Fix unit tests

hapi-fhir-base/TODO.txt

@@ -28,3 +28,5 @@
  * Support slices in the model
  
  * Support extensions (declared and undeclared) in primitives, narratives, etc. 
+ 
+ * Create a Maven archetype for a server project and a client project

hapi-fhir-base/pom.xml

@@ -151,6 +151,8 @@
 				<version>3.3</version>
 			</plugin>
 			<!-- 
+
+			-->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-report-plugin</artifactId>
@@ -176,7 +178,6 @@
 				<artifactId>maven-jxr-plugin</artifactId>
 				<version>2.3</version>
 			</plugin>
-			-->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-project-info-reports-plugin</artifactId>

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

@@ -24,6 +24,9 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IComposite
 		if (theNext == null) {
 			throw new NullPointerException();
 		}
+//		if (theNext.getValidChildNames().contains("performetPractitioner")) {
+//			throw new NullPointerException();
+//		}
 		if (theNext.getExtensionUrl() != null) {
 			throw new IllegalArgumentException("Shouldn't haven an extension URL, use addExtension instead");
 		}

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

@@ -27,7 +27,7 @@ import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.IResourceBlock;
 import ca.uhn.fhir.model.api.IValueSetEnumBinder;
-import ca.uhn.fhir.model.api.ResourceReference;
+import ca.uhn.fhir.model.api.BaseResourceReference;
 import ca.uhn.fhir.model.api.annotation.Block;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.CodeTableDef;
@@ -37,6 +37,7 @@ import ca.uhn.fhir.model.api.annotation.Extension;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.BoundCodeDt;
+import ca.uhn.fhir.model.primitive.BoundCodeableConceptDt;
 import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.ICodedDatatype;
@@ -323,7 +324,7 @@ class ModelScanner {
 				if (IElement.class.isAssignableFrom(nextElementType)) {
 					addScanAlso((Class<? extends IElement>) nextElementType);
 				}
-			} else if (ResourceReference.class.isAssignableFrom(nextElementType)) {
+			} else if (BaseResourceReference.class.isAssignableFrom(nextElementType)) {
 				/*
 				 * Child is a resource reference
 				 */
@@ -361,9 +362,14 @@ class ModelScanner {
 					} else {
 						def = new RuntimeChildPrimitiveDatatypeDefinition(next, elementName, descriptionAnnotation, childAnnotation, nextDatatype);
 					}
+				} else {
+					if (nextElementType.equals(BoundCodeableConceptDt.class)) {
+						IValueSetEnumBinder<Enum<?>> binder = getBoundCodeBinder(next);
+						def = new RuntimeChildCompositeBoundDatatypeDefinition(next, elementName, childAnnotation, descriptionAnnotation, nextDatatype, binder);
 					} else {
 						def = new RuntimeChildCompositeDatatypeDefinition(next, elementName, childAnnotation, descriptionAnnotation, nextDatatype);
 					}
+				}
 
 				CodeableConceptElement concept = next.getAnnotation(CodeableConceptElement.class);
 				if (concept != null) {

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

@@ -0,0 +1,27 @@
+package ca.uhn.fhir.context;
+
+import java.lang.reflect.Field;
+
+import ca.uhn.fhir.model.api.IDatatype;
+import ca.uhn.fhir.model.api.IValueSetEnumBinder;
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+
+public class RuntimeChildCompositeBoundDatatypeDefinition extends RuntimeChildCompositeDatatypeDefinition {
+
+	private IValueSetEnumBinder<Enum<?>> myBinder;
+
+	public RuntimeChildCompositeBoundDatatypeDefinition(Field theField, String theElementName, Child theChildAnnotation, Description theDescriptionAnnotation, Class<? extends IDatatype> theDatatype, IValueSetEnumBinder<Enum<?>> theBinder) {
+		super(theField, theElementName, theChildAnnotation, theDescriptionAnnotation, theDatatype);
+		myBinder = theBinder;
+		if (theBinder==null) {
+			throw new IllegalArgumentException("Binder must not be null");
+		}
+	}
+
+	@Override
+	public IValueSetEnumBinder<Enum<?>> getInstanceConstructorArguments() {
+		return myBinder;
+	}
+
+}

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

@@ -8,7 +8,7 @@ import java.util.Set;
 
 import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.ResourceReference;
+import ca.uhn.fhir.model.api.BaseResourceReference;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.Description;
 
@@ -28,7 +28,7 @@ public class RuntimeChildResourceDefinition extends BaseRuntimeDeclaredChildDefi
 
 	@Override
 	public String getChildNameByDatatype(Class<? extends IElement> theDatatype) {
-		if (ResourceReference.class.equals(theDatatype)) {
+		if (BaseResourceReference.class.isAssignableFrom(theDatatype)) {
 			return getElementName();
 		}
 		return null;
@@ -36,7 +36,7 @@ public class RuntimeChildResourceDefinition extends BaseRuntimeDeclaredChildDefi
 
 	@Override
 	public BaseRuntimeElementDefinition<?> getChildElementDefinitionByDatatype(Class<? extends IElement> theDatatype) {
-		if (ResourceReference.class.equals(theDatatype)) {
+		if (BaseResourceReference.class.isAssignableFrom(theDatatype)) {
 			return myRuntimeDef;
 		}
 		return null;

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

@@ -11,7 +11,7 @@ import java.util.Set;
 import ca.uhn.fhir.model.api.IDatatype;
 import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.ResourceReference;
+import ca.uhn.fhir.model.api.BaseResourceReference;
 import ca.uhn.fhir.model.api.UndeclaredExtension;
 
 public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildDefinition {
@@ -70,13 +70,13 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 		}
 		
 		// Resource Reference
-		myDatatypeToAttributeName.put(ResourceReference.class, "valueReference");
+		myDatatypeToAttributeName.put(BaseResourceReference.class, "valueReference");
 		List<Class<? extends IResource>> types = new ArrayList<Class<? extends IResource>>();
 		types.add(IResource.class);
 		RuntimeResourceReferenceDefinition def = new RuntimeResourceReferenceDefinition("valueResource", types);
 		def.sealAndInitialize(theClassToElementDefinitions);
 		myAttributeNameToDefinition.put("valueResource", def);
-		myDatatypeToDefinition.put(ResourceReference.class, def);
+		myDatatypeToDefinition.put(BaseResourceReference.class, def);
 	}
 
 

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

@@ -208,6 +208,7 @@ public class RuntimeResourceDefinition extends BaseRuntimeElementCompositeDefini
 			StructureElement extSlice = theStruct.addElement();
 			extSlice.setName(elementName);
 			extSlice.setPath(join(path, '.') + '.' + elementName);
+			extSlice.getDefinition().setIsModifier(theIsModifier);
 			extSlice.getDefinition().addType().setCode(DataTypeEnum.EXTENSION);
 			extSlice.getDefinition().setMin(0);
 			extSlice.getDefinition().setMax("*");

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

@@ -6,15 +6,15 @@ import java.util.Map;
 
 import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.ResourceReference;
+import ca.uhn.fhir.model.api.BaseResourceReference;
 
-public class RuntimeResourceReferenceDefinition extends BaseRuntimeElementDefinition<ResourceReference> {
+public class RuntimeResourceReferenceDefinition extends BaseRuntimeElementDefinition<BaseResourceReference> {
 
 	private final List<Class<? extends IResource>> myResourceTypes;
 	private HashMap<Class<? extends IResource>, RuntimeResourceDefinition> myResourceTypeToDefinition;
 
 	public RuntimeResourceReferenceDefinition(String theName, List<Class<? extends IResource>> theResourceTypes) {
-		super(theName, ResourceReference.class);
+		super(theName, BaseResourceReference.class);
 		if (theResourceTypes == null || theResourceTypes.isEmpty()) {
 			throw new ConfigurationException("Element '" + theName + "' has no resource types noted");
 		}

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

@@ -1,11 +1,25 @@
 package ca.uhn.fhir.model.api;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 public abstract class BaseElement implements IElement, ISupportsUndeclaredExtensions {
 
 	private List<UndeclaredExtension> myUndeclaredExtensions;
+	private List<UndeclaredExtension> myUndeclaredModifierExtensions;
+
+	@Override
+	public List<UndeclaredExtension> getAllUndeclaredExtensions() {
+		ArrayList<UndeclaredExtension> retVal = new ArrayList<UndeclaredExtension>();
+		if (myUndeclaredExtensions != null) {
+			retVal.addAll(myUndeclaredExtensions);
+		}
+		if (myUndeclaredModifierExtensions != null) {
+			retVal.addAll(myUndeclaredModifierExtensions);
+		}
+		return Collections.unmodifiableList(retVal);
+	}
 
 	@Override
 	public List<UndeclaredExtension> getUndeclaredExtensions() {
@@ -15,6 +29,14 @@ public abstract class BaseElement implements IElement, ISupportsUndeclaredExtens
 		return myUndeclaredExtensions;
 	}
 
+	@Override
+	public List<UndeclaredExtension> getUndeclaredModifierExtensions() {
+		if (myUndeclaredModifierExtensions == null) {
+			myUndeclaredModifierExtensions = new ArrayList<UndeclaredExtension>();
+		}
+		return myUndeclaredModifierExtensions;
+	}
+
 	/**
 	 * 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()}.
@@ -27,6 +49,13 @@ public abstract class BaseElement implements IElement, ISupportsUndeclaredExtens
 				}
 			}
 		}
+		if (myUndeclaredModifierExtensions != null) {
+			for (UndeclaredExtension next : myUndeclaredModifierExtensions) {
+				if (!next.isEmpty()) {
+					return false;
+				}
+			}
+		}
 		return true;
 	}
 

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

@@ -0,0 +1,8 @@
+package ca.uhn.fhir.model.api;
+
+
+
+public abstract class BaseResourceReference extends BaseElement {
+
+
+}

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

@@ -5,8 +5,18 @@ import java.util.List;
 public interface ISupportsUndeclaredExtensions {
 	
 	/**
-	 * Returns a list containing all undeclared extensions
+	 * Returns a list containing all undeclared non-modifier extensions
 	 */
 	List<UndeclaredExtension> getUndeclaredExtensions();
 
+	/**
+	 * Returns an <b>immutable</b> list containing all extensions (modifier and non-modifier)
+	 */
+	List<UndeclaredExtension> getAllUndeclaredExtensions();
+
+	/**
+	 * Returns a list containing all undeclared modifier extensions
+	 */
+	List<UndeclaredExtension> getUndeclaredModifierExtensions();
+	
 }

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

@@ -1,32 +0,0 @@
-package ca.uhn.fhir.model.api;
-
-import org.apache.commons.lang3.StringUtils;
-
-
-public class ResourceReference implements IDatatype {
-
-	private String myDisplay;
-	private String myReference;
-
-	public String getDisplay() {
-		return myDisplay;
-	}
-
-	public String getReference() {
-		return myReference;
-	}
-
-	public void setDisplay(String theDisplay) {
-		myDisplay = theDisplay;
-	}
-
-	public void setReference(String theReference) {
-		myReference = theReference;
-	}
-
-	@Override
-	public boolean isEmpty() {
-		return StringUtils.isBlank(myDisplay) && StringUtils.isBlank(myReference);
-	}
-
-}

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

@@ -1,27 +1,54 @@
 package ca.uhn.fhir.model.api;
 
-
 public class UndeclaredExtension extends BaseElement {
 
 	private String myUrl;
 	private IElement myValue;
+	private boolean myIsModifier;
 
-	public UndeclaredExtension() {
+	public UndeclaredExtension(boolean theIsModifier) {
-		super();
+		myIsModifier = theIsModifier;
 	}
 
-	public UndeclaredExtension(String theUrl) {
+	public UndeclaredExtension(boolean theIsModifier, String theUrl) {
-		myUrl=theUrl;
+		myIsModifier = theIsModifier;
+		myUrl = theUrl;
+	}
+
+	public boolean isModifier() {
+		return myIsModifier;
 	}
 
 	public String getUrl() {
 		return myUrl;
 	}
 
+	/**
+	 * Returns the value of this extension, if one exists.
+	 * <p>
+	 * Note that if this extension contains extensions (instead of a datatype) then <b>this method will return null</b>. In that case, you must use {@link #getUndeclaredExtensions()} and
+	 * {@link #getUndeclaredModifierExtensions()} to retrieve the child extensions.
+	 * </p>
+	 */
 	public IElement getValue() {
 		return myValue;
 	}
 
+	/**
+	 * Returns the value of this extension, casted to a primitive datatype. This is a convenience method which should only be called if you are sure that the value for this particular extension will
+	 * be a primitive.
+	 * <p>
+	 * Note that if this extension contains extensions (instead of a datatype) then <b>this method will return null</b>. In that case, you must use {@link #getUndeclaredExtensions()} and
+	 * {@link #getUndeclaredModifierExtensions()} to retrieve the child extensions.
+	 * </p>
+	 * 
+	 * @throws ClassCastException
+	 *             If the value of this extension is not a primitive datatype
+	 */
+	public IPrimitiveDatatype<?> getValueAsPrimitive() {
+		return (IPrimitiveDatatype<?>) getValue();
+	}
+
 	public void setUrl(String theUrl) {
 		myUrl = theUrl;
 	}
@@ -32,7 +59,7 @@ public class UndeclaredExtension extends BaseElement {
 
