Merge branch 'master' into jaxrs-client

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

@@ -70,6 +70,8 @@ import ca.uhn.fhir.model.api.IResourceBlock;
 import ca.uhn.fhir.model.api.IValueSetEnumBinder;
 import ca.uhn.fhir.model.api.annotation.Block;
 import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Compartment;
+import ca.uhn.fhir.model.api.annotation.Compartments;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.api.annotation.Extension;
@@ -87,7 +89,6 @@ import ca.uhn.fhir.util.ReflectionUtil;
 class ModelScanner {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ModelScanner.class);
 
-	private final Map<Class<? extends Annotation>, Class<? extends Annotation>> myAnnotationForwards = new HashMap<Class<? extends Annotation>, Class<? extends Annotation>>();
 	private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinitions = new HashMap<Class<? extends IBase>, BaseRuntimeElementDefinition<?>>();
 	private FhirContext myContext;
 	private Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = new HashMap<String, RuntimeResourceDefinition>();
@@ -101,7 +102,8 @@ class ModelScanner {
 
 	private Set<Class<? extends IBase>> myVersionTypes;
 
-	ModelScanner(FhirContext theContext, FhirVersionEnum theVersion, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theExistingDefinitions, Collection<Class<? extends IElement>> theResourceTypes) throws ConfigurationException {
+	ModelScanner(FhirContext theContext, FhirVersionEnum theVersion, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theExistingDefinitions,
+			Collection<Class<? extends IElement>> theResourceTypes) throws ConfigurationException {
 		myContext = theContext;
 		myVersion = theVersion;
 		Set<Class<? extends IBase>> toScan;
@@ -233,68 +235,13 @@ class ModelScanner {
 	}
 
 	/**
-	 * There are two implementations of all of the annotations (e.g. {@link Child} and
+	 * There are two implementations of all of the annotations (e.g. {@link Child} and {@link org.hl7.fhir.instance.model.annotations.Child}) since the HL7.org ones will eventually replace the HAPI
-	 * {@link org.hl7.fhir.instance.model.annotations.Child}) since the HL7.org ones will eventually replace the HAPI
+	 * ones. Annotations can't extend each other or implement interfaces or anything like that, so rather than duplicate all of the annotation processing code this method just creates an interface
-	 * ones. Annotations can't extend each other or implement interfaces or anything like that, so rather than duplicate
+	 * Proxy to simulate the HAPI annotations if the HL7.org ones are found instead.
-	 * all of the annotation processing code this method just creates an interface Proxy to simulate the HAPI
-	 * annotations if the HL7.org ones are found instead.
 	 */
-	@SuppressWarnings("unchecked")
+	private <T extends Annotation> T pullAnnotation(AnnotatedElement theTarget, Class<T> theAnnotationType) {
-	private <T extends Annotation> T pullAnnotation(Class<?> theContainer, AnnotatedElement theTarget, Class<T> theAnnotationType) {
-
 		T retVal = theTarget.getAnnotation(theAnnotationType);
-//		if (myContext.getVersion().getVersion() != FhirVersionEnum.DSTU2_HL7ORG) {
 		return retVal;
-//		}
-//
-//		if (retVal == null) {
-//			final Class<? extends Annotation> altAnnotationClass;
-//			/*
-//			 * Use a cache to minimize Class.forName calls, since they are slow and expensive..
-//			 */
-//			if (myAnnotationForwards.containsKey(theAnnotationType) == false) {
-//				String sourceClassName = theAnnotationType.getName();
-//				String candidateAltClassName = sourceClassName.replace("ca.uhn.fhir.model.api.annotation", "org.hl7.fhir.instance.model.annotations");
-//				if (!sourceClassName.equals(candidateAltClassName)) {
-//					Class<?> forName;
-//					try {
-//						forName = Class.forName(candidateAltClassName);
-//						ourLog.debug("Forwarding annotation request for [{}] to class [{}]", theAnnotationType, forName);
-//					} catch (ClassNotFoundException e) {
-//						forName = null;
-//					}
-//					altAnnotationClass = (Class<? extends Annotation>) forName;
-//				} else {
-//					altAnnotationClass = null;
-//				}
-//				myAnnotationForwards.put(theAnnotationType, altAnnotationClass);
-//			} else {
-//				altAnnotationClass = myAnnotationForwards.get(theAnnotationType);
-//			}
-//
-//			if (altAnnotationClass == null) {
-//				return null;
-//			}
-//
-//			final Annotation altAnnotation;
-//			altAnnotation = theTarget.getAnnotation(altAnnotationClass);
-//			if (altAnnotation == null) {
-//				return null;
-//			}
-//
-//			InvocationHandler h = new InvocationHandler() {
-//
-//				@Override
-//				public Object invoke(Object theProxy, Method theMethod, Object[] theArgs) throws Throwable {
-//					Method altMethod = altAnnotationClass.getMethod(theMethod.getName(), theMethod.getParameterTypes());
-//					return altMethod.invoke(altAnnotation, theArgs);
-//				}
-//			};
-//			retVal = (T) Proxy.newProxyInstance(theAnnotationType.getClassLoader(), new Class<?>[] { theAnnotationType }, h);
-//
-//		}
-//
-//		return retVal;
 	}
 
 	private void scan(Class<? extends IBase> theClass) throws ConfigurationException {
@@ -303,17 +250,18 @@ class ModelScanner {
 			return;
 		}
 
