p>
-	 * Description: <b>the _id of a resource</b><br>
-	 * Type: <b>string</b><br>
-	 * Path: <b>Resource._id</b><br>
-	 * </p>
-	 */
-	public static final StringClientParam RES_ID = new StringClientParam(BaseResource.SP_RES_ID);
-
-
-	@Child(name = "contained", order = 2, min = 0, max = 1)
-	private ContainedDt myContained;
-
-	private IdDt myId;
-
-	@Child(name = "language", order = 0, min = 0, max = Child.MAX_UNLIMITED)
-	private CodeDt myLanguage;
-
-	private ResourceMetadataMap myResourceMetadata;
-
-	@Child(name = "text", order = 1, min = 0, max = 1)
-	private NarrativeDt myText;
-
-	@Override
-	public ContainedDt getContained() {
-		if (myContained == null) {
-			myContained = new ContainedDt();
-		}
-		return myContained;
-	}
-
-	public IdDt getId() {
-		if (myId == null) {
-			myId = new IdDt();
-		}
-		return myId;
-	}
-
-	@Override
-	public IIdType getIdElement() {
-		return getId();
-	}
-
-	@Override
-	public CodeDt getLanguage() {
-		if (myLanguage == null) {
-			myLanguage = new CodeDt();
-		}
-		return myLanguage;
-	}
-
-	@Override
-	public ResourceMetadataMap getResourceMetadata() {
-		if (myResourceMetadata == null) {
-			myResourceMetadata = new ResourceMetadataMap();
-		}
-		return myResourceMetadata;
-	}
-
-	@Override
-	public NarrativeDt getText() {
-		if (myText == null) {
-			myText = new NarrativeDt();
-		}
-		return myText;
-	}
-
-	public void setContained(ContainedDt theContained) {
-		myContained = theContained;
-	}
-
-	public void setId(IdDt theId) {
-		myId = theId;
-	}
-	
-	public BaseResource setId(IIdType theId) {
-		if (theId instanceof IdDt) {
-			myId = (IdDt) theId;
-		} else if (theId != null) {
-			myId = new IdDt(theId.getValue());
-		}
-		return this;
-	}
-
-	public BaseResource setId(String theId) {
-		if (theId == null) {
-			myId = null;
-		} else {
-			myId = new IdDt(theId);
-		}
-		return this;
-	}
-
-	@Override
-	public void setLanguage(CodeDt theLanguage) {
-		myLanguage = theLanguage;
-	}
-
-	@Override
-	public void setResourceMetadata(ResourceMetadataMap theMap) {
-		Validate.notNull(theMap, "The Map must not be null");
-		myResourceMetadata = theMap;
-	}
-
-	public void setText(NarrativeDt theText) {
-		myText = theText;
-	}
-
-	@Override
-	public String toString() {
-		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
-		b.append("id", getId().toUnqualified());
-		return b.toString();
-	}
-
-	/**
-	 * Intended to be called by extending classes {@link #isEmpty()} implementations, returns <code>true</code> if all
-	 * content in this superclass instance is empty per the semantics of {@link #isEmpty()}.
-	 */
-	@Override
-	protected boolean isBaseEmpty() {
-		return super.isBaseEmpty() && ElementUtil.isEmpty(myLanguage, myText, myId);
-	}
-
-}

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

@@ -51,6 +51,7 @@
 	}
 
 #foreach ( $child in $childElements )
+#if (${child.methodName} != 'Meta')
 	/**
 	 * Gets the value(s) for <b>${child.elementName}</b> ($esc.html(${child.shortName})).
 	 * creating it if it does
@@ -73,7 +74,7 @@
 #end
 		return ${child.variableName};
 	}
-
+#end
 
 	/**
 	 * Gets the value(s) for <b>${child.elementName}</b> ($esc.html(${child.shortName})).