 	@Override
 	public boolean isEmpty() {
-		return myValue == null || myValue.isEmpty();
+		return super.isBaseEmpty() && myValue == null || myValue.isEmpty();
 	}
 
 }

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

@@ -13,6 +13,8 @@ public @interface ResourceDef {
 
 	String name();
 
+	String id() default "";
+	
 	String profile() default "";
 	
 	int identifierOrder() default ORDER_NOT_SPECIFIED;

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/AddressDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Address") 
-public class AddressDt extends BaseElement implements ICompositeDatatype  {
+public class AddressDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="use", type=CodeDt.class, order=0, min=0, max=1)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/AttachmentDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Attachment") 
-public class AttachmentDt extends BaseElement implements ICompositeDatatype  {
+public class AttachmentDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="contentType", type=CodeDt.class, order=0, min=1, max=1)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/CodeableConceptDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="CodeableConcept") 
-public class CodeableConceptDt extends BaseElement implements ICompositeDatatype  {
+public class CodeableConceptDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="coding", type=CodingDt.class, order=0, min=0, max=Child.MAX_UNLIMITED)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/CodingDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Coding") 
-public class CodingDt extends BaseElement implements ICompositeDatatype  {
+public class CodingDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="system", type=UriDt.class, order=0, min=0, max=1)	
@@ -83,7 +84,7 @@ public class CodingDt extends BaseElement implements ICompositeDatatype  {
 		shortDefinition="Set this coding was chosen from",
 		formalDefinition="The set of possible coded values this coding was chosen from or constrained by"
 	)
-	private ResourceReference myValueSet;
+	private ResourceReferenceDt myValueSet;
 	
 
 	@Override
@@ -316,9 +317,9 @@ public class CodingDt extends BaseElement implements ICompositeDatatype  {
      * The set of possible coded values this coding was chosen from or constrained by
      * </p> 
 	 */
-	public ResourceReference getValueSet() {  
+	public ResourceReferenceDt getValueSet() {  
 		if (myValueSet == null) {
-			myValueSet = new ResourceReference();
+			myValueSet = new ResourceReferenceDt();
 		}
 		return myValueSet;
 	}
@@ -331,7 +332,7 @@ public class CodingDt extends BaseElement implements ICompositeDatatype  {
      * The set of possible coded values this coding was chosen from or constrained by
      * </p> 
 	 */
-	public void setValueSet(ResourceReference theValue) {
+	public void setValueSet(ResourceReferenceDt theValue) {
 		myValueSet = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/ContactDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Contact") 
-public class ContactDt extends BaseElement implements ICompositeDatatype  {
+public class ContactDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="system", type=CodeDt.class, order=0, min=0, max=1)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/HumanNameDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="HumanName") 
-public class HumanNameDt extends BaseElement implements ICompositeDatatype  {
+public class HumanNameDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="use", type=CodeDt.class, order=0, min=0, max=1)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/IdentifierDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Identifier") 
-public class IdentifierDt extends BaseElement implements ICompositeDatatype  , IQueryParameterType {
+public class IdentifierDt 
+        extends  BaseElement         implements ICompositeDatatype  , IQueryParameterType {
 
 	/**
 	 * Creates a new identifier
@@ -97,7 +98,7 @@ public class IdentifierDt extends BaseElement implements ICompositeDatatype  , I
 		shortDefinition="Organization that issued id (may be just text)",
 		formalDefinition="Organization that issued/manages the identifier"
 	)
-	private ResourceReference myAssigner;
+	private ResourceReferenceDt myAssigner;
 	
 
 	@Override
@@ -318,9 +319,9 @@ public class IdentifierDt extends BaseElement implements ICompositeDatatype  , I
      * Organization that issued/manages the identifier
      * </p> 
 	 */
-	public ResourceReference getAssigner() {  
+	public ResourceReferenceDt getAssigner() {  
 		if (myAssigner == null) {
-			myAssigner = new ResourceReference();
+			myAssigner = new ResourceReferenceDt();
 		}
 		return myAssigner;
 	}
@@ -333,7 +334,7 @@ public class IdentifierDt extends BaseElement implements ICompositeDatatype  , I
      * Organization that issued/manages the identifier
      * </p> 
 	 */
-	public void setAssigner(ResourceReference theValue) {
+	public void setAssigner(ResourceReferenceDt theValue) {
 		myAssigner = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/PeriodDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Period") 
-public class PeriodDt extends BaseElement implements ICompositeDatatype  {
+public class PeriodDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="start", type=DateTimeDt.class, order=0, min=0, max=1)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/QuantityDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Quantity") 
-public class QuantityDt extends BaseElement implements ICompositeDatatype  {
+public class QuantityDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="value", type=DecimalDt.class, order=0, min=0, max=1)	
@@ -120,7 +121,7 @@ public class QuantityDt extends BaseElement implements ICompositeDatatype  {
      * The value of the measured amount. The value includes an implicit precision in the presentation of the value
      * </p> 
 	 */
-	public void setValue( long theValue) {
+	public void setValue( java.math.BigDecimal theValue) {
 		myValue = new DecimalDt(theValue); 
 	}
 
@@ -144,7 +145,7 @@ public class QuantityDt extends BaseElement implements ICompositeDatatype  {
      * The value of the measured amount. The value includes an implicit precision in the presentation of the value
      * </p> 
 	 */
-	public void setValue( java.math.BigDecimal theValue) {
+	public void setValue( long theValue) {
 		myValue = new DecimalDt(theValue); 
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/RangeDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Range") 
-public class RangeDt extends BaseElement implements ICompositeDatatype  {
+public class RangeDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="low", type=QuantityDt.class, order=0, min=0, max=1)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/RatioDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Ratio") 
-public class RatioDt extends BaseElement implements ICompositeDatatype  {
+public class RatioDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="numerator", type=QuantityDt.class, order=0, min=0, max=1)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/ResourceReferenceDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="ResourceReference") 
-public class ResourceReferenceDt extends BaseElement implements ICompositeDatatype  {
+public class ResourceReferenceDt 
+        extends  BaseResourceReference         implements ICompositeDatatype  {
 
 
 	@Child(name="reference", type=StringDt.class, order=0, min=0, max=1)	

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/SampledDataDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="SampledData") 
-public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
+public class SampledDataDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="origin", type=QuantityDt.class, order=0, min=1, max=1)	
@@ -165,7 +166,7 @@ public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
      * The length of time between sampling times, measured in milliseconds
      * </p> 
 	 */
-	public void setPeriod( long theValue) {
+	public void setPeriod( java.math.BigDecimal theValue) {
 		myPeriod = new DecimalDt(theValue); 
 	}
 
@@ -189,7 +190,7 @@ public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
      * The length of time between sampling times, measured in milliseconds
      * </p> 
 	 */
-	public void setPeriod( java.math.BigDecimal theValue) {
+	public void setPeriod( long theValue) {
 		myPeriod = new DecimalDt(theValue); 
 	}
 
@@ -232,7 +233,7 @@ public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
      * A correction factor that is applied to the sampled data points before they are added to the origin
      * </p> 
 	 */
-	public void setFactor( long theValue) {
+	public void setFactor( java.math.BigDecimal theValue) {
 		myFactor = new DecimalDt(theValue); 
 	}
 
@@ -256,7 +257,7 @@ public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
      * A correction factor that is applied to the sampled data points before they are added to the origin
      * </p> 
 	 */
-	public void setFactor( java.math.BigDecimal theValue) {
+	public void setFactor( long theValue) {
 		myFactor = new DecimalDt(theValue); 
 	}
 
@@ -299,7 +300,7 @@ public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
      * The lower limit of detection of the measured points. This is needed if any of the data points have the value \"L\" (lower than detection limit)
      * </p> 
 	 */
-	public void setLowerLimit( long theValue) {
+	public void setLowerLimit( java.math.BigDecimal theValue) {
 		myLowerLimit = new DecimalDt(theValue); 
 	}
 
@@ -323,7 +324,7 @@ public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
      * The lower limit of detection of the measured points. This is needed if any of the data points have the value \"L\" (lower than detection limit)
      * </p> 
 	 */
-	public void setLowerLimit( java.math.BigDecimal theValue) {
+	public void setLowerLimit( long theValue) {
 		myLowerLimit = new DecimalDt(theValue); 
 	}
 
@@ -366,7 +367,7 @@ public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
      * The upper limit of detection of the measured points. This is needed if any of the data points have the value \"U\" (higher than detection limit)
      * </p> 
 	 */
-	public void setUpperLimit( long theValue) {
+	public void setUpperLimit( java.math.BigDecimal theValue) {
 		myUpperLimit = new DecimalDt(theValue); 
 	}
 
@@ -390,7 +391,7 @@ public class SampledDataDt extends BaseElement implements ICompositeDatatype  {
      * The upper limit of detection of the measured points. This is needed if any of the data points have the value \"U\" (higher than detection limit)
      * </p> 
 	 */
-	public void setUpperLimit( java.math.BigDecimal theValue) {
+	public void setUpperLimit( long theValue) {
 		myUpperLimit = new DecimalDt(theValue); 
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/ScheduleDt.java

@@ -38,7 +38,8 @@ import ca.uhn.fhir.model.dstu.resource.*;
  * </p> 
  */
 @DatatypeDef(name="Schedule") 
-public class ScheduleDt extends BaseElement implements ICompositeDatatype  {
+public class ScheduleDt 
+        extends  BaseElement         implements ICompositeDatatype  {
 
 
 	@Child(name="event", type=PeriodDt.class, order=0, min=0, max=Child.MAX_UNLIMITED)	
@@ -319,7 +320,7 @@ public class ScheduleDt extends BaseElement implements ICompositeDatatype  {
      * How long each repetition should last
      * </p> 
 	 */
-	public void setDuration( long theValue) {
+	public void setDuration( java.math.BigDecimal theValue) {
 		myDuration = new DecimalDt(theValue); 
 	}
 
@@ -343,7 +344,7 @@ public class ScheduleDt extends BaseElement implements ICompositeDatatype  {
      * How long each repetition should last
      * </p> 
 	 */
-	public void setDuration( java.math.BigDecimal theValue) {
+	public void setDuration( long theValue) {
 		myDuration = new DecimalDt(theValue); 
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Device.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * Allows institutions to track their devices. 
  * </p> 
  */
-@ResourceDef(name="Device", profile="http://hl7.org/fhir/profiles/Device")
+@ResourceDef(name="Device", profile="http://hl7.org/fhir/profiles/Device", id="device")
 public class Device extends BaseResource implements IResource {
 
 	/**
@@ -184,7 +184,7 @@ public class Device extends BaseResource implements IResource {
 		shortDefinition="Organization responsible for device",
 		formalDefinition="An organization that is responsible for the provision and ongoing maintenance of the device"
 	)
-	private ResourceReference myOwner;
+	private ResourceReferenceDt myOwner;
 	
 	@Child(name="location", order=9, min=0, max=1, type={
 		Location.class,
@@ -193,7 +193,7 @@ public class Device extends BaseResource implements IResource {
 		shortDefinition="Where the resource is found",
 		formalDefinition="The resource may be found in a literal location (i.e. GPS coordinates), a logical place (i.e. \"in/with the patient\"), or a coded location"
 	)
-	private ResourceReference myLocation;
+	private ResourceReferenceDt myLocation;
 	
 	@Child(name="patient", order=10, min=0, max=1, type={
 		Patient.class,
@@ -202,7 +202,7 @@ public class Device extends BaseResource implements IResource {
 		shortDefinition="If the resource is affixed to a person",
 		formalDefinition="Patient information, if the resource is affixed to a person"
 	)
-	private ResourceReference myPatient;
+	private ResourceReferenceDt myPatient;
 	
 	@Child(name="contact", type=ContactDt.class, order=11, min=0, max=Child.MAX_UNLIMITED)	
 	@Description(
@@ -579,9 +579,9 @@ public class Device extends BaseResource implements IResource {
      * An organization that is responsible for the provision and ongoing maintenance of the device
      * </p> 
 	 */
-	public ResourceReference getOwner() {  
+	public ResourceReferenceDt getOwner() {  
 		if (myOwner == null) {
-			myOwner = new ResourceReference();
+			myOwner = new ResourceReferenceDt();
 		}
 		return myOwner;
 	}
@@ -594,7 +594,7 @@ public class Device extends BaseResource implements IResource {
      * An organization that is responsible for the provision and ongoing maintenance of the device
      * </p> 
 	 */
-	public void setOwner(ResourceReference theValue) {
+	public void setOwner(ResourceReferenceDt theValue) {
 		myOwner = theValue;
 	}
 
@@ -610,9 +610,9 @@ public class Device extends BaseResource implements IResource {
      * The resource may be found in a literal location (i.e. GPS coordinates), a logical place (i.e. \"in/with the patient\"), or a coded location
      * </p> 
 	 */
-	public ResourceReference getLocation() {  
+	public ResourceReferenceDt getLocation() {  
 		if (myLocation == null) {
-			myLocation = new ResourceReference();
+			myLocation = new ResourceReferenceDt();
 		}
 		return myLocation;
 	}
@@ -625,7 +625,7 @@ public class Device extends BaseResource implements IResource {
      * The resource may be found in a literal location (i.e. GPS coordinates), a logical place (i.e. \"in/with the patient\"), or a coded location
      * </p> 
 	 */
-	public void setLocation(ResourceReference theValue) {
+	public void setLocation(ResourceReferenceDt theValue) {
 		myLocation = theValue;
 	}
 