-		ResourceDef resourceDefinition = pullAnnotation(theClass, theClass, ResourceDef.class);
+		ResourceDef resourceDefinition = pullAnnotation(theClass, ResourceDef.class);
 		if (resourceDefinition != null) {
 			if (!IBaseResource.class.isAssignableFrom(theClass)) {
-				throw new ConfigurationException("Resource type contains a @" + ResourceDef.class.getSimpleName() + " annotation but does not implement " + IResource.class.getCanonicalName() + ": " + theClass.getCanonicalName());
+				throw new ConfigurationException(
+						"Resource type contains a @" + ResourceDef.class.getSimpleName() + " annotation but does not implement " + IResource.class.getCanonicalName() + ": " + theClass.getCanonicalName());
 			}
 			@SuppressWarnings("unchecked")
 			Class<? extends IBaseResource> resClass = (Class<? extends IBaseResource>) theClass;
 			scanResource(resClass, resourceDefinition);
 		}
 
-		DatatypeDef datatypeDefinition = pullAnnotation(theClass, theClass, DatatypeDef.class);
+		DatatypeDef datatypeDefinition = pullAnnotation(theClass, DatatypeDef.class);
 		if (datatypeDefinition != null) {
 			if (ICompositeType.class.isAssignableFrom(theClass)) {
 				@SuppressWarnings("unchecked")
@@ -325,17 +273,19 @@ class ModelScanner {
 				scanPrimitiveDatatype(resClass, datatypeDefinition);
 			} else {
 				return;
-//				throw new ConfigurationException("Resource type contains a @" + DatatypeDef.class.getSimpleName() + " annotation but does not implement " + IDatatype.class.getCanonicalName() + ": " + theClass.getCanonicalName());
+				// throw new ConfigurationException("Resource type contains a @" + DatatypeDef.class.getSimpleName() + " annotation but does not implement " + IDatatype.class.getCanonicalName() + ": " +
+				// theClass.getCanonicalName());
 			}
 		}
 
-		Block blockDefinition = pullAnnotation(theClass, theClass, Block.class);
+		Block blockDefinition = pullAnnotation(theClass, Block.class);
 
 		if (blockDefinition != null) {
 			if (IResourceBlock.class.isAssignableFrom(theClass) || IBaseBackboneElement.class.isAssignableFrom(theClass) || IBaseDatatypeElement.class.isAssignableFrom(theClass)) {
 				scanBlock(theClass);
 			} else {
-				throw new ConfigurationException("Type contains a @" + Block.class.getSimpleName() + " annotation but does not implement " + IResourceBlock.class.getCanonicalName() + ": " + theClass.getCanonicalName());
+				throw new ConfigurationException(
+						"Type contains a @" + Block.class.getSimpleName() + " annotation but does not implement " + IResourceBlock.class.getCanonicalName() + ": " + theClass.getCanonicalName());
 			}
 		}
 
@@ -364,8 +314,8 @@ class ModelScanner {
 		RuntimeCompositeDatatypeDefinition resourceDef;
 		if (theClass.equals(ExtensionDt.class)) {
 			resourceDef = new RuntimeExtensionDtDefinition(theDatatypeDefinition, theClass, true);
-//		} else if (IBaseMetaType.class.isAssignableFrom(theClass)) {
+			// } else if (IBaseMetaType.class.isAssignableFrom(theClass)) {
-//			resourceDef = new RuntimeMetaDefinition(theDatatypeDefinition, theClass, isStandardType(theClass));
+			// resourceDef = new RuntimeMetaDefinition(theDatatypeDefinition, theClass, isStandardType(theClass));
 		} else {
 			resourceDef = new RuntimeCompositeDatatypeDefinition(theDatatypeDefinition, theClass, isStandardType(theClass));
 		}
@@ -429,7 +379,8 @@ class ModelScanner {
 	}
 
 	@SuppressWarnings("unchecked")
-	private void scanCompositeElementForChildren(Class<? extends IBase> theClass, Set<String> elementNames, TreeMap<Integer, BaseRuntimeDeclaredChildDefinition> theOrderToElementDef, TreeMap<Integer, BaseRuntimeDeclaredChildDefinition> theOrderToExtensionDef) {
+	private void scanCompositeElementForChildren(Class<? extends IBase> theClass, Set<String> elementNames, TreeMap<Integer, BaseRuntimeDeclaredChildDefinition> theOrderToElementDef,
+			TreeMap<Integer, BaseRuntimeDeclaredChildDefinition> theOrderToExtensionDef) {
 		int baseElementOrder = theOrderToElementDef.isEmpty() ? 0 : theOrderToElementDef.lastEntry().getKey() + 1;
 
 		for (Field next : theClass.getDeclaredFields()) {
@@ -439,16 +390,16 @@ class ModelScanner {
 				continue;
 			}
 
-			Child childAnnotation = pullAnnotation(theClass, next, Child.class);
+			Child childAnnotation = pullAnnotation(next, Child.class);
 			if (childAnnotation == null) {
 				ourLog.trace("Ignoring non @Child field {} on target type {}", next.getName(), theClass);
 				continue;
 			}
 