src/changes/changes.xml

@@ -261,6 +261,44 @@
 				header containing "application/xml" as some browsers
 				do.
 			</action>
+			<action type="add">
+				DSTU2 resources now have a 
+				<![CDATA[<code>getMeta()</code>]]> method which returns a
+				modifiable view of the resource metadata for convenience. This
+				matches the equivalent method in the DSTU3 structures.
+			</action>
+			<action type="add" issue="315">
+				Add a new method to FhirContext called
+				<![CDATA[
+				<code><a href="./apidocs/ca/uhn/fhir/context/FhirContext.html#setDefaultTypeForProfile-java.lang.String-java.lang.Class-">setDefaultTypeForProfile</a></code>
+				]]>
+				which can be used to specify that when recources are received which declare
+				support for specific profiles, a specific custom structures should be used 
+				instead of the default. For example, if you have created a custom Observation
+				class for a specific profile, you could use this method to cause your custom
+				type to be used by the parser for resources in a search bundle you receive.
+				<![CDATA[
+				<br/><br/>
+				See the documentation page on
+				<a href="./doc_extensions.html">Profiles and Extensions</a>
+				for more information.
+				]]>
+			</action>
+			<action type="fix" issue="315">
+				Parsing/Encoding a custom resource type which extends a
+				base type sometimes caused the FhirContext to treat all future
+				parses of the same resource as using the custom type even when
+				this was not wanted.
+				<![CDATA[<br/><br/>]]>
+				Custom structures may now be explicitly declared by profile
+				using the
+				<![CDATA[
+				<code><a href="./apidocs/ca/uhn/fhir/context/FhirContext.html#setDefaultTypeForProfile-java.lang.String-java.lang.Class-">setDefaultTypeForProfile</a></code>
+				]]>
+				method.
+				<![CDATA[<br/><br/>]]>
+				This issue was discovered and fixed as a part of the implementation of issue #315.
+			</action>
 		</release>
 		<release version="1.4" date="2016-02-04">
 			<action type="add">

src/site/xdoc/doc_extensions.xml

@@ -3,13 +3,20 @@
 
 	<properties>
 		<title>Profiles and Extensions</title>
-		<author email="jamesagnew@users.sourceforge.net">James Agnew</author>
+		<author email="jamesagnew@gmail.com">James Agnew</author>
 	</properties>
 
 	<body>
 
 		<section name="Undeclared Extensions">
 			
+			<p class="doc_info_bubble">
+				Note on FHIR Versions: Because of the differences in the way the structures
+				work between DSTU2 and DSTU3, we have provided two versions of many of the
+				examples on this page. See the <a href="./download.html">download page</a>
+				for more information on FHIR versions.
+			</p>
+			
 			<p>
 				Extensions are a key part of the FHIR specification, providing a standardized
 				way of placing additional data in a resource. 
@@ -21,17 +28,40 @@
 				Undeclared extensions can be added to any of the built in FHIR resource types that come with HAPI-FHIR.
 			</p>
 			
+			<p>
+				<b>DSTU2</b>
+			</p>
 			<macro name="snippet">
 				<param name="id" value="resourceExtension" />
-				<param name="file" value="examples/src/main/java/example/Extensions.java" />
+				<param name="file" value="examples/src/main/java/example/ExtensionsDstu2.java" />
+			</macro>
+
+			<p>
+				<b>DSTU3</b>
+			</p>
+			<macro name="snippet">
+				<param name="id" value="resourceExtension" />
+				<param name="file" value="examples/src/main/java/example/ExtensionsDstu3.java" />
 			</macro>
 			
 			<p>
 				Undeclared extensions can also be added to datatypes (composite or primitive).
 			</p>
+
+			<p>
+				<b>DSTU2</b>
+			</p>
 			<macro name="snippet">
 				<param name="id" value="resourceStringExtension" />
-				<param name="file" value="examples/src/main/java/example/Extensions.java" />
+				<param name="file" value="examples/src/main/java/example/ExtensionsDstu2.java" />
+			</macro>
+			
+			<p>
+				<b>DSTU3</b>
+			</p>
+			<macro name="snippet">
+				<param name="id" value="resourceStringExtension" />
+				<param name="file" value="examples/src/main/java/example/ExtensionsDstu3.java" />
 			</macro>
 
 			<subsection name="Sub-Extensions">
@@ -41,9 +71,21 @@
 					of a datatype. This is done by adding a child undeclared extension to the
 					parent extension.
 				</p>
+
+				<p>
+					<b>DSTU2</b>
+				</p>
 				<macro name="snippet">
 					<param name="id" value="subExtension" />
-					<param name="file" value="examples/src/main/java/example/Extensions.java" />
+					<param name="file" value="examples/src/main/java/example/ExtensionsDstu2.java" />
+				</macro>
+			
+				<p>
+					<b>DSTU3</b>
+				</p>
+				<macro name="snippet">
+					<param name="id" value="subExtension" />
+					<param name="file" value="examples/src/main/java/example/ExtensionsDstu3.java" />
 				</macro>
 