@@ -641,9 +641,9 @@ public class Device extends BaseResource implements IResource {
      * Patient information, if the resource is affixed to a person
      * </p> 
 	 */
-	public ResourceReference getPatient() {  
+	public ResourceReferenceDt getPatient() {  
 		if (myPatient == null) {
-			myPatient = new ResourceReference();
+			myPatient = new ResourceReferenceDt();
 		}
 		return myPatient;
 	}
@@ -656,7 +656,7 @@ public class Device extends BaseResource implements IResource {
      * Patient information, if the resource is affixed to a person
      * </p> 
 	 */
-	public void setPatient(ResourceReference theValue) {
+	public void setPatient(ResourceReferenceDt theValue) {
 		myPatient = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Group.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * 
  * </p> 
  */
-@ResourceDef(name="Group", profile="http://hl7.org/fhir/profiles/Group")
+@ResourceDef(name="Group", profile="http://hl7.org/fhir/profiles/Group", id="group")
 public class Group extends BaseResource implements IResource {
 
 	/**
@@ -191,7 +191,7 @@ public class Group extends BaseResource implements IResource {
 		shortDefinition="Who is in group",
 		formalDefinition="Identifies the resource instances that are members of the group."
 	)
-	private List<ResourceReference> myMember;
+	private List<ResourceReferenceDt> myMember;
 	
 
 	@Override
@@ -487,7 +487,7 @@ public class Group extends BaseResource implements IResource {
      * Identifies the resource instances that are members of the group.
      * </p> 
 	 */
-	public List<ResourceReference> getMember() {  
+	public List<ResourceReferenceDt> getMember() {  
 		return myMember;
 	}
 
@@ -499,7 +499,7 @@ public class Group extends BaseResource implements IResource {
      * Identifies the resource instances that are members of the group.
      * </p> 
 	 */
-	public void setMember(List<ResourceReference> theValue) {
+	public void setMember(List<ResourceReferenceDt> theValue) {
 		myMember = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Location.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * 
  * </p> 
  */
-@ResourceDef(name="Location", profile="http://hl7.org/fhir/profiles/Location")
+@ResourceDef(name="Location", profile="http://hl7.org/fhir/profiles/Location", id="location")
 public class Location extends BaseResource implements IResource {
 
 	/**
@@ -184,7 +184,7 @@ public class Location extends BaseResource implements IResource {
 		shortDefinition="The organization that is responsible for the provisioning and upkeep of the location",
 		formalDefinition=""
 	)
-	private ResourceReference myManagingOrganization;
+	private ResourceReferenceDt myManagingOrganization;
 	
 	@Child(name="status", type=CodeDt.class, order=9, min=0, max=1)	
 	@Description(
@@ -200,7 +200,7 @@ public class Location extends BaseResource implements IResource {
 		shortDefinition="Another Location which this Location is physically part of",
 		formalDefinition=""
 	)
-	private ResourceReference myPartOf;
+	private ResourceReferenceDt myPartOf;
 	
 	@Child(name="mode", type=CodeDt.class, order=11, min=0, max=1)	
 	@Description(
@@ -522,9 +522,9 @@ public class Location extends BaseResource implements IResource {
      * 
      * </p> 
 	 */
-	public ResourceReference getManagingOrganization() {  
+	public ResourceReferenceDt getManagingOrganization() {  
 		if (myManagingOrganization == null) {
-			myManagingOrganization = new ResourceReference();
+			myManagingOrganization = new ResourceReferenceDt();
 		}
 		return myManagingOrganization;
 	}
@@ -537,7 +537,7 @@ public class Location extends BaseResource implements IResource {
      * 
      * </p> 
 	 */
-	public void setManagingOrganization(ResourceReference theValue) {
+	public void setManagingOrganization(ResourceReferenceDt theValue) {
 		myManagingOrganization = theValue;
 	}
 
@@ -596,9 +596,9 @@ public class Location extends BaseResource implements IResource {
      * 
      * </p> 
 	 */
-	public ResourceReference getPartOf() {  
+	public ResourceReferenceDt getPartOf() {  
 		if (myPartOf == null) {
-			myPartOf = new ResourceReference();
+			myPartOf = new ResourceReferenceDt();
 		}
 		return myPartOf;
 	}
@@ -611,7 +611,7 @@ public class Location extends BaseResource implements IResource {
      * 
      * </p> 
 	 */
-	public void setPartOf(ResourceReference theValue) {
+	public void setPartOf(ResourceReferenceDt theValue) {
 		myPartOf = theValue;
 	}
 
@@ -736,7 +736,7 @@ public class Location extends BaseResource implements IResource {
      * Longitude. The value domain and the interpretation are the same as for the text of the longitude element in KML (see notes below)
      * </p> 
 	 */
-	public void setLongitude( long theValue) {
+	public void setLongitude( java.math.BigDecimal theValue) {
 		myLongitude = new DecimalDt(theValue); 
 	}
 
@@ -760,7 +760,7 @@ public class Location extends BaseResource implements IResource {
      * Longitude. The value domain and the interpretation are the same as for the text of the longitude element in KML (see notes below)
      * </p> 
 	 */
-	public void setLongitude( java.math.BigDecimal theValue) {
+	public void setLongitude( long theValue) {
 		myLongitude = new DecimalDt(theValue); 
 	}
 
@@ -803,7 +803,7 @@ public class Location extends BaseResource implements IResource {
      * Latitude. The value domain and the interpretation are the same as for the text of the latitude element in KML (see notes below)
      * </p> 
 	 */
-	public void setLatitude( long theValue) {
+	public void setLatitude( java.math.BigDecimal theValue) {
 		myLatitude = new DecimalDt(theValue); 
 	}
 
@@ -827,7 +827,7 @@ public class Location extends BaseResource implements IResource {
      * Latitude. The value domain and the interpretation are the same as for the text of the latitude element in KML (see notes below)
      * </p> 
 	 */
-	public void setLatitude( java.math.BigDecimal theValue) {
+	public void setLatitude( long theValue) {
 		myLatitude = new DecimalDt(theValue); 
 	}
 
@@ -870,7 +870,7 @@ public class Location extends BaseResource implements IResource {
      * Altitude. The value domain and the interpretation are the same as for the text of the altitude element in KML (see notes below)
      * </p> 
 	 */
-	public void setAltitude( long theValue) {
+	public void setAltitude( java.math.BigDecimal theValue) {
 		myAltitude = new DecimalDt(theValue); 
 	}
 
@@ -894,7 +894,7 @@ public class Location extends BaseResource implements IResource {
      * Altitude. The value domain and the interpretation are the same as for the text of the altitude element in KML (see notes below)
      * </p> 
 	 */
-	public void setAltitude( java.math.BigDecimal theValue) {
+	public void setAltitude( long theValue) {
 		myAltitude = new DecimalDt(theValue); 
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Medication.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * 
  * </p> 
  */
-@ResourceDef(name="Medication", profile="http://hl7.org/fhir/profiles/Medication")
+@ResourceDef(name="Medication", profile="http://hl7.org/fhir/profiles/Medication", id="medication")
 public class Medication extends BaseResource implements IResource {
 
 	/**
@@ -139,7 +139,7 @@ public class Medication extends BaseResource implements IResource {
 		shortDefinition="Manufacturer of the item",
 		formalDefinition="Describes the details of the manufacturer"
 	)
-	private ResourceReference myManufacturer;
+	private ResourceReferenceDt myManufacturer;
 	
 	@Child(name="kind", type=CodeDt.class, order=4, min=0, max=1)	
 	@Description(
@@ -295,9 +295,9 @@ public class Medication extends BaseResource implements IResource {
      * Describes the details of the manufacturer
      * </p> 
 	 */
-	public ResourceReference getManufacturer() {  
+	public ResourceReferenceDt getManufacturer() {  
 		if (myManufacturer == null) {
-			myManufacturer = new ResourceReference();
+			myManufacturer = new ResourceReferenceDt();
 		}
 		return myManufacturer;
 	}
@@ -310,7 +310,7 @@ public class Medication extends BaseResource implements IResource {
      * Describes the details of the manufacturer
      * </p> 
 	 */
-	public void setManufacturer(ResourceReference theValue) {
+	public void setManufacturer(ResourceReferenceDt theValue) {
 		myManufacturer = theValue;
 	}
 
@@ -561,7 +561,7 @@ public class Medication extends BaseResource implements IResource {
 		shortDefinition="The product contained",
 		formalDefinition="The actual ingredient - either a substance (simple ingredient) or another medication"
 	)
-	private ResourceReference myItem;
+	private ResourceReferenceDt myItem;
 	
 	@Child(name="amount", type=RatioDt.class, order=1, min=0, max=1)	
 	@Description(
@@ -586,7 +586,7 @@ public class Medication extends BaseResource implements IResource {
      * The actual ingredient - either a substance (simple ingredient) or another medication
      * </p> 
 	 */
-	public ResourceReference getItem() {  
+	public ResourceReferenceDt getItem() {  
 		return myItem;
 	}
 
@@ -598,7 +598,7 @@ public class Medication extends BaseResource implements IResource {
      * The actual ingredient - either a substance (simple ingredient) or another medication
      * </p> 
 	 */
-	public void setItem(ResourceReference theValue) {
+	public void setItem(ResourceReferenceDt theValue) {
 		myItem = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Observation.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * Observations are a key aspect of healthcare.  This resource is used to capture those that do not require more sophisticated mechanisms.
  * </p> 
  */
-@ResourceDef(name="Observation", profile="http://hl7.org/fhir/profiles/Observation")
+@ResourceDef(name="Observation", profile="http://hl7.org/fhir/profiles/Observation", id="observation")
 public class Observation extends BaseResource implements IResource {
 
 	/**
@@ -289,7 +289,7 @@ public class Observation extends BaseResource implements IResource {
 		shortDefinition="Who and/or what this is about",
 		formalDefinition="The thing the observation is being made about"
 	)
-	private ResourceReference mySubject;
+	private ResourceReferenceDt mySubject;
 	
 	@Child(name="specimen", order=12, min=0, max=1, type={
 		Specimen.class,
@@ -298,7 +298,7 @@ public class Observation extends BaseResource implements IResource {
 		shortDefinition="Specimen used for this observation",
 		formalDefinition="The specimen that was used when this observation was made"
 	)
-	private ResourceReference mySpecimen;
+	private ResourceReferenceDt mySpecimen;
 	
 	@Child(name="performer", order=13, min=0, max=Child.MAX_UNLIMITED, type={
 		Practitioner.class,
@@ -309,7 +309,7 @@ public class Observation extends BaseResource implements IResource {
 		shortDefinition="Who did the observation",
 		formalDefinition="Who was responsible for asserting the observed value as \"true\""
 	)
-	private List<ResourceReference> myPerformer;
+	private List<ResourceReferenceDt> myPerformer;
 	
 	@Child(name="referenceRange", order=14, min=0, max=Child.MAX_UNLIMITED)	
 	@Description(
@@ -748,7 +748,7 @@ public class Observation extends BaseResource implements IResource {
      * The thing the observation is being made about
      * </p> 
 	 */
-	public ResourceReference getSubject() {  
+	public ResourceReferenceDt getSubject() {  
 		return mySubject;
 	}
 
@@ -760,7 +760,7 @@ public class Observation extends BaseResource implements IResource {
      * The thing the observation is being made about
      * </p> 
 	 */
-	public void setSubject(ResourceReference theValue) {
+	public void setSubject(ResourceReferenceDt theValue) {
 		mySubject = theValue;
 	}
 
@@ -776,9 +776,9 @@ public class Observation extends BaseResource implements IResource {
      * The specimen that was used when this observation was made
      * </p> 
 	 */
-	public ResourceReference getSpecimen() {  
+	public ResourceReferenceDt getSpecimen() {  
 		if (mySpecimen == null) {
-			mySpecimen = new ResourceReference();
+			mySpecimen = new ResourceReferenceDt();
 		}
 		return mySpecimen;
 	}
@@ -791,7 +791,7 @@ public class Observation extends BaseResource implements IResource {
      * The specimen that was used when this observation was made
      * </p> 
 	 */
-	public void setSpecimen(ResourceReference theValue) {
+	public void setSpecimen(ResourceReferenceDt theValue) {
 		mySpecimen = theValue;
 	}
 
@@ -807,7 +807,7 @@ public class Observation extends BaseResource implements IResource {
      * Who was responsible for asserting the observed value as \"true\"
      * </p> 
 	 */
-	public List<ResourceReference> getPerformer() {  
+	public List<ResourceReferenceDt> getPerformer() {  
 		return myPerformer;
 	}
 
@@ -819,7 +819,7 @@ public class Observation extends BaseResource implements IResource {
      * Who was responsible for asserting the observed value as \"true\"
      * </p> 
 	 */
-	public void setPerformer(List<ResourceReference> theValue) {
+	public void setPerformer(List<ResourceReferenceDt> theValue) {
 		myPerformer = theValue;
 	}
 
@@ -1111,7 +1111,7 @@ public class Observation extends BaseResource implements IResource {
 		shortDefinition="Observation that is related to this one",
 		formalDefinition="A reference to the observation that is related to this observation"
 	)
-	private ResourceReference myTarget;
+	private ResourceReferenceDt myTarget;
 	