-			Description descriptionAnnotation = pullAnnotation(theClass, next, Description.class);
+			Description descriptionAnnotation = pullAnnotation(next, Description.class);
 
 			TreeMap<Integer, BaseRuntimeDeclaredChildDefinition> orderMap = theOrderToElementDef;
-			Extension extensionAttr = pullAnnotation(theClass, next, Extension.class);
+			Extension extensionAttr = pullAnnotation(next, Extension.class);
 			if (extensionAttr != null) {
 				orderMap = theOrderToExtensionDef;
 			}
@@ -471,8 +422,8 @@ class ModelScanner {
 						}
 					}
 					if (order == Child.REPLACE_PARENT) {
-						throw new ConfigurationException("Field " + next.getName() + "' on target type " + theClass.getSimpleName() + " has order() of REPLACE_PARENT (" + Child.REPLACE_PARENT + ") but no parent element with extension URL " + extensionAttr.url() + " could be found on type "
+						throw new ConfigurationException("Field " + next.getName() + "' on target type " + theClass.getSimpleName() + " has order() of REPLACE_PARENT (" + Child.REPLACE_PARENT
-								+ next.getDeclaringClass().getSimpleName());
+								+ ") but no parent element with extension URL " + extensionAttr.url() + " could be found on type " + next.getDeclaringClass().getSimpleName());
 					}
 
 				} else {
@@ -487,8 +438,8 @@ class ModelScanner {
 						}
 					}
 					if (order == Child.REPLACE_PARENT) {
-						throw new ConfigurationException("Field " + next.getName() + "' on target type " + theClass.getSimpleName() + " has order() of REPLACE_PARENT (" + Child.REPLACE_PARENT + ") but no parent element with name " + elementName + " could be found on type "
+						throw new ConfigurationException("Field " + next.getName() + "' on target type " + theClass.getSimpleName() + " has order() of REPLACE_PARENT (" + Child.REPLACE_PARENT
-								+ next.getDeclaringClass().getSimpleName());
+								+ ") but no parent element with name " + elementName + " could be found on type " + next.getDeclaringClass().getSimpleName());
 					}
 
 				}
@@ -504,8 +455,7 @@ class ModelScanner {
 			// int max = childAnnotation.max();
 
 			/*
-			 * Anything that's marked as unknown is given a new ID that is <0 so that it doesn't conflict with any given
+			 * Anything that's marked as unknown is given a new ID that is <0 so that it doesn't conflict with any given IDs and can be figured out later
-			 * IDs and can be figured out later
 			 */
 			if (order == Child.ORDER_UNKNOWN) {
 				order = Integer.MIN_VALUE;
@@ -572,7 +522,8 @@ class ModelScanner {
 					binder = getBoundCodeBinder(next);
 				}
 
-				RuntimeChildDeclaredExtensionDefinition def = new RuntimeChildDeclaredExtensionDefinition(next, childAnnotation, descriptionAnnotation, extensionAttr, elementName, extensionAttr.url(), et, binder);
+				RuntimeChildDeclaredExtensionDefinition def = new RuntimeChildDeclaredExtensionDefinition(next, childAnnotation, descriptionAnnotation, extensionAttr, elementName, extensionAttr.url(), et,
+						binder);
 
 				if (IBaseEnumeration.class.isAssignableFrom(nextElementType)) {
 					def.setEnumerationType(ReflectionUtil.getGenericCollectionTypeOfFieldWithSecondOrderForList(next));
@@ -600,10 +551,10 @@ class ModelScanner {
 				RuntimeChildResourceDefinition def = new RuntimeChildResourceDefinition(next, elementName, childAnnotation, descriptionAnnotation, refTypesList);
 				orderMap.put(order, def);
 
-			} else if (IResourceBlock.class.isAssignableFrom(nextElementType) || IBaseBackboneElement.class.isAssignableFrom(nextElementType) || IBaseDatatypeElement.class.isAssignableFrom(nextElementType)) {
+			} else if (IResourceBlock.class.isAssignableFrom(nextElementType) || IBaseBackboneElement.class.isAssignableFrom(nextElementType)
+					|| IBaseDatatypeElement.class.isAssignableFrom(nextElementType)) {
 				/*
-				 * Child is a resource block (i.e. a sub-tag within a resource) TODO: do these have a better name
+				 * Child is a resource block (i.e. a sub-tag within a resource) TODO: do these have a better name according to HL7?
-				 * according to HL7?
 				 */
 
 				Class<? extends IBase> blockDef = (Class<? extends IBase>) nextElementType;
@@ -611,13 +562,14 @@ class ModelScanner {
 				RuntimeChildResourceBlockDefinition def = new RuntimeChildResourceBlockDefinition(next, childAnnotation, descriptionAnnotation, elementName, blockDef);
 				orderMap.put(order, def);
 
-			} else if (IDatatype.class.equals(nextElementType) || IElement.class.equals(nextElementType) || "Type".equals(nextElementType.getSimpleName()) || IBaseDatatype.class.equals(nextElementType)) {
+			} else if (IDatatype.class.equals(nextElementType) || IElement.class.equals(nextElementType) || "Type".equals(nextElementType.getSimpleName())
+					|| IBaseDatatype.class.equals(nextElementType)) {
 
 				RuntimeChildAny def = new RuntimeChildAny(next, elementName, childAnnotation, descriptionAnnotation);
 				orderMap.put(order, def);
 