 			</subsection>
@@ -52,11 +94,23 @@
 
 				<p>
 					HAPI provides a few ways of accessing extension values in resources 
-					which are receieved from other sources (i.e. downloaded by a client).
+					which are received from other sources (i.e. downloaded by a client).
+				</p>
+
+				<p>
+					<b>DSTU2</b>
 				</p>
 				<macro name="snippet">
 					<param name="id" value="parseExtension" />
-					<param name="file" value="examples/src/main/java/example/Extensions.java" />
+					<param name="file" value="examples/src/main/java/example/ExtensionsDstu2.java" />
+				</macro>
+			
+				<p>
+					<b>DSTU3</b>
+				</p>
+				<macro name="snippet">
+					<param name="id" value="parseExtension" />
+					<param name="file" value="examples/src/main/java/example/ExtensionsDstu3.java" />
 				</macro>
 
 			</subsection>
@@ -119,84 +173,43 @@
 					<param name="file" value="examples/src/main/java/example/MyPatientUse.java" />
 				</macro>
 
-			<subsection name="Documentation">
+			<subsection name="Using Custom Types in a Client">
 				
 				<p>
-					Note in the example above the use of the <code>@Description</code>
+					If you are using a client and wish to use a specific custom structure,
-					annotation on the extension fields. This documentation is important,
+					you may simply use the custom structure as you would a build in
-					as the FHIR Server will automatically add it to the generated Profile
+					HAPI type.
-					resources which are exported by the server.  
 				</p>
+				<macro name="snippet">
+					<param name="id" value="customTypeClientSimple" />
+					<param name="file" value="examples/src/main/java/example/ExtensionsDstu3.java" />
+				</macro>
 				
 				<p>
-					These bits of documentation will then be re-added to any automatically
+					Sometimes you may not know in advance exactly which
-					generated clients built using <a href="./doc_tinder.html">Tinder</a>
+					type you will be receiving. For example, there are Patient resources
-					against your server.
+					which conform to several different profiles on a server and you 
+					aren't sure which profile you will get back for a specific read,
+					you can declare the "primary" type for a given profile.
 				</p>
+				<macro name="snippet">
+					<param name="id" value="customTypeClientDeclared" />
+					<param name="file" value="examples/src/main/java/example/ExtensionsDstu3.java" />
+				</macro>
+				
+			</subsection>
+
+			<subsection name="Using Custom Types in a Server">
 				
 				<p>
-					The following is a snippet from the generated Profile resource
+					If you are using a client and wish to use a specific custom structure,
-					which is automatically created by a HAPI RESTful server using
+					you may simply use the custom structure as you would a build in
-					your new type. (Don't worry if this part doens't make sense to you
+					HAPI type.
-					yet, this is an advanced feature)
 				</p>
-				
+				<macro name="snippet">
-				<source><![CDATA[<element>
+					<param name="id" value="customTypeClientSimple" />
-   <path value="Patient.extension"/>
+					<param name="file" value="examples/src/main/java/example/ExtensionsDstu3.java" />
-   <name value="extension"/>
+				</macro>
-   <slicing>
-      <discriminator value="url"/>
-      <ordered value="false"/>
-      <rules value="open"/>
-   </slicing>
-   <definition>
-      <type>
-         <code value="Extension"/>
-      </type>
-   </definition>
-</element>
-<element>
-   <path value="Patient.extension"/>
-   <name value="extension"/>
-   <definition>
-      <short value="The name of the patient's favourite pet"/>
-      <min value="0"/>
-      <max value="1"/>
-      <type>
-         <code value="Extension"/>
-         <profile value="http://example.com/dontuse#petname"/>
-      </type>
-      <isModifier value="false"/>
-   </definition>
-</element>
-<element>
-   <path value="Patient.modifierExtension"/>
-   <name value="modifierExtension"/>
-   <slicing>
-      <discriminator value="url"/>
-      <ordered value="false"/>
-      <rules value="open"/>
-   </slicing>
-   <definition>
-      <type>
-         <code value="Extension"/>
-      </type>
-   </definition>
-</element>
-<element>
-   <path value="Patient.modifierExtension"/>
-   <name value="modifierExtension"/>
-   <definition>
-      <short value="Some dates of note for the patient"/>
-      <min value="0"/>
-      <max value="*"/>
-      <type>
-         <code value="Extension"/>
-         <profile value="http://example.com/dontuse#importantDates"/>
-      </type>
-      <isModifier value="true"/>
-   </definition>
-</element>]]></source>	
 
 			</subsection>