 
 	@Override
@@ -1172,9 +1172,9 @@ public class Observation extends BaseResource implements IResource {
      * A reference to the observation that is related to this observation
      * </p> 
 	 */
-	public ResourceReference getTarget() {  
+	public ResourceReferenceDt getTarget() {  
 		if (myTarget == null) {
-			myTarget = new ResourceReference();
+			myTarget = new ResourceReferenceDt();
 		}
 		return myTarget;
 	}
@@ -1187,7 +1187,7 @@ public class Observation extends BaseResource implements IResource {
      * A reference to the observation that is related to this observation
      * </p> 
 	 */
-	public void setTarget(ResourceReference theValue) {
+	public void setTarget(ResourceReferenceDt theValue) {
 		myTarget = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Organization.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * 
  * </p> 
  */
-@ResourceDef(name="Organization", profile="http://hl7.org/fhir/profiles/Organization")
+@ResourceDef(name="Organization", profile="http://hl7.org/fhir/profiles/Organization", id="organization")
 public class Organization extends BaseResource implements IResource {
 
 	/**
@@ -153,7 +153,7 @@ public class Organization extends BaseResource implements IResource {
 		shortDefinition="The organization of which this organization forms a part",
 		formalDefinition="The organization of which this organization forms a part"
 	)
-	private ResourceReference myPartOf;
+	private ResourceReferenceDt myPartOf;
 	
 	@Child(name="contact", order=6, min=0, max=Child.MAX_UNLIMITED)	
 	@Description(
@@ -169,7 +169,7 @@ public class Organization extends BaseResource implements IResource {
 		shortDefinition="Location(s) the organization uses to provide services",
 		formalDefinition="Location(s) the organization uses to provide services"
 	)
-	private List<ResourceReference> myLocation;
+	private List<ResourceReferenceDt> myLocation;
 	
 	@Child(name="active", type=BooleanDt.class, order=8, min=0, max=1)	
 	@Description(
@@ -412,9 +412,9 @@ public class Organization extends BaseResource implements IResource {
      * The organization of which this organization forms a part
      * </p> 
 	 */
-	public ResourceReference getPartOf() {  
+	public ResourceReferenceDt getPartOf() {  
 		if (myPartOf == null) {
-			myPartOf = new ResourceReference();
+			myPartOf = new ResourceReferenceDt();
 		}
 		return myPartOf;
 	}
@@ -427,7 +427,7 @@ public class Organization extends BaseResource implements IResource {
      * The organization of which this organization forms a part
      * </p> 
 	 */
-	public void setPartOf(ResourceReference theValue) {
+	public void setPartOf(ResourceReferenceDt theValue) {
 		myPartOf = theValue;
 	}
 
@@ -487,9 +487,9 @@ public class Organization extends BaseResource implements IResource {
      * Location(s) the organization uses to provide services
      * </p> 
 	 */
-	public List<ResourceReference> getLocation() {  
+	public List<ResourceReferenceDt> getLocation() {  
 		if (myLocation == null) {
-			myLocation = new ArrayList<ResourceReference>();
+			myLocation = new ArrayList<ResourceReferenceDt>();
 		}
 		return myLocation;
 	}
@@ -502,7 +502,7 @@ public class Organization extends BaseResource implements IResource {
      * Location(s) the organization uses to provide services
      * </p> 
 	 */
-	public void setLocation(List<ResourceReference> theValue) {
+	public void setLocation(List<ResourceReferenceDt> theValue) {
 		myLocation = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Patient.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * Tracking patient is the center of the healthcare process
  * </p> 
  */
-@ResourceDef(name="Patient", profile="http://hl7.org/fhir/profiles/Patient")
+@ResourceDef(name="Patient", profile="http://hl7.org/fhir/profiles/Patient", id="patient")
 public class Patient extends BaseResource implements IResource {
 
 	/**
@@ -296,7 +296,7 @@ public class Patient extends BaseResource implements IResource {
 		shortDefinition="Patient's nominated care provider",
 		formalDefinition="Patient's nominated care provider"
 	)
-	private List<ResourceReference> myCareProvider;
+	private List<ResourceReferenceDt> myCareProvider;
 	
 	@Child(name="managingOrganization", order=14, min=0, max=1, type={
 		Organization.class,
@@ -305,7 +305,7 @@ public class Patient extends BaseResource implements IResource {
 		shortDefinition="Organization that is the custodian of the patient record",
 		formalDefinition="Organization that is the custodian of the patient record"
 	)
-	private ResourceReference myManagingOrganization;
+	private ResourceReferenceDt myManagingOrganization;
 	
 	@Child(name="link", order=15, min=0, max=Child.MAX_UNLIMITED)	
 	@Description(
@@ -873,7 +873,7 @@ public class Patient extends BaseResource implements IResource {
      * Patient's nominated care provider
      * </p> 
 	 */
-	public List<ResourceReference> getCareProvider() {  
+	public List<ResourceReferenceDt> getCareProvider() {  
 		return myCareProvider;
 	}
 
@@ -885,7 +885,7 @@ public class Patient extends BaseResource implements IResource {
      * Patient's nominated care provider
      * </p> 
 	 */
-	public void setCareProvider(List<ResourceReference> theValue) {
+	public void setCareProvider(List<ResourceReferenceDt> theValue) {
 		myCareProvider = theValue;
 	}
 
@@ -901,9 +901,9 @@ public class Patient extends BaseResource implements IResource {
      * Organization that is the custodian of the patient record
      * </p> 
 	 */
-	public ResourceReference getManagingOrganization() {  
+	public ResourceReferenceDt getManagingOrganization() {  
 		if (myManagingOrganization == null) {
-			myManagingOrganization = new ResourceReference();
+			myManagingOrganization = new ResourceReferenceDt();
 		}
 		return myManagingOrganization;
 	}
@@ -916,7 +916,7 @@ public class Patient extends BaseResource implements IResource {
      * Organization that is the custodian of the patient record
      * </p> 
 	 */
-	public void setManagingOrganization(ResourceReference theValue) {
+	public void setManagingOrganization(ResourceReferenceDt theValue) {
 		myManagingOrganization = theValue;
 	}
 
@@ -1062,7 +1062,7 @@ public class Patient extends BaseResource implements IResource {
 		shortDefinition="Organization that is associated with the contact",
 		formalDefinition="Organization on behalf of which the contact is acting or for which the contact is working."
 	)
-	private ResourceReference myOrganization;
+	private ResourceReferenceDt myOrganization;
 	
 
 	@Override
@@ -1273,9 +1273,9 @@ public class Patient extends BaseResource implements IResource {
      * Organization on behalf of which the contact is acting or for which the contact is working.
      * </p> 
 	 */
-	public ResourceReference getOrganization() {  
+	public ResourceReferenceDt getOrganization() {  
 		if (myOrganization == null) {
-			myOrganization = new ResourceReference();
+			myOrganization = new ResourceReferenceDt();
 		}
 		return myOrganization;
 	}
@@ -1288,7 +1288,7 @@ public class Patient extends BaseResource implements IResource {
      * Organization on behalf of which the contact is acting or for which the contact is working.
      * </p> 
 	 */
-	public void setOrganization(ResourceReference theValue) {
+	public void setOrganization(ResourceReferenceDt theValue) {
 		myOrganization = theValue;
 	}
 
@@ -1463,7 +1463,7 @@ public class Patient extends BaseResource implements IResource {
 		shortDefinition="The other patient resource that the link refers to",
 		formalDefinition="The other patient resource that the link refers to"
 	)
-	private ResourceReference myOther;
+	private ResourceReferenceDt myOther;
 	
 	@Child(name="type", type=CodeDt.class, order=1, min=1, max=1)	
 	@Description(
@@ -1488,9 +1488,9 @@ public class Patient extends BaseResource implements IResource {
      * The other patient resource that the link refers to
      * </p> 
 	 */
-	public ResourceReference getOther() {  
+	public ResourceReferenceDt getOther() {  
 		if (myOther == null) {
-			myOther = new ResourceReference();
+			myOther = new ResourceReferenceDt();
 		}
 		return myOther;
 	}
@@ -1503,7 +1503,7 @@ public class Patient extends BaseResource implements IResource {
      * The other patient resource that the link refers to
      * </p> 
 	 */
-	public void setOther(ResourceReference theValue) {
+	public void setOther(ResourceReferenceDt theValue) {
 		myOther = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Practitioner.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * Need to track doctors, staff, locums etc. for both healthcare practitioners, funders, etc.
  * </p> 
  */
-@ResourceDef(name="Practitioner", profile="http://hl7.org/fhir/profiles/Practitioner")
+@ResourceDef(name="Practitioner", profile="http://hl7.org/fhir/profiles/Practitioner", id="practitioner")
 public class Practitioner extends BaseResource implements IResource {
 
 	/**
@@ -187,7 +187,7 @@ public class Practitioner extends BaseResource implements IResource {
 		shortDefinition="The represented organization",
 		formalDefinition="The organization that the practitioner represents"
 	)
-	private ResourceReference myOrganization;
+	private ResourceReferenceDt myOrganization;
 	
 	@Child(name="role", type=CodeableConceptDt.class, order=8, min=0, max=Child.MAX_UNLIMITED)	
 	@Description(
@@ -217,7 +217,7 @@ public class Practitioner extends BaseResource implements IResource {
 		shortDefinition="The location(s) at which this practitioner provides care",
 		formalDefinition="The location(s) at which this practitioner provides care"
 	)
-	private List<ResourceReference> myLocation;
+	private List<ResourceReferenceDt> myLocation;
 	
 	@Child(name="qualification", order=12, min=0, max=Child.MAX_UNLIMITED)	
 	@Description(
@@ -541,9 +541,9 @@ public class Practitioner extends BaseResource implements IResource {
      * The organization that the practitioner represents
      * </p> 
 	 */
-	public ResourceReference getOrganization() {  
+	public ResourceReferenceDt getOrganization() {  
 		if (myOrganization == null) {
-			myOrganization = new ResourceReference();
+			myOrganization = new ResourceReferenceDt();
 		}
 		return myOrganization;
 	}
@@ -556,7 +556,7 @@ public class Practitioner extends BaseResource implements IResource {
      * The organization that the practitioner represents
      * </p> 
 	 */
-	public void setOrganization(ResourceReference theValue) {
+	public void setOrganization(ResourceReferenceDt theValue) {
 		myOrganization = theValue;
 	}
 
@@ -715,9 +715,9 @@ public class Practitioner extends BaseResource implements IResource {
      * The location(s) at which this practitioner provides care
      * </p> 
 	 */
-	public List<ResourceReference> getLocation() {  
+	public List<ResourceReferenceDt> getLocation() {  
 		if (myLocation == null) {
-			myLocation = new ArrayList<ResourceReference>();
+			myLocation = new ArrayList<ResourceReferenceDt>();
 		}
 		return myLocation;
 	}
@@ -730,7 +730,7 @@ public class Practitioner extends BaseResource implements IResource {
      * The location(s) at which this practitioner provides care
      * </p> 
 	 */
-	public void setLocation(List<ResourceReference> theValue) {
+	public void setLocation(List<ResourceReferenceDt> theValue) {
 		myLocation = theValue;
 	}
 
@@ -856,7 +856,7 @@ public class Practitioner extends BaseResource implements IResource {
 		shortDefinition="Organization that regulates and issues the qualification",
 		formalDefinition="Organization that regulates and issues the qualification"
 	)
-	private ResourceReference myIssuer;
+	private ResourceReferenceDt myIssuer;
 	
 
 	@Override
@@ -936,9 +936,9 @@ public class Practitioner extends BaseResource implements IResource {
      * Organization that regulates and issues the qualification
      * </p> 
 	 */
-	public ResourceReference getIssuer() {  
+	public ResourceReferenceDt getIssuer() {  
 		if (myIssuer == null) {
-			myIssuer = new ResourceReference();
+			myIssuer = new ResourceReferenceDt();
 		}
 		return myIssuer;
 	}
@@ -951,7 +951,7 @@ public class Practitioner extends BaseResource implements IResource {
      * Organization that regulates and issues the qualification
      * </p> 
 	 */
-	public void setIssuer(ResourceReference theValue) {
+	public void setIssuer(ResourceReferenceDt theValue) {
 		myIssuer = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Profile.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * 
  * </p> 
  */
-@ResourceDef(name="Profile", profile="http://hl7.org/fhir/profiles/Profile")
+@ResourceDef(name="Profile", profile="http://hl7.org/fhir/profiles/Profile", id="profile")
 public class Profile extends BaseResource implements IResource {
 
 	/**

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Specimen.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * 
  * </p> 
  */
-@ResourceDef(name="Specimen", profile="http://hl7.org/fhir/profiles/Specimen")
+@ResourceDef(name="Specimen", profile="http://hl7.org/fhir/profiles/Specimen", id="specimen")
 public class Specimen extends BaseResource implements IResource {
 
 	/**
@@ -82,7 +82,7 @@ public class Specimen extends BaseResource implements IResource {
 		shortDefinition="Where the specimen came from. This may be the patient(s) or from the environment or  a device",
 		formalDefinition=""
 	)
-	private ResourceReference mySubject;
+	private ResourceReferenceDt mySubject;
 	