-			} else if (IDatatype.class.isAssignableFrom(nextElementType) || IPrimitiveType.class.isAssignableFrom(nextElementType) || ICompositeType.class.isAssignableFrom(nextElementType) || IBaseDatatype.class.isAssignableFrom(nextElementType)
+			} else if (IDatatype.class.isAssignableFrom(nextElementType) || IPrimitiveType.class.isAssignableFrom(nextElementType) || ICompositeType.class.isAssignableFrom(nextElementType)
-					|| IBaseExtension.class.isAssignableFrom(nextElementType)) {
+					|| IBaseDatatype.class.isAssignableFrom(nextElementType) || IBaseExtension.class.isAssignableFrom(nextElementType)) {
 				Class<? extends IBase> nextDatatype = (Class<? extends IBase>) nextElementType;
 
 				addScanAlso(nextDatatype);
@@ -645,10 +597,11 @@ class ModelScanner {
 					}
 				}
 
-				CodeableConceptElement concept = pullAnnotation(theClass, next, CodeableConceptElement.class);
+				CodeableConceptElement concept = pullAnnotation(next, CodeableConceptElement.class);
 				if (concept != null) {
 					if (!ICodedDatatype.class.isAssignableFrom(nextDatatype)) {
-						throw new ConfigurationException("Field '" + elementName + "' in type '" + theClass.getCanonicalName() + "' is marked as @" + CodeableConceptElement.class.getCanonicalName() + " but type is not a subtype of " + ICodedDatatype.class.getName());
+						throw new ConfigurationException("Field '" + elementName + "' in type '" + theClass.getCanonicalName() + "' is marked as @" + CodeableConceptElement.class.getCanonicalName()
+								+ " but type is not a subtype of " + ICodedDatatype.class.getName());
 					} else {
 						Class<? extends ICodeEnum> type = concept.type();
 						myScanAlsoCodeTable.add(type);
@@ -711,21 +664,23 @@ class ModelScanner {
 			Class<?> parent = theClass.getSuperclass();
 			primaryNameProvider = false;
 			while (parent.equals(Object.class) == false && isBlank(resourceName)) {
-				ResourceDef nextDef = pullAnnotation(theClass, parent, ResourceDef.class);
+				ResourceDef nextDef = pullAnnotation(parent, ResourceDef.class);
 				if (nextDef != null) {
 					resourceName = nextDef.name();
 				}
 				parent = parent.getSuperclass();
 			}
 			if (isBlank(resourceName)) {
-				throw new ConfigurationException("Resource type @" + ResourceDef.class.getSimpleName() + " annotation contains no resource name(): " + theClass.getCanonicalName() + " - This is only allowed for types that extend other resource types ");
+				throw new ConfigurationException("Resource type @" + ResourceDef.class.getSimpleName() + " annotation contains no resource name(): " + theClass.getCanonicalName()
+						+ " - This is only allowed for types that extend other resource types ");
 			}
 		}
 
 		String resourceId = resourceDefinition.id();
 		if (!isBlank(resourceId)) {
 			if (myIdToResourceDefinition.containsKey(resourceId)) {
-				throw new ConfigurationException("The following resource types have the same ID of '" + resourceId + "' - " + theClass.getCanonicalName() + " and " + myIdToResourceDefinition.get(resourceId).getImplementingClass().getCanonicalName());
+				throw new ConfigurationException("The following resource types have the same ID of '" + resourceId + "' - " + theClass.getCanonicalName() + " and "
+						+ myIdToResourceDefinition.get(resourceId).getImplementingClass().getCanonicalName());
 			}
 		}
 
@@ -751,7 +706,7 @@ class ModelScanner {
 		Map<Field, SearchParamDefinition> compositeFields = new LinkedHashMap<Field, SearchParamDefinition>();
 
 		for (Field nextField : theClass.getFields()) {
-			SearchParamDefinition searchParam = pullAnnotation(theClass, nextField, SearchParamDefinition.class);
+			SearchParamDefinition searchParam = pullAnnotation(nextField, SearchParamDefinition.class);
 			if (searchParam != null) {
 				RestSearchParameterTypeEnum paramType = RestSearchParameterTypeEnum.valueOf(searchParam.type().toUpperCase());
 				if (paramType == null) {
@@ -761,7 +716,17 @@ class ModelScanner {
 					compositeFields.put(nextField, searchParam);
 					continue;
 				}
-				RuntimeSearchParam param = new RuntimeSearchParam(searchParam.name(), searchParam.description(), searchParam.path(), paramType);
+
+				Set<String> providesMembershipInCompartments = null;
+				Compartments compartmentsAnnotation = pullAnnotation(nextField, Compartments.class);
+				if (compartmentsAnnotation != null) {
+					providesMembershipInCompartments = new HashSet<String>();
+					for (Compartment next : compartmentsAnnotation.providesMembershipIn()) {
+						providesMembershipInCompartments.add(next.name());
+					}
+				}
+
+				RuntimeSearchParam param = new RuntimeSearchParam(searchParam.name(), searchParam.description(), searchParam.path(), paramType, providesMembershipInCompartments);
 				theResourceDef.addSearchParam(param);
 				nameToParam.put(param.getName(), param);
 			}
@@ -774,13 +739,14 @@ class ModelScanner {
 			for (String nextName : searchParam.compositeOf()) {
 				RuntimeSearchParam param = nameToParam.get(nextName);
 				if (param == null) {
-					ourLog.warn("Search parameter {}.{} declares that it is a composite with compositeOf value '{}' but that is not a valid parametr name itself. Valid values are: {}", new Object[] { theResourceDef.getName(), searchParam.name(), nextName, nameToParam.keySet() });
+					ourLog.warn("Search parameter {}.{} declares that it is a composite with compositeOf value '{}' but that is not a valid parametr name itself. Valid values are: {}",
+							new Object[] { theResourceDef.getName(), searchParam.name(), nextName, nameToParam.keySet() });
 					continue;
 				}
 				compositeOf.add(param);
 			}
 