 	@Child(name="accessionIdentifier", type=IdentifierDt.class, order=4, min=0, max=1)	
 	@Description(
@@ -254,7 +254,7 @@ public class Specimen extends BaseResource implements IResource {
      * 
      * </p> 
 	 */
-	public ResourceReference getSubject() {  
+	public ResourceReferenceDt getSubject() {  
 		return mySubject;
 	}
 
@@ -266,7 +266,7 @@ public class Specimen extends BaseResource implements IResource {
      * 
      * </p> 
 	 */
-	public void setSubject(ResourceReference theValue) {
+	public void setSubject(ResourceReferenceDt theValue) {
 		mySubject = theValue;
 	}
 
@@ -502,7 +502,7 @@ public class Specimen extends BaseResource implements IResource {
 		shortDefinition="The subject of the relationship",
 		formalDefinition="The specimen resource that is the target of this relationship"
 	)
-	private List<ResourceReference> myTarget;
+	private List<ResourceReferenceDt> myTarget;
 	
 
 	@Override
@@ -563,9 +563,9 @@ public class Specimen extends BaseResource implements IResource {
      * The specimen resource that is the target of this relationship
      * </p> 
 	 */
-	public List<ResourceReference> getTarget() {  
+	public List<ResourceReferenceDt> getTarget() {  
 		if (myTarget == null) {
-			myTarget = new ArrayList<ResourceReference>();
+			myTarget = new ArrayList<ResourceReferenceDt>();
 		}
 		return myTarget;
 	}
@@ -578,7 +578,7 @@ public class Specimen extends BaseResource implements IResource {
      * The specimen resource that is the target of this relationship
      * </p> 
 	 */
-	public void setTarget(List<ResourceReference> theValue) {
+	public void setTarget(List<ResourceReferenceDt> theValue) {
 		myTarget = theValue;
 	}
 
@@ -606,7 +606,7 @@ public class Specimen extends BaseResource implements IResource {
 		shortDefinition="Who collected the specimen",
 		formalDefinition="Person who collected the specimen"
 	)
-	private ResourceReference myCollector;
+	private ResourceReferenceDt myCollector;
 	
 	@Child(name="comment", type=StringDt.class, order=1, min=0, max=Child.MAX_UNLIMITED)	
 	@Description(
@@ -662,9 +662,9 @@ public class Specimen extends BaseResource implements IResource {
      * Person who collected the specimen
      * </p> 
 	 */
-	public ResourceReference getCollector() {  
+	public ResourceReferenceDt getCollector() {  
 		if (myCollector == null) {
-			myCollector = new ResourceReference();
+			myCollector = new ResourceReferenceDt();
 		}
 		return myCollector;
 	}
@@ -677,7 +677,7 @@ public class Specimen extends BaseResource implements IResource {
      * Person who collected the specimen
      * </p> 
 	 */
-	public void setCollector(ResourceReference theValue) {
+	public void setCollector(ResourceReferenceDt theValue) {
 		myCollector = theValue;
 	}
 
@@ -911,7 +911,7 @@ public class Specimen extends BaseResource implements IResource {
 		shortDefinition="Material used in the processing step",
 		formalDefinition=""
 	)
-	private List<ResourceReference> myAdditive;
+	private List<ResourceReferenceDt> myAdditive;
 	
 
 	@Override
@@ -1015,9 +1015,9 @@ public class Specimen extends BaseResource implements IResource {
      * 
      * </p> 
 	 */
-	public List<ResourceReference> getAdditive() {  
+	public List<ResourceReferenceDt> getAdditive() {  
 		if (myAdditive == null) {
-			myAdditive = new ArrayList<ResourceReference>();
+			myAdditive = new ArrayList<ResourceReferenceDt>();
 		}
 		return myAdditive;
 	}
@@ -1030,7 +1030,7 @@ public class Specimen extends BaseResource implements IResource {
      * 
      * </p> 
 	 */
-	public void setAdditive(List<ResourceReference> theValue) {
+	public void setAdditive(List<ResourceReferenceDt> theValue) {
 		myAdditive = theValue;
 	}
 
@@ -1093,7 +1093,7 @@ public class Specimen extends BaseResource implements IResource {
 		shortDefinition="Additive associated with container",
 		formalDefinition="Additive associated with the container"
 	)
-	private ResourceReference myAdditive;
+	private ResourceReferenceDt myAdditive;
 	
 
 	@Override
@@ -1291,9 +1291,9 @@ public class Specimen extends BaseResource implements IResource {
      * Additive associated with the container
      * </p> 
 	 */
-	public ResourceReference getAdditive() {  
+	public ResourceReferenceDt getAdditive() {  
 		if (myAdditive == null) {
-			myAdditive = new ResourceReference();
+			myAdditive = new ResourceReferenceDt();
 		}
 		return myAdditive;
 	}
@@ -1306,7 +1306,7 @@ public class Specimen extends BaseResource implements IResource {
      * Additive associated with the container
      * </p> 
 	 */
-	public void setAdditive(ResourceReference theValue) {
+	public void setAdditive(ResourceReferenceDt theValue) {
 		myAdditive = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Substance.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * 
  * </p> 
  */
-@ResourceDef(name="Substance", profile="http://hl7.org/fhir/profiles/Substance")
+@ResourceDef(name="Substance", profile="http://hl7.org/fhir/profiles/Substance", id="substance")
 public class Substance extends BaseResource implements IResource {
 
 	/**
@@ -470,7 +470,7 @@ public class Substance extends BaseResource implements IResource {
 		shortDefinition="A component of the substance",
 		formalDefinition="Another substance that is a component of this substance"
 	)
-	private ResourceReference mySubstance;
+	private ResourceReferenceDt mySubstance;
 	
 
 	@Override
@@ -519,9 +519,9 @@ public class Substance extends BaseResource implements IResource {
      * Another substance that is a component of this substance
      * </p> 
 	 */
-	public ResourceReference getSubstance() {  
+	public ResourceReferenceDt getSubstance() {  
 		if (mySubstance == null) {
-			mySubstance = new ResourceReference();
+			mySubstance = new ResourceReferenceDt();
 		}
 		return mySubstance;
 	}
@@ -534,7 +534,7 @@ public class Substance extends BaseResource implements IResource {
      * Another substance that is a component of this substance
      * </p> 
 	 */
-	public void setSubstance(ResourceReference theValue) {
+	public void setSubstance(ResourceReferenceDt theValue) {
 		mySubstance = theValue;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/ValueSet.java

@@ -37,7 +37,7 @@ import ca.uhn.fhir.model.dstu.valueset.*;
  * 
  * </p> 
  */
-@ResourceDef(name="ValueSet", profile="http://hl7.org/fhir/profiles/ValueSet")
+@ResourceDef(name="ValueSet", profile="http://hl7.org/fhir/profiles/ValueSet", id="valueset")
 public class ValueSet extends BaseResource implements IResource {
 
 	/**

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

@@ -30,8 +30,9 @@ import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.IResourceBlock;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
-import ca.uhn.fhir.model.api.ResourceReference;
+import ca.uhn.fhir.model.api.BaseResourceReference;
 import ca.uhn.fhir.model.api.UndeclaredExtension;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
 
 class ParserState<T extends IElement> {
@@ -58,8 +59,8 @@ class ParserState<T extends IElement> {
 		myState.enteringNewElement(theNamespaceURI, theName);
 	}
 
-	public void enteringNewElementExtension(StartElement theElem, String theUrlAttr) {
+	public void enteringNewElementExtension(StartElement theElem, String theUrlAttr, boolean theIsModifier) {
-		myState.enteringNewElementExtension(theElem, theUrlAttr);
+		myState.enteringNewElementExtension(theElem, theUrlAttr, theIsModifier);
 	}
 
 	public T getObject() {
@@ -370,15 +371,19 @@ class ParserState<T extends IElement> {
 		/**
 		 * Default implementation just handles undeclared extensions
 		 */
-		public void enteringNewElementExtension(@SuppressWarnings("unused") StartElement theElement, String theUrlAttr) {
+		public void enteringNewElementExtension(@SuppressWarnings("unused") StartElement theElement, String theUrlAttr, boolean theIsModifier) {
 			if (getCurrentElement() instanceof ISupportsUndeclaredExtensions) {
-				UndeclaredExtension newExtension = new UndeclaredExtension(theUrlAttr);
+				UndeclaredExtension newExtension = new UndeclaredExtension(theIsModifier, theUrlAttr);
-				// TODO: fail if we don't support undeclared extensions
+				ISupportsUndeclaredExtensions elem = (ISupportsUndeclaredExtensions) getCurrentElement();
-				((ISupportsUndeclaredExtensions) getCurrentElement()).getUndeclaredExtensions().add(newExtension);
+				if (theIsModifier) {
+					elem.getUndeclaredModifierExtensions().add(newExtension);
+				} else {
+					elem.getUndeclaredExtensions().add(newExtension);
+				}
 				ExtensionState newState = new ExtensionState(newExtension);
 				push(newState);
 			} else {
-				throw new DataFormatException("Extension is not supported at this position");
+				throw new DataFormatException("Type " + getCurrentElement() + " does not support undeclared extentions, and found an extension with URL: " + theUrlAttr);
 			}
 		}
 
@@ -446,7 +451,7 @@ class ParserState<T extends IElement> {
 			}
 			case RESOURCE_REF: {
 				RuntimeResourceReferenceDefinition resourceRefTarget = (RuntimeResourceReferenceDefinition) target;
-				ResourceReference newChildInstance = new ResourceReference();
+				ResourceReferenceDt newChildInstance = new ResourceReferenceDt();
 				myDefinition.getMutator().addValue(myParentInstance, newChildInstance);
 				ResourceReferenceState newState = new ResourceReferenceState(resourceRefTarget, newChildInstance);
 				push(newState);
@@ -463,7 +468,7 @@ class ParserState<T extends IElement> {
 		}
 
 		@Override
-		public void enteringNewElementExtension(StartElement theElement, String theUrlAttr) {
+		public void enteringNewElementExtension(StartElement theElement, String theUrlAttr, boolean theIsModifier) {
 			RuntimeChildDeclaredExtensionDefinition declaredExtension = myDefinition.getChildExtensionForUrl(theUrlAttr);
 			if (declaredExtension != null) {
 				if (myChildInstance == null) {
@@ -473,7 +478,7 @@ class ParserState<T extends IElement> {
 				BaseState newState = new DeclaredExtensionState(declaredExtension, myChildInstance);
 				push(newState);
 			} else {
-				super.enteringNewElementExtension(theElement, theUrlAttr);
+				super.enteringNewElementExtension(theElement, theUrlAttr, theIsModifier);
 			}
 		}
 
@@ -514,7 +519,7 @@ class ParserState<T extends IElement> {
 			switch (target.getChildType()) {
 			case COMPOSITE_DATATYPE: {
 				BaseRuntimeElementCompositeDefinition<?> compositeTarget = (BaseRuntimeElementCompositeDefinition<?>) target;
-				ICompositeDatatype newChildInstance = (ICompositeDatatype) compositeTarget.newInstance();
+				ICompositeDatatype newChildInstance = (ICompositeDatatype) compositeTarget.newInstance(child.getInstanceConstructorArguments());
 				child.getMutator().addValue(myInstance, newChildInstance);
 				ElementCompositeState newState = new ElementCompositeState(compositeTarget, newChildInstance);
 				push(newState);
@@ -531,7 +536,7 @@ class ParserState<T extends IElement> {
 			}
 			case RESOURCE_REF: {
 				RuntimeResourceReferenceDefinition resourceRefTarget = (RuntimeResourceReferenceDefinition) target;
-				ResourceReference newChildInstance = new ResourceReference();
+				ResourceReferenceDt newChildInstance = new ResourceReferenceDt();
 				child.getMutator().addValue(myInstance, newChildInstance);
 				ResourceReferenceState newState = new ResourceReferenceState(resourceRefTarget, newChildInstance);
 				push(newState);
@@ -564,13 +569,13 @@ class ParserState<T extends IElement> {
 		}
 
 		@Override
-		public void enteringNewElementExtension(StartElement theElement, String theUrlAttr) {
+		public void enteringNewElementExtension(StartElement theElement, String theUrlAttr, boolean theIsModifier) {
 			RuntimeChildDeclaredExtensionDefinition declaredExtension = myDefinition.getDeclaredExtension(theUrlAttr);
 			if (declaredExtension != null) {
 				BaseState newState = new DeclaredExtensionState(declaredExtension, myInstance);
 				push(newState);
 			} else {
-				super.enteringNewElementExtension(theElement, theUrlAttr);
+				super.enteringNewElementExtension(theElement, theUrlAttr, theIsModifier);
 			}
 		}
 
@@ -623,7 +628,7 @@ class ParserState<T extends IElement> {
 			}
 			case RESOURCE_REF: {
 				RuntimeResourceReferenceDefinition resourceRefTarget = (RuntimeResourceReferenceDefinition) target;
-				ResourceReference newChildInstance = new ResourceReference();
+				ResourceReferenceDt newChildInstance = new ResourceReferenceDt();
 				myExtension.setValue(newChildInstance);
 				ResourceReferenceState newState = new ResourceReferenceState(resourceRefTarget, newChildInstance);
 				push(newState);
@@ -784,10 +789,10 @@ class ParserState<T extends IElement> {
 	private class ResourceReferenceState extends BaseState {
 
 		private RuntimeResourceReferenceDefinition myDefinition;
-		private ResourceReference myInstance;
+		private ResourceReferenceDt myInstance;
 		private ResourceReferenceSubState mySubState;
 
-		public ResourceReferenceState(RuntimeResourceReferenceDefinition theDefinition, ResourceReference theInstance) {
+		public ResourceReferenceState(RuntimeResourceReferenceDefinition theDefinition, ResourceReferenceDt theInstance) {
 			myDefinition = theDefinition;
 			myInstance = theInstance;
 			mySubState = ResourceReferenceSubState.INITIAL;

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

@@ -34,6 +34,7 @@ import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeChildDeclaredExtensionDefinition;
 import ca.uhn.fhir.context.RuntimeChildUndeclaredExtensionDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.api.Bundle;
@@ -42,8 +43,9 @@ import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IPrimitiveDatatype;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
-import ca.uhn.fhir.model.api.ResourceReference;
+import ca.uhn.fhir.model.api.BaseResourceReference;
 import ca.uhn.fhir.model.api.UndeclaredExtension;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
@@ -89,7 +91,14 @@ public class XmlParser implements IParser {
 							if (urlAttr == null || isBlank(urlAttr.getValue())) {
 								throw new DataFormatException("Extension element has no 'url' attribute");
 							}
-							parserState.enteringNewElementExtension(elem, urlAttr.getValue());
+							parserState.enteringNewElementExtension(elem, urlAttr.getValue(),false);
+						} else if ("modifierExtension".equals(elem.getName().getLocalPart())) {
+							Attribute urlAttr = elem.getAttributeByName(new QName("url"));
+							if (urlAttr == null || isBlank(urlAttr.getValue())) {
+								throw new DataFormatException("Extension element has no 'url' attribute");
+							}
+							parserState.enteringNewElementExtension(elem, urlAttr.getValue(),true);
+
 						} else {
 
 							String elementName = elem.getName().getLocalPart();
@@ -131,7 +140,7 @@ public class XmlParser implements IParser {
 					parserState.xmlEvent(nextEvent);
 
 				} catch (DataFormatException e) {
-					throw new DataFormatException("DataFormatException at [" + nextEvent.getLocation().toString() + "]: "+e.getMessage(), e);
+					throw new DataFormatException("DataFormatException at [" + nextEvent.getLocation().toString() + "]: " + e.getMessage(), e);
 				}
 			}
 			return null;
@@ -140,7 +149,9 @@ public class XmlParser implements IParser {
 		}
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see ca.uhn.fhir.parser.IParser#encodeBundleToString(ca.uhn.fhir.model.api.Bundle)
 	 */
 	@Override
@@ -151,7 +162,9 @@ public class XmlParser implements IParser {
 		return stringWriter.toString();
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see ca.uhn.fhir.parser.IParser#encodeBundleToWriter(ca.uhn.fhir.model.api.Bundle, java.io.Writer)
 	 */
 	@Override
@@ -211,9 +224,8 @@ public class XmlParser implements IParser {
 		}
 	}
 
-
+	private void encodeChildElementToStreamWriter(XMLStreamWriter theEventWriter, IElement nextValue, String childName, BaseRuntimeElementDefinition<?> childDef, String theExtensionUrl)
-
+			throws XMLStreamException, DataFormatException {
-	private void encodeChildElementToStreamWriter(XMLStreamWriter theEventWriter, IElement nextValue, String childName, BaseRuntimeElementDefinition<?> childDef, String theExtensionUrl) throws XMLStreamException, DataFormatException {
 		if (nextValue.isEmpty()) {
 			return;
 		}
@@ -243,7 +255,7 @@ public class XmlParser implements IParser {
 			break;
 		}
 		case RESOURCE_REF: {
-			ResourceReference ref = (ResourceReference) nextValue;
+			ResourceReferenceDt ref = (ResourceReferenceDt) nextValue;
 			if (!ref.isEmpty()) {
 				theEventWriter.writeStartElement(childName);
 				encodeResourceReferenceToStreamWriter(theEventWriter, ref);
@@ -268,7 +280,8 @@ public class XmlParser implements IParser {
 
 	}
 
-	private void encodeCompositeElementChildrenToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> children) throws XMLStreamException, DataFormatException {
+	private void encodeCompositeElementChildrenToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> children) throws XMLStreamException,
+			DataFormatException {
 		for (BaseRuntimeChildDefinition nextChild : children) {
 			List<? extends IElement> values = nextChild.getAccessor().getValues(theElement);
 			if (values == null || values.isEmpty()) {
@@ -288,7 +301,13 @@ public class XmlParser implements IParser {
 				}
 
 				if (extensionUrl != null && childName.equals("extension") == false) {
+					RuntimeChildDeclaredExtensionDefinition extDef = (RuntimeChildDeclaredExtensionDefinition) nextChild;
+					if (extDef.isModifier()) {
+						theEventWriter.writeStartElement("modifierExtension");
+					}else {
 						theEventWriter.writeStartElement("extension");
+					}
+					
 					theEventWriter.writeAttribute("url", extensionUrl);
 					encodeChildElementToStreamWriter(theEventWriter, nextValue, childName, childDef, null);
 					theEventWriter.writeEndElement();
@@ -299,18 +318,24 @@ public class XmlParser implements IParser {
 		}
 	}
 
-	private void encodeCompositeElementToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> resDef) throws XMLStreamException, DataFormatException {
+	private void encodeCompositeElementToStreamWriter(IElement theElement, XMLStreamWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> resDef) throws XMLStreamException,
+			DataFormatException {
 		encodeExtensionsIfPresent(theEventWriter, theElement);
 		encodeCompositeElementChildrenToStreamWriter(theElement, theEventWriter, resDef.getExtensions());
 		encodeCompositeElementChildrenToStreamWriter(theElement, theEventWriter, resDef.getChildren());
 	}
 
 	private void encodeExtensionsIfPresent(XMLStreamWriter theWriter, IElement theResource) throws XMLStreamException, DataFormatException {
-		boolean retVal = false;
 		if (theResource instanceof ISupportsUndeclaredExtensions) {
-			for (UndeclaredExtension next : ((ISupportsUndeclaredExtensions) theResource).getUndeclaredExtensions()) {
+			ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theResource;
-				retVal = true;
+			encodeUndeclaredExtensions(theWriter, res.getUndeclaredExtensions(), "extension");
-				theWriter.writeStartElement("extension");
+			encodeUndeclaredExtensions(theWriter, res.getUndeclaredModifierExtensions(), "modifierExtension");
+		}
+	}
+
+	private void encodeUndeclaredExtensions(XMLStreamWriter theWriter, List<UndeclaredExtension> extensions, String tagName) throws XMLStreamException {
+		for (UndeclaredExtension next : extensions) {
+			theWriter.writeStartElement(tagName);
 			theWriter.writeAttribute("url", next.getUrl());
 
 			if (next.getValue() != null) {
@@ -327,22 +352,23 @@ public class XmlParser implements IParser {
 			theWriter.writeEndElement();
 		}
 	}
-	}
 
-	private void encodeResourceReferenceToStreamWriter(XMLStreamWriter theEventWriter, ResourceReference theRef) throws XMLStreamException {
+	private void encodeResourceReferenceToStreamWriter(XMLStreamWriter theEventWriter, ResourceReferenceDt theRef) throws XMLStreamException {
-		if (StringUtils.isNotBlank(theRef.getDisplay())) {
+		if (!(theRef.getDisplay().isEmpty())) {
 			theEventWriter.writeStartElement("display");
-			theEventWriter.writeAttribute("value", theRef.getDisplay());
+			theEventWriter.writeAttribute("value", theRef.getDisplay().getValue());
 			theEventWriter.writeEndElement();
 		}
-		if (StringUtils.isNotBlank(theRef.getReference())) {
+		if (!(theRef.getReference().isEmpty())) {
 			theEventWriter.writeStartElement("reference");
-			theEventWriter.writeAttribute("value", theRef.getReference());
+			theEventWriter.writeAttribute("value", theRef.getReference().getValue());
 			theEventWriter.writeEndElement();
 		}
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see ca.uhn.fhir.parser.IParser#encodeResourceToString(ca.uhn.fhir.model.api.IResource)
 	 */
 	@Override
@@ -352,7 +378,9 @@ public class XmlParser implements IParser {
 		return stringWriter.toString();
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see ca.uhn.fhir.parser.IParser#encodeResourceToWriter(ca.uhn.fhir.model.api.IResource, java.io.Writer)
 	 */
 	@Override
@@ -368,7 +396,9 @@ public class XmlParser implements IParser {
 		}
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see ca.uhn.fhir.parser.IParser#encodeResourceToXmlStreamWriter(ca.uhn.fhir.model.api.IResource, javax.xml.stream.XMLStreamWriter)
 	 */
 	@Override
@@ -431,7 +461,7 @@ public class XmlParser implements IParser {
 					theEventWriter.writeStartElement(se.getName().getLocalPart());
 					if (StringUtils.isBlank(se.getName().getPrefix())) {
 						theEventWriter.writeDefaultNamespace(se.getName().getNamespaceURI());
-					}else {
+					} else {
 						theEventWriter.writeNamespace(se.getName().getPrefix(), se.getName().getNamespaceURI());
 					}
 				} else {
@@ -442,7 +472,7 @@ public class XmlParser implements IParser {
 							if (StringUtils.isBlank(se.getName().getPrefix())) {
 								theEventWriter.writeStartElement(se.getName().getLocalPart());
 								theEventWriter.writeDefaultNamespace(se.getName().getNamespaceURI());
-							}else {
+							} else {
 								theEventWriter.writeStartElement(se.getName().getNamespaceURI(), se.getName().getLocalPart());
 							}
 						}
@@ -464,7 +494,9 @@ public class XmlParser implements IParser {
 		}
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see ca.uhn.fhir.parser.IParser#parseBundle(java.lang.String)
 	 */
 	@Override
@@ -478,7 +510,9 @@ public class XmlParser implements IParser {
 		return doXmlLoop(theStreamReader, parserState);
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see ca.uhn.fhir.parser.IParser#parseResource(java.lang.String)
 	 */
 	@Override
@@ -486,7 +520,9 @@ public class XmlParser implements IParser {
 		return parseResource(null, theMessageString);
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see ca.uhn.fhir.parser.IParser#parseResource(javax.xml.stream.XMLEventReader)
 	 */
 	@Override

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

@@ -17,6 +17,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import ca.uhn.fhir.rest.server.exceptions.*;
+
 import org.apache.commons.lang3.StringUtils;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -98,9 +99,18 @@ public abstract class RestfulServer extends HttpServlet {
 		}
 	}
 
+	/**
+	 * This method must be overridden to provide one or more resource providers
+	 */
 	public abstract Collection<IResourceProvider> getResourceProviders();
 
-    public abstract ISecurityManager getSecurityManager();
+	/**
+	 * This method should be overridden to provide a security manager
+	 * instance. By default, returns null.
+	 */
+    public ISecurityManager getSecurityManager() {
+        return null;
+    }
 
 	protected void handleRequest(SearchMethodBinding.RequestType requestType, HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
 		try {

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

@@ -8,17 +8,16 @@ public class ElementUtil {
 
 	@SuppressWarnings("unchecked")
 	public static boolean isEmpty(Object... theElements) {
-		if (theElements ==null) {
+		if (theElements == null) {
 			return true;
 		}
 		for (int i = 0; i < theElements.length; i++) {
 			Object next = theElements[i];
 			if (next instanceof List) {
-				if (!isEmpty((List<? extends IElement>)next)) {
+				if (!isEmpty((List<? extends IElement>) next)) {
 					return false;
 				}
-			}
+			} else if (next != null && !((IElement) next).isEmpty()) {
-			if (next != null && !((IElement)next).isEmpty()) {
 				return false;
 			}
 		}
@@ -26,7 +25,7 @@ public class ElementUtil {
 	}
 
 	public static boolean isEmpty(IElement... theElements) {
-		if (theElements ==null) {
+		if (theElements == null) {
 			return true;
 		}
 		for (int i = 0; i < theElements.length; i++) {
@@ -39,7 +38,7 @@ public class ElementUtil {
 	}
 
 	public static boolean isEmpty(List<? extends IElement> theElements) {
-		if (theElements ==null) {
+		if (theElements == null) {
 			return true;
 		}
 		for (int i = 0; i < theElements.size(); i++) {

hapi-fhir-base/src/site/example/java/example/ExampleRestfulServlet.java

@@ -0,0 +1,38 @@
+package example;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.servlet.annotation.WebServlet;
+
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+
+//START SNIPPET: servlet
+/**
+ * In this example, we are using Servlet 3.0 annotations to define
+ * the URL pattern for this servlet, but we could also
+ * define this in a web.xml file.
+ */
+@WebServlet(urlPatterns= {"/fhir/*"}, displayName="FHIR Server")
+public class ExampleRestfulServlet extends RestfulServer {
+
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * Restful servers must provide an implementation of this method, which
+	 * returns all resource providers to be used by this server. In the example
+	 * below, we are creating a RESTful server which is able to serve
+	 * Patient and Observation resources.
+	 */
+	@Override
+	public Collection<IResourceProvider> getResourceProviders() {
+		List<IResourceProvider> retVal = new ArrayList<IResourceProvider>();
+		retVal.add(new RestfulPatientResourceProvider());
+		retVal.add(new RestfulObservationResourceProvider());
+		return retVal;
+	}
+
+}
+//END SNIPPET: servlet

hapi-fhir-base/src/site/example/java/example/RestfulObservationResourceProvider.java