-			RuntimeSearchParam param = new RuntimeSearchParam(searchParam.name(), searchParam.description(), searchParam.path(), RestSearchParameterTypeEnum.COMPOSITE, compositeOf);
+			RuntimeSearchParam param = new RuntimeSearchParam(searchParam.name(), searchParam.description(), searchParam.path(), RestSearchParameterTypeEnum.COMPOSITE, compositeOf, null);
 			theResourceDef.addSearchParam(param);
 		}
 	}

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

@@ -3,6 +3,7 @@ package ca.uhn.fhir.context;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Set;
 import java.util.StringTokenizer;
 
 import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
@@ -29,23 +30,30 @@ import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
 
 public class RuntimeSearchParam {
 
+	private List<RuntimeSearchParam> myCompositeOf;
 	private String myDescription;
 	private String myName;
 	private RestSearchParameterTypeEnum myParamType;
 	private String myPath;
-	private List<RuntimeSearchParam> myCompositeOf;
+	private Set<String> myProvidesMembershipInCompartments;
 
-	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType) {
+	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, List<RuntimeSearchParam> theCompositeOf,
-		this(theName, theDescription, thePath, theParamType, null);
+			Set<String> theProvidesMembershipInCompartments) {
-	}
-
-	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, List<RuntimeSearchParam> theCompositeOf) {
 		super();
 		myName = theName;
 		myDescription = theDescription;
 		myPath = thePath;
 		myParamType = theParamType;
 		myCompositeOf = theCompositeOf;
+		if (theProvidesMembershipInCompartments != null && !theProvidesMembershipInCompartments.isEmpty()) {
+			myProvidesMembershipInCompartments = Collections.unmodifiableSet(theProvidesMembershipInCompartments);
+		} else {
+			myProvidesMembershipInCompartments = null;
+		}
+	}
+
+	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, Set<String> theProvidesMembershipInCompartments) {
+		this(theName, theDescription, thePath, theParamType, null, theProvidesMembershipInCompartments);
 	}
 
 	public List<RuntimeSearchParam> getCompositeOf() {
@@ -70,7 +78,7 @@ public class RuntimeSearchParam {
 
 	public List<String> getPathsSplit() {
 		String path = getPath();
-		if (path.indexOf('|')==-1) {
+		if (path.indexOf('|') == -1) {
 			return Collections.singletonList(path);
 		}
 
@@ -83,4 +91,11 @@ public class RuntimeSearchParam {
 		return retVal;
 	}
 
+	/**
+	 * Can return null
+	 */
+	public Set<String> getProvidesMembershipInCompartments() {
+		return myProvidesMembershipInCompartments;
+	}
+
 }

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

@@ -0,0 +1,19 @@
+package ca.uhn.fhir.model.api.annotation;
+
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+@Retention(RetentionPolicy.RUNTIME)
+@Target(value= {})
+public @interface Compartment {
+
+	/**
+	 * This may only be populated on a reference field. On such a field, places the containing
+	 * resource in a compartment with the name(s) specified by the given strings, where the compartment
+	 * belongs to the target resource. For example, this field could be populated with <code>Patient</code> on 
+	 * the <code>Observation.subject</code> field.
+	 */
+	String name();
+	
+}

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

@@ -0,0 +1,14 @@
+package ca.uhn.fhir.model.api.annotation;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+@Retention(RetentionPolicy.RUNTIME)
+@Target(value= {ElementType.FIELD})
+public @interface Compartments {
+
+	Compartment[] providesMembershipIn();
+	
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/ResourceParam.java

@@ -25,6 +25,29 @@ import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
 import java.lang.annotation.Target;
 
+import ca.uhn.fhir.rest.server.IResourceProvider;
+
+/**
+ * Denotes a parameter for a REST method which will contain the resource actually 
+ * being created/updated/etc in an operation which contains a resource in the HTTP request.
+ * <p>
+ * For example, in a {@link Create} operation the method parameter annotated with this
+ * annotation will contain the actual resource being created.
+ * </p>
+ * <p>
+ * Parameters with this annotation should typically be of the type of resource being
+ * operated on (see below for an exception when raw data is required). For example, in a
+ * {@link IResourceProvider} for Patient resources, the parameter annotated with this
+ * annotation should be of type Patient. 
+ * </p>
+ * <p>
+ * Note that in servers it is also acceptable to have parameters with this annotation
+ * which are of type {@link String} or of type <code>byte[]</code>. Parameters of
+ * these types will contain the raw/unparsed HTTP request body. It is fine to
+ * have multiple parameters with this annotation, so you can have one parameter
+ * which accepts the parsed resource, and another which accepts the raw request.
+ * </p>
+ */
 @Target(value=ElementType.PARAMETER)
 @Retention(RetentionPolicy.RUNTIME)
 public @interface ResourceParam {