@@ -0,0 +1,86 @@
+package example;
+
+import java.util.Collections;
+import java.util.List;
+
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu.valueset.AdministrativeGenderCodesEnum;
+import ca.uhn.fhir.model.dstu.valueset.IdentifierUseEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.primitive.UriDt;
+import ca.uhn.fhir.rest.annotation.Read;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.operations.Search;
+import ca.uhn.fhir.rest.server.parameters.Required;
+
+//START SNIPPET: provider
+/**
+ * All resource providers must implement IResourceProvider
+ */
+public class RestfulObservationResourceProvider implements IResourceProvider {
+
+	/**
+	 * The getResourceType method comes from IResourceProvider, and must
+	 * be overridden to indicate what type of resource this provider
+	 * supplies.
+	 */
+	@Override
+	public Class<Patient> getResourceType() {
+		return Patient.class;
+	}
+	
+	/**
+	 * The "@Read" annotation indicates that this method supports the
+	 * read operation. It takes one argument, the Resource type being returned. 
+	 * 
+	 * @param theId
+	 *    The read operation takes one parameter, which must be of type
+	 *    IdDt and must be annotated with the "@Read.IdParam" annotation.
+	 * @return 
+	 *    Returns a resource matching this identifier, or null if none exists.
+	 */
+	@Read(Patient.class)
+	public Patient getResourceById(@Read.IdParam IdDt theId) {
+		Patient patient = new Patient();
+		patient.addIdentifier();
+		patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
+		patient.getIdentifier().get(0).setValue("00002");
+		patient.addName().addFamily("Test");
+		patient.getName().get(0).addGiven("PatientOne");
+		patient.setGender(AdministrativeGenderCodesEnum.F);
+		return patient;
+	}
+
+	/**
+	 * The "@Search" annotation indicates that this method supports the 
+	 * search operation. You may have many different method annotated with 
+	 * this annotation, to support many different search criteria. This
+	 * example searches by family name.
+	 * 
+	 * @param theIdentifier
+	 *    This operation takes one parameter which is the search criteria. It is
+	 *    annotated with the "@Required" annotation. This annotation takes one argument,
+	 *    a string containing the name of the search criteria. The datatype here
+	 *    is StringDt, but there are other possible parameter types depending on the
+	 *    specific search criteria.
+	 * @return
+	 *    This method returns a list of Patients. This list may contain multiple
+	 *    matching resources, or it may also be empty.
+	 */
+	@Search(Patient.class)
+	public List<Patient> getPatient(@Required(name = Patient.SP_FAMILY) StringDt theFamilyName) {
+		Patient patient = new Patient();
+		patient.addIdentifier();
+		patient.getIdentifier().get(0).setUse(IdentifierUseEnum.OFFICIAL);
+		patient.getIdentifier().get(0).setSystem(new UriDt("urn:hapitest:mrns"));
+		patient.getIdentifier().get(0).setValue("00001");
+		patient.addName();
+		patient.getName().get(0).addFamily("Test");
+		patient.getName().get(0).addGiven("PatientOne");
+		patient.getGender().setText("M");
+		return Collections.singletonList(patient);
+	}
+
+}
+//END SNIPPET: provider

hapi-fhir-base/src/site/example/java/example/RestfulServlet.java

@@ -1,30 +0,0 @@
-package example;
-
-import java.util.Arrays;
-import java.util.Collection;
-
-import ca.uhn.fhir.rest.server.IResourceProvider;
-import ca.uhn.fhir.rest.server.ISecurityManager;
-import ca.uhn.fhir.rest.server.RestfulServer;
-
-public class RestfulServlet extends RestfulServer {
-
-	private static final long serialVersionUID = 1L;
-	
-	private Collection<IResourceProvider> myResourceProviders;
-
-	public RestfulServlet(IResourceProvider... theResourceProviders) {
-		myResourceProviders = Arrays.asList(theResourceProviders);
-	}
-
-	@Override
-	public Collection<IResourceProvider> getResourceProviders() {
-		return myResourceProviders;
-	}
-
-    @Override
-    public ISecurityManager getSecurityManager() {
-        return null;
-    }
-
-}

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

@@ -9,7 +9,7 @@
 	<body>
 
 		<!-- The body of the document contains a number of sections -->
-		<section name="Working with Resources">
+		<section name="Creating a RESTful Server">
 			
 			<macro name="toc">
 			</macro>
@@ -26,7 +26,7 @@
 				be possible to create a FHIR compliant server quickly and easily.
 			</p>
 			
-			<subsection name="Creating A Server">
+			<subsection name="Defining Resource Providers">
 			
 				<p>
 					The first step in creating a FHIR RESTful Server is to define one or
@@ -41,7 +41,9 @@
 				</p>
 				
 				<p>
-					Resource providers each contain one or more methods which have been
+					A Resource provider class must implement the 
+					<a href="./apidocs/ca/uhn/fhir/rest/server/IResourceProvider.html">IResourceProvider</a> interface,
+					and will contain one or more methods which have been
 					annotated with special annotations indicating which RESTful operation
 					that method supports. Below is a simple example of a resource provider
 					which supports the
@@ -59,6 +61,36 @@
 
 			</subsection>
 
+			<subsection name="Create a Server">
+			
+				<p>
+					Once your resource providers are created, your next step is to
+					define a server class. 
+				</p>
+				
+				<p>
+					HAPI provides a class called
+					<a href="./apidocs/ca/uhn/fhir/rest/server/RestfulServer.html">RestfulServer</a>, which
+					is a specialized Java Servlet. To create a server, you simply create a class
+					which extends RestfulServer as shown in the example below.
+				</p>
+				
+				<macro name="snippet">
+					<param name="id" value="servlet" />
+					<param name="file" value="src/site/example/java/example/ExampleRestfulServlet.java" />
+				</macro>
+
+			</subsection>	
+			
+			<subsection name="Deploy">
+				
+				<p>
+					Once you have created your resource providers and your restful server class,
+					you can bundle these into a WAR file and you are ready to deploy to 
+					any JEE container (Tomcat, Websphere, Glassfish, etc).
+				</p>
+			
+			</subsection>
 					
 		</section>
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/context/ModelScannerTest.java

@@ -20,25 +20,25 @@ public class ModelScannerTest {
 		
 		assertEquals(RuntimeChildCompositeDatatypeDefinition.class, def.getChildByNameOrThrowDataFormatException("identifier").getClass());
 		
-		RuntimeChildDeclaredExtensionDefinition ext = def.getDeclaredExtension("http://foo/1");
+		RuntimeChildDeclaredExtensionDefinition ext = def.getDeclaredExtension("http://foo/#f1");
 		assertNotNull(ext);
 		BaseRuntimeElementDefinition<?> valueString = ext.getChildByName("valueString");
 		assertNotNull(valueString);
 		
-		ext = def.getDeclaredExtension("http://foo/2");
+		ext = def.getDeclaredExtension("http://foo/#f2");
 		assertNotNull(ext);
 		valueString = ext.getChildByName("valueString");
 		assertNotNull(valueString);
 
-		ext = def.getDeclaredExtension("http://bar/1");
+		ext = def.getDeclaredExtension("http://bar/#b1");
 		assertNotNull(ext);
-		RuntimeChildDeclaredExtensionDefinition childExt = ext.getChildExtensionForUrl("http://bar/1/1");
+		RuntimeChildDeclaredExtensionDefinition childExt = ext.getChildExtensionForUrl("http://bar/#b1/1");
 		assertNotNull(childExt);
 		BaseRuntimeElementDefinition<?> valueDate = childExt.getChildByName("valueDate");
 		assertNotNull(valueDate);
-		childExt = ext.getChildExtensionForUrl("http://bar/1/2");
+		childExt = ext.getChildExtensionForUrl("http://bar/#b1/2");
 		assertNotNull(childExt);
-		childExt = childExt.getChildExtensionForUrl("http://bar/1/2/1");
+		childExt = childExt.getChildExtensionForUrl("http://bar/#b1/2/1");
 		assertNotNull(childExt);
 		valueDate = childExt.getChildByName("valueDate");
 		assertNotNull(valueDate);

hapi-fhir-base/src/test/java/ca/uhn/fhir/context/ResourceWithExtensionsA.java

@@ -21,19 +21,19 @@ public class ResourceWithExtensionsA implements IResource {
 	 */
 	
 	@Child(name = "bar1", type = Bar1.class, order = 2, min = 1, max = Child.MAX_UNLIMITED)
-	@Extension(url = "http://bar/#b1", definedLocally=true)
+	@Extension(url = "http://bar/#b1", definedLocally=true, isModifier=false)
 	private List<Bar1> myBar1;
 
 	@Child(name = "bar2", type = Bar1.class, order = 3, min = 1, max = Child.MAX_UNLIMITED)
-	@Extension(url = "http://bar/#b2", definedLocally=true)
+	@Extension(url = "http://bar/#b2", definedLocally=true, isModifier=false)
 	private Bar1 myBar2;
 
 	@Child(name = "foo1", type = StringDt.class, order = 0, min = 0, max = Child.MAX_UNLIMITED)
-	@Extension(url = "http://foo/#f1", definedLocally=true)
+	@Extension(url = "http://foo/#f1", definedLocally=true, isModifier=false)
 	private List<StringDt> myFoo1;
 
 	@Child(name = "foo2", type = StringDt.class, order = 1, min = 0, max = 1)
-	@Extension(url = "http://foo/#f2", definedLocally=true)
+	@Extension(url = "http://foo/#f2", definedLocally=true, isModifier=true)
 	private StringDt myFoo2;
 
 	@Child(name = "identifier", type = IdentifierDt.class, order = 0, min = 0, max = Child.MAX_UNLIMITED)
@@ -87,11 +87,11 @@ public class ResourceWithExtensionsA implements IResource {
 		}
 		
 		@Child(name = "bar11", type = DateDt.class, order = 0, min = 0, max = Child.MAX_UNLIMITED)
-		@Extension(url = "http://bar/#1/1", definedLocally=true)
+		@Extension(url = "http://bar/#b1/1", definedLocally=true, isModifier=false)
 		private List<DateDt> myBar11;
 
 		@Child(name = "bar12", type = DateDt.class, order = 1, min = 0, max = Child.MAX_UNLIMITED)
-		@Extension(url = "http://bar/#1/2", definedLocally=true)
+		@Extension(url = "http://bar/#b1/2", definedLocally=true, isModifier=false)
 		private List<Bar2> myBar12;
 
 		@Override
@@ -121,11 +121,11 @@ public class ResourceWithExtensionsA implements IResource {
 	public static class Bar2 implements IExtension {
 
 		@Child(name = "bar121", type = DateDt.class, order = 0, min = 0, max = Child.MAX_UNLIMITED)
-		@Extension(url = "http://bar/#1/2/1", definedLocally=true)
+		@Extension(url = "http://bar/#b1/2/1", definedLocally=true, isModifier=false)
 		private List<DateDt> myBar121;
 
 		@Child(name = "bar122", type = DateDt.class, order = 1, min = 0, max = Child.MAX_UNLIMITED)
-		@Extension(url = "http://bar/#1/2/2", definedLocally=true)
+		@Extension(url = "http://bar/#b1/2/2", definedLocally=true, isModifier=false)
 		private List<DateDt> myBar122;
 
 		@Override

hapi-fhir-base/src/test/java/ca/uhn/fhir/context/RuntimeResourceDefinitionTest.java

@@ -7,6 +7,7 @@ import org.junit.Test;
 import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.dstu.resource.Profile;
 import ca.uhn.fhir.model.dstu.resource.Profile.ExtensionDefn;
+import ca.uhn.fhir.model.dstu.resource.Profile.Structure;
 import ca.uhn.fhir.model.dstu.valueset.DataTypeEnum;
 
 public class RuntimeResourceDefinitionTest {
@@ -21,6 +22,14 @@ public class RuntimeResourceDefinitionTest {
 
 		ourLog.info(ctx.newXmlParser().encodeResourceToString(profile));
 		
+		Structure struct = profile.getStructure().get(0);
+		assertEquals("Patient", struct.getElement().get(0).getPath().getValue());
+		assertEquals("Patient.extension", struct.getElement().get(1).getPath().getValue());
+		assertEquals("Patient.modifierExtension", struct.getElement().get(2).getPath().getValue());
+		assertEquals("Patient.text", struct.getElement().get(3).getPath().getValue());
+		assertEquals("Patient.contained", struct.getElement().get(4).getPath().getValue());
+		assertEquals("Patient.language", struct.getElement().get(5).getPath().getValue());
+		
 	}
 	
 	@Test
@@ -30,35 +39,35 @@ public class RuntimeResourceDefinitionTest {
 
 		Profile profile = def.toProfile();
 
-		ourLog.debug(ctx.newXmlParser().encodeResourceToString(profile));
+		ourLog.info(ctx.newXmlParser().encodeResourceToString(profile));
 		
 		assertEquals(1, profile.getStructure().get(0).getElement().get(0).getDefinition().getType().size());
 		assertEquals("Resource", profile.getStructure().get(0).getElement().get(0).getDefinition().getType().get(0).getCode().getValue());
 
-		ExtensionDefn ext = profile.getExtensionDefn().get(0);
+		ExtensionDefn ext = profile.getExtensionDefn().get(1);
-		assertEquals("1/1", ext.getCode().getValue());
+		assertEquals("b1/1", ext.getCode().getValue());
 		assertEquals(DataTypeEnum.DATE.getCode(), ext.getDefinition().getType().get(0).getCode().getValue());
 		
-		ext = profile.getExtensionDefn().get(1);
+		ext = profile.getExtensionDefn().get(2);
-		assertEquals("1/2", ext.getCode().getValue());
+		assertEquals("b1/2", ext.getCode().getValue());
 		assertEquals(DataTypeEnum.EXTENSION, ext.getDefinition().getType().get(0).getCode().getValueAsEnum());
-		assertEquals("#1/2/1", ext.getDefinition().getType().get(0).getProfile().getValueAsString());
+		assertEquals("#b1/2/1", ext.getDefinition().getType().get(0).getProfile().getValueAsString());
 		assertEquals(DataTypeEnum.EXTENSION, ext.getDefinition().getType().get(1).getCode().getValueAsEnum());
-		assertEquals("#1/2/2", ext.getDefinition().getType().get(1).getProfile().getValueAsString());
+		assertEquals("#b1/2/2", ext.getDefinition().getType().get(1).getProfile().getValueAsString());
 		
 		assertEquals("ResourceWithExtensionsA.extension", profile.getStructure().get(0).getElement().get(1).getPath().getValue());
 		assertEquals("ResourceWithExtensionsA.extension", profile.getStructure().get(0).getElement().get(2).getPath().getValue());
 		assertEquals("ResourceWithExtensionsA.extension", profile.getStructure().get(0).getElement().get(3).getPath().getValue());
 		assertEquals("ResourceWithExtensionsA.extension", profile.getStructure().get(0).getElement().get(4).getPath().getValue());
-		assertEquals("ResourceWithExtensionsA.extension", profile.getStructure().get(0).getElement().get(5).getPath().getValue());
+		assertEquals("ResourceWithExtensionsA.modifierExtension", profile.getStructure().get(0).getElement().get(5).getPath().getValue());
 
 		assertEquals(DataTypeEnum.EXTENSION, profile.getStructure().get(0).getElement().get(1).getDefinition().getType().get(0).getCode().getValueAsEnum());
 		assertEquals("url", profile.getStructure().get(0).getElement().get(1).getSlicing().getDiscriminator().getValue());
 
 		assertEquals(DataTypeEnum.EXTENSION, profile.getStructure().get(0).getElement().get(2).getDefinition().getType().get(0).getCode().getValueAsEnum());
-		assertEquals("f1", profile.getStructure().get(0).getElement().get(2).getDefinition().getType().get(0).getProfile().getValueAsString());
+		assertEquals("#f1", profile.getStructure().get(0).getElement().get(2).getDefinition().getType().get(0).getProfile().getValueAsString());
 		
-		assertEquals("ResourceWithExtensionsA.identifier", profile.getStructure().get(0).getElement().get(6).getPath().getValue());
+		assertEquals("ResourceWithExtensionsA.identifier", profile.getStructure().get(0).getElement().get(9).getPath().getValue());
 
 	}
 

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

@@ -146,33 +146,33 @@ public class XmlParserTest {
 	}
 	
 	@Test
-	public void testLoadAndEncodeExtensions() throws ConfigurationException, DataFormatException, SAXException, IOException {
+	public void testLoadAndEncodeDeclaredExtensions() throws ConfigurationException, DataFormatException, SAXException, IOException {
 		FhirContext ctx = new FhirContext(ResourceWithExtensionsA.class);
 		IParser p = new XmlParser(ctx);
 
 		//@formatter:off
 		String msg = "<ResourceWithExtensionsA xmlns=\"http://hl7.org/fhir\">\n" + 
-				"	<extension url=\"http://foo/1\">\n" + 
+				"	<extension url=\"http://foo/#f1\">\n" + 
 				"		<valueString value=\"Foo1Value\"/>\n" + 
 				"	</extension>\n" + 
-				"	<extension url=\"http://foo/1\">\n" + 
+				"	<extension url=\"http://foo/#f1\">\n" + 
 				"		<valueString value=\"Foo1Value2\"/>\n" + 
 				"	</extension>\n" + 
-				"	<extension url=\"http://foo/2\">\n" + 
+				"	<modifierExtension url=\"http://foo/#f2\">\n" + 
 				"		<valueString value=\"Foo2Value1\"/>\n" + 
-				"	</extension>\n" + 
+				"	</modifierExtension>\n" + 
-				"	<extension url=\"http://bar/1\">\n" + 
+				"	<extension url=\"http://bar/#b1\">\n" + 
-				"		<extension url=\"http://bar/1/1\">\n" +
+				"		<extension url=\"http://bar/#b1/1\">\n" +
 				"			<valueDate value=\"2013-01-01\"/>\n" +
 				"		</extension>\n" + 
-				"		<extension url=\"http://bar/1/2\">\n" + 
+				"		<extension url=\"http://bar/#b1/2\">\n" + 
-				"			<extension url=\"http://bar/1/2/1\">\n" + 
+				"			<extension url=\"http://bar/#b1/2/1\">\n" + 
 				"				<valueDate value=\"2013-01-02\"/>\n" +
 				"			</extension>\n" + 
-				"			<extension url=\"http://bar/1/2/1\">\n" + 
+				"			<extension url=\"http://bar/#b1/2/1\">\n" + 
 				"				<valueDate value=\"2013-01-12\"/>\n" +
 				"			</extension>\n" + 
-				"			<extension url=\"http://bar/1/2/2\">\n" + 
+				"			<extension url=\"http://bar/#b1/2/2\">\n" + 
 				"				<valueDate value=\"2013-01-03\"/>\n" +
 				"			</extension>\n" + 
 				"		</extension>\n" + 
@@ -200,6 +200,60 @@ public class XmlParserTest {
 		assertTrue(d.toString(), d.identical());
 	}
 
+	@Test
+	public void testLoadAndEncodeUndeclaredExtensions() throws ConfigurationException, DataFormatException, SAXException, IOException {
+		FhirContext ctx = new FhirContext(Patient.class);
+		IParser p = new XmlParser(ctx);
+
+		//@formatter:off
+		String msg = "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
+				"	<extension url=\"http://foo/#f1\">\n" + 
+				"		<valueString value=\"Foo1Value\"/>\n" + 
+				"	</extension>\n" + 
+				"	<extension url=\"http://foo/#f1\">\n" + 
+				"		<valueString value=\"Foo1Value2\"/>\n" + 
+				"	</extension>\n" + 
+				"	<extension url=\"http://bar/#b1\">\n" + 
+				"		<extension url=\"http://bar/#b1/1\">\n" +
+				"			<valueDate value=\"2013-01-01\"/>\n" +
+				"		</extension>\n" + 
+				"		<extension url=\"http://bar/#b1/2\">\n" + 
+				"			<extension url=\"http://bar/#b1/2/1\">\n" + 
+				"				<valueDate value=\"2013-01-02\"/>\n" +
+				"			</extension>\n" + 
+				"			<extension url=\"http://bar/#b1/2/1\">\n" + 
+				"				<valueDate value=\"2013-01-12\"/>\n" +
+				"			</extension>\n" + 
+				"			<extension url=\"http://bar/#b1/2/2\">\n" + 
+				"				<valueDate value=\"2013-01-03\"/>\n" +
+				"			</extension>\n" + 
+				"		</extension>\n" + 
+				"	</extension>\n" + 
+				"	<modifierExtension url=\"http://foo/#f2\">\n" + 
+				"		<valueString value=\"Foo2Value1\"/>\n" + 
+				"	</modifierExtension>\n" + 
+				"	<identifier>\n" + 
+				"		<label value=\"IdentifierLabel\"/>\n" + 
+				"	</identifier>\n" + 
+				"</Patient>";
+		//@formatter:on
+
+		Patient resource = (Patient) p.parseResource(msg);
+		assertEquals("IdentifierLabel", resource.getIdentifier().get(0).getLabel().getValue());
+		assertEquals("Foo1Value", resource.getUndeclaredExtensions().get(0).getValueAsPrimitive().getValueAsString());
+		assertEquals("Foo1Value2", resource.getUndeclaredExtensions().get(1).getValueAsPrimitive().getValueAsString());
+		assertEquals("Foo2Value1", resource.getUndeclaredModifierExtensions().get(0).getValueAsPrimitive().getValueAsString());
+		
+		assertEquals("2013-01-01", resource.getUndeclaredExtensions().get(2).getUndeclaredExtensions().get(0).getValueAsPrimitive().getValueAsString());
+		assertEquals("2013-01-02", resource.getUndeclaredExtensions().get(2).getUndeclaredExtensions().get(1).getUndeclaredExtensions().get(0).getValueAsPrimitive().getValueAsString());
+
+		String encoded = p.encodeResourceToString(resource);
+		ourLog.info(encoded);
+
+		Diff d = new Diff(new StringReader(msg), new StringReader(encoded));
+		assertTrue(d.toString(), d.identical());
+	}
+
 	@BeforeClass
 	public static void beforeClass() {
 		XMLUnit.setIgnoreAttributeOrder(true);

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

@@ -1,18 +1,15 @@
 package ca.uhn.fhir.rest.server;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.HttpGet;
-import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.entity.ContentType;
+import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
-import org.apache.http.impl.client.DefaultHttpClient;
-import org.apache.http.impl.conn.PoolingClientConnectionManager;
-import org.apache.http.impl.conn.SchemeRegistryFactory;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
@@ -33,7 +30,7 @@ public class ResfulServerTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResfulServerTest.class);
 	private static int ourPort;
 	private static Server ourServer;
-	private static DefaultHttpClient ourClient;
+	private static CloseableHttpClient ourClient;
 	private static FhirContext ourCtx;
 
 	@BeforeClass
@@ -49,8 +46,10 @@ public class ResfulServerTest {
 		ourServer.setHandler(proxyHandler);
 		ourServer.start();
 
-		PoolingClientConnectionManager connectionManager = new PoolingClientConnectionManager(SchemeRegistryFactory.createDefault(), 5000, TimeUnit.MILLISECONDS);
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
-		ourClient = new DefaultHttpClient(connectionManager);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
 
 		ourCtx = new FhirContext(Patient.class);
 		

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

@@ -148,6 +148,7 @@ public abstract class BaseStructureParser {
 		ctx.put("includeDescriptionAnnotations", true);
 		ctx.put("packageBase", thePackageBase);
 		ctx.put("profile", theResource.getProfile());
+		ctx.put("id", StringUtils.defaultString(theResource.getId()));
 		ctx.put("className", theResource.getName());
 		ctx.put("shortName", defaultString(theResource.getShortName()));
 		ctx.put("definition", defaultString(theResource.getDefinition()));

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

@@ -53,6 +53,8 @@ public abstract class BaseStructureSpreadsheetParser extends BaseStructureParser
 
 			parseBasicElements(resourceRow, resource);
 
+			resource.setId(resource.getName().toLowerCase());
+			
 			if (this instanceof ResourceGeneratorUsingSpreadsheet) {
 				resource.setProfile("http://hl7.org/fhir/profiles/" + resource.getElementName());
 			}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/Child.java

@@ -67,7 +67,7 @@ public class Child extends BaseElement {
 	public String getReferenceType() {
 		String retVal;
 		if (this.isResourceRef()) {
-			retVal = (ResourceReference.class.getSimpleName());
+			retVal = "ResourceReferenceDt"; // (ResourceReferenceDt.class.getSimpleName());
 		} else if (this.getType().size() == 1 || this instanceof ResourceBlock) {
 			if (isBoundCode()) {
 				retVal = "Bound" + getSingleType() + "<" + getBindingClass() + ">";

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/Resource.java

@@ -5,9 +5,14 @@ import java.util.List;
 
 public class Resource extends BaseElement {
 
+	private String myId;
 	private String myProfile;
+
 	private List<SearchParameter> mySearchParameters;
 
+	public String getId() {
+		return myId;
+	}
 	public String getProfile() {
 		return myProfile;
 	}
@@ -24,6 +29,10 @@ public class Resource extends BaseElement {
 		return "";
 	}
 
+	public void setId(String theId) {
+		myId = theId;
+	}
+
 	public void setProfile(String theProfile) {
 		myProfile = theProfile;
 	}

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

@@ -24,7 +24,9 @@ import ${packageBase}.resource.*;
  * </p> 
  */
 @DatatypeDef(name="${className}") 
-public class ${className}Dt extends BaseElement implements ICompositeDatatype  #{if}( ${className} == "Identifier" ), IQueryParameterType #{end}
+public class ${className}Dt 
+        extends #{if}(${className}=="ResourceReference") BaseResourceReference #{else} BaseElement #{end} 
+        implements ICompositeDatatype  #{if}( ${className} == "Identifier" ), IQueryParameterType #{end}
 {
 
 #########################

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

@@ -23,7 +23,7 @@ import ${packageBase}.valueset.*;
  * ${requirements}
  * </p> 
  */
-@ResourceDef(name="${className}", profile="${profile}")
+@ResourceDef(name="${className}", profile="${profile}", id="${id}")
 public class ${className} extends BaseResource implements IResource {
 
 #foreach ( $param in $searchParams )