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

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.rest.method;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -46,6 +49,7 @@ import ca.uhn.fhir.rest.server.IVersionSpecificBundleFactory;
  * @author Doug Martin (Regenstrief Center for Biomedical Informatics)
  */
 abstract class BaseHttpClientInvocationWithContents extends BaseHttpClientInvocation {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHttpClientInvocationWithContents.class);
 
 	private final Bundle myBundle;
 	private final BundleTypeEnum myBundleType;

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

@@ -117,7 +117,7 @@ abstract class BaseOutcomeReturningMethodBindingWithResourceParam extends BaseOu
 
 	@Override
 	public BaseHttpClientInvocation invokeClient(Object[] theArgs) throws InternalErrorException {
-		IResource resource = (IResource) theArgs[myResourceParameterIndex];
+		IResource resource = (IResource) theArgs[myResourceParameterIndex]; // TODO: use IBaseResource
 		if (resource == null) {
 			throw new NullPointerException("Resource can not be null");
 		}

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

@@ -451,10 +451,20 @@ public class MethodUtil {
 							mode = Mode.RESOURCE;
 						} else if (String.class.equals(parameterType)) {
 							mode = ResourceParameter.Mode.BODY;
+						} else if (byte[].class.equals(parameterType)) {
+							mode = ResourceParameter.Mode.BODY_BYTE_ARRAY;
 						} else if (EncodingEnum.class.equals(parameterType)) {
 							mode = Mode.ENCODING;
 						} else {
-							throw new ConfigurationException("Method '" + theMethod.getName() + "' is annotated with @" + ResourceParam.class.getSimpleName() + " but has a type that is not an implemtation of " + IResource.class.getCanonicalName());
+							StringBuilder b = new StringBuilder();
+							b.append("Method '");
+							b.append(theMethod.getName());
+							b.append("' is annotated with @");
+							b.append(ResourceParam.class.getSimpleName());
+							b.append(" but has a type that is not an implemtation of ");
+							b.append(IBaseResource.class.getCanonicalName());
+							b.append(" or String or byte[]");
+							throw new ConfigurationException(b.toString());
 						}
 						param = new ResourceParameter((Class<? extends IResource>) parameterType, theProvider, mode);
 					} else if (nextAnnotation instanceof IdParam || nextAnnotation instanceof VersionIdParam) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ResourceParameter.java

@@ -105,8 +105,10 @@ public class ResourceParameter implements IParameter {
 				return IOUtils.toString(createRequestReader(theRequest));
 			} catch (IOException e) {
 				// Shouldn't happen since we're reading from a byte array
-				throw new InternalErrorException("Failed to load request");
+				throw new InternalErrorException("Failed to load request", e);
 			}
+		case BODY_BYTE_ARRAY:
+			return theRequest.loadRequestContents();
 		case ENCODING:
 			return RestfulServerUtils.determineRequestEncoding(theRequest);
 		case RESOURCE:
@@ -201,23 +203,27 @@ public class ResourceParameter implements IParameter {
 	}
 
 	public static IBaseResource parseResourceFromRequest(RequestDetails theRequest, BaseMethodBinding<?> theMethodBinding, Class<? extends IBaseResource> theResourceType) {
-		IBaseResource retVal;
+		IBaseResource retVal = null;
+		
 		if (IBaseBinary.class.isAssignableFrom(theResourceType)) {
-			FhirContext ctx = theRequest.getServer().getFhirContext();
 			String ct = theRequest.getHeader(Constants.HEADER_CONTENT_TYPE);
+			if (EncodingEnum.forContentTypeStrict(ct) == null) {
+			FhirContext ctx = theRequest.getServer().getFhirContext();
 			IBaseBinary binary = (IBaseBinary) ctx.getResourceDefinition("Binary").newInstance();
 			binary.setContentType(ct);
 			binary.setContent(theRequest.loadRequestContents());
-
 			retVal = binary;
-		} else {
+			}
+		}
+		
+		if (retVal == null) {
 			retVal = loadResourceFromRequest(theRequest, theMethodBinding, theResourceType);
 		}
 		return retVal;
 	}
 
 	public enum Mode {
-		BODY, ENCODING, RESOURCE
+		BODY, BODY_BYTE_ARRAY, ENCODING, RESOURCE
 	}
 
 }

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

@@ -54,7 +54,7 @@ public class Constants {
 	public static final String FORMAT_XML = "xml";
 	public static final String HEADER_ACCEPT = "Accept";
 	public static final String HEADER_ACCEPT_ENCODING = "Accept-Encoding";
-	public static final String HEADER_ACCEPT_VALUE_ALL = CT_FHIR_XML + ";q=1.0, " + CT_FHIR_JSON + ";q=1.0";
+	public static final String HEADER_ACCEPT_VALUE_XML_OR_JSON = CT_FHIR_XML + ";q=1.0, " + CT_FHIR_JSON + ";q=1.0";
 	public static final String HEADER_ALLOW = "Allow";
 	public static final String HEADER_AUTHORIZATION = "Authorization";
 	public static final String HEADER_AUTHORIZATION_VALPREFIX_BASIC = "Basic ";

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

@@ -44,6 +44,7 @@ public enum EncodingEnum {
 	;
 
 	private static HashMap<String, EncodingEnum> ourContentTypeToEncoding;
+	private static HashMap<String, EncodingEnum> ourContentTypeToEncodingStrict;
 
 	static {
 		ourContentTypeToEncoding = new HashMap<String, EncodingEnum>();
@@ -52,6 +53,9 @@ public enum EncodingEnum {
 			ourContentTypeToEncoding.put(next.getResourceContentType(), next);
 		}
 		
+		// Add before we add the lenient ones
+		ourContentTypeToEncodingStrict = new HashMap<String, EncodingEnum>(ourContentTypeToEncoding);
+
 		/*
 		 * These are wrong, but we add them just to be tolerant of other
 		 * people's mistakes
@@ -88,10 +92,30 @@ public enum EncodingEnum {
 		return myResourceContentType;
 	}
 
+	/**
+	 * Returns the encoding for a given content type, or <code>null</code> if no encoding
+	 * is found. 
+	 * <p>
+	 * <b>This method is lenient!</b> Things like "application/xml" will return {@link EncodingEnum#XML}
+	 * even if the "+fhir" part is missing from the expected content type.
+	 * </p>
+	 */
 	public static EncodingEnum forContentType(String theContentType) {
 		return ourContentTypeToEncoding.get(theContentType);
 	}
 
+	/**
+	 * Returns the encoding for a given content type, or <code>null</code> if no encoding
+	 * is found. 
+	 * <p>
+	 * <b>This method is NOT lenient!</b> Things like "application/xml" will return <code>null</code>
+	 * </p>
+	 * @see #forContentType(String)
+	 */
+	public static EncodingEnum forContentTypeStrict(String theContentType) {
+		return ourContentTypeToEncodingStrict.get(theContentType);
+	}
+
 	public String getFormatContentType() {
 		return myFormatContentType;
 	}

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

@@ -517,7 +517,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 
 	protected void handleRequest(RequestTypeEnum theRequestType, HttpServletRequest theRequest, HttpServletResponse theResponse) throws ServletException, IOException {
 		String fhirServerBase = null;
-		boolean requestIsBrowser = requestIsBrowser(theRequest);
 		ServletRequestDetails requestDetails = new ServletRequestDetails();
 		requestDetails.setServer(this);
 		requestDetails.setRequestType(theRequestType);
@@ -651,10 +650,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 				}
 			}
 
-			if (requestIsBrowser) {
-				// if request is coming from a browser, prompt the user to enter login credentials
-				theResponse.setHeader("WWW-Authenticate", "BASIC realm=\"FHIR\"");
-			}
 			writeExceptionToResponse(theResponse, e);
 
 		} catch (Throwable e) {
@@ -1399,9 +1394,4 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		return nextString.length() > 0 && (nextString.charAt(0) == '_' || nextString.charAt(0) == '$' || nextString.equals(Constants.URL_TOKEN_METADATA));
 	}
 
-	public static boolean requestIsBrowser(HttpServletRequest theRequest) {
-		String userAgent = theRequest.getHeader("User-Agent");
-		return userAgent != null && userAgent.contains("Mozilla");
-	}
-
 }

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -43,6 +43,9 @@ ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected duri
 # JPA Messages
 
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request.
+ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
+ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
+ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlMultipleMatches=Invalid match URL "{0}" - Multiple resources match this search
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided 
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1} 

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

@@ -34,32 +34,39 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 
 public class DaoConfig {
 
+	// ***
+	// update setter javadoc if default changes
+	// ***
+	private boolean myAllowInlineMatchUrlReferences = false; 
+
 	private boolean myAllowMultipleDelete; 
 	private int myHardSearchLimit = 1000;
 	private int myHardTagListLimit = 1000;
 	private int myIncludeLimit = 2000;
+
+	// ***
+	// update setter javadoc if default changes
+	// ***
+	private boolean myIndexContainedResources = true;
+
 	private List<IServerInterceptor> myInterceptors;
 	private ResourceEncodingEnum myResourceEncoding = ResourceEncodingEnum.JSONC;
 	private boolean mySchedulingDisabled;
 	private boolean mySubscriptionEnabled;
 	private long mySubscriptionPollDelay = 1000;
 	private Long mySubscriptionPurgeInactiveAfterMillis;
-
 	/**
 	 * See {@link #setIncludeLimit(int)}
 	 */
 	public int getHardSearchLimit() {
 		return myHardSearchLimit;
 	}
-
 	public int getHardTagListLimit() {
 		return myHardTagListLimit;
 	}
-
 	public int getIncludeLimit() {
 		return myIncludeLimit;
 	}
-
 	/**
 	 * Returns the interceptors which will be notified of operations.
 	 * 
@@ -84,10 +91,25 @@ public class DaoConfig {
 		return mySubscriptionPurgeInactiveAfterMillis;
 	}
 
+	/**
+	 * @see #setAllowInlineMatchUrlReferences(boolean)
+	 */
+	public boolean isAllowInlineMatchUrlReferences() {
+		return myAllowInlineMatchUrlReferences;
+	}
+
 	public boolean isAllowMultipleDelete() {
 		return myAllowMultipleDelete;
 	}
 
+	/**
+	 * Should contained IDs be indexed the same way that non-contained IDs are (default is
+	 * <code>true</code>) 
+	 */
+	public boolean isIndexContainedResources() {
+		return myIndexContainedResources;
+	}
+
 	public boolean isSchedulingDisabled() {
 		return mySchedulingDisabled;
 	}
@@ -99,6 +121,20 @@ public class DaoConfig {
 		return mySubscriptionEnabled;
 	}
 
+	/**
+	 * Should references containing match URLs be resolved and replaced in create and update operations. For
+	 * example, if this property is set to true and a resource is created containing a reference
+	 * to "Patient?identifier=12345", this is reference match URL will be resolved and replaced according
+	 * to the usual match URL rules.
+	 * <p>
+	 * Default is false for now, as this is an experimental feature.
+	 * </p>
+	 * @since 1.5
+	 */
+	public void setAllowInlineMatchUrlReferences(boolean theAllowInlineMatchUrlReferences) {
+		myAllowInlineMatchUrlReferences = theAllowInlineMatchUrlReferences;
+	}
+
 	public void setAllowMultipleDelete(boolean theAllowMultipleDelete) {
 		myAllowMultipleDelete = theAllowMultipleDelete;
 	}
@@ -120,6 +156,14 @@ public class DaoConfig {
 		myIncludeLimit = theIncludeLimit;
 	}
 
+	/**
+	 * Should contained IDs be indexed the same way that non-contained IDs are (default is
+	 * <code>true</code>) 
+	 */
+	public void setIndexContainedResources(boolean theIndexContainedResources) {
+		myIndexContainedResources = theIndexContainedResources;
+	}
+
 	/**
 	 * This may be used to optionally register server interceptors directly against the DAOs.
 	 * <p>

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

@@ -0,0 +1,34 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2016 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+import ca.uhn.fhir.jpa.entity.ForcedId;
+
+public interface IForcedIdDao extends JpaRepository<ForcedId, Long> {
+	
+	@Query("SELECT f FROM ForcedId f WHERE f.myResourcePid = :resource_pid")
+	public ForcedId findByResourcePid(@Param("resource_pid") Long theResourcePid);
+	
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java

@@ -462,7 +462,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 		FhirTerser terser = getContext().newTerser();
 		for (DaoMethodOutcome nextOutcome : idToPersistedOutcome.values()) {
-			IBaseResource nextResource = (IBaseResource) nextOutcome.getResource();
+			IBaseResource nextResource = nextOutcome.getResource();
 			if (nextResource == null) {
 				continue;
 			}

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

@@ -35,7 +35,8 @@ import javax.persistence.UniqueConstraint;
 //@formatter:off
 @Entity()
 @Table(name = "HFJ_FORCED_ID", uniqueConstraints = {
-		@UniqueConstraint(name = "IDX_FORCEDID", columnNames = {"FORCED_ID"})
+	@UniqueConstraint(name = "IDX_FORCEDID", columnNames = {"FORCED_ID"}),
+	@UniqueConstraint(name = "IDX_FORCEDID_RESID", columnNames = {"RESOURCE_PID"})
 })
 @NamedQueries(value = {
 		@NamedQuery(name = "Q_GET_FORCED_ID", query = "SELECT f FROM ForcedId f WHERE myForcedId = :ID")

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.entity;
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.Index;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.builder.EqualsBuilder;
@@ -34,9 +35,8 @@ import org.hibernate.search.annotations.Field;
 //@formatter:off
 @Embeddable
 @Entity
-@Table(name = "HFJ_SPIDX_COORDS" /* , indexes = { @Index(name = "IDX_SP_TOKEN", columnList = "SP_SYSTEM,SP_VALUE") } */)
+@Table(name = "HFJ_SPIDX_COORDS", indexes = { 
-@org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_COORDS", indexes = { 
+	@Index(name = "IDX_SP_COORDS", columnList = "RES_TYPE,SP_NAME,SP_LATITUDE,SP_LONGITUDE") 
-	@org.hibernate.annotations.Index(name = "IDX_SP_COORDS", columnNames = { "RES_TYPE", "SP_NAME", "SP_LATITUDE" }) 
 })
 //@formatter:on
 public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchParam {

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

@@ -144,6 +144,9 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	//@formatter:on
 	private String myContentText;
 
+	@Column(name = "HAS_CONTAINED", nullable = true)
+	private boolean myHasContainedResource;
+
 	@Column(name = "SP_HAS_LINKS")
 	private boolean myHasLinks;
 
@@ -158,6 +161,9 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	@Column(name = "SP_INDEX_STATUS", nullable = true)
 	private Long myIndexStatus;
 
+	@Column(name = "IS_CONTAINED", nullable = true)
+	private boolean myIsContainedResource;
+
 	@Column(name = "RES_LANGUAGE", length = MAX_LANGUAGE_LENGTH, nullable = true)
 	private String myLanguage;
 
@@ -340,10 +346,18 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		return false;
 	}
 
+	public boolean isHasContainedResource() {
+		return myHasContainedResource;
+	}
+
 	public boolean isHasLinks() {
 		return myHasLinks;
 	}
 
+	public boolean isIsContainedResource() {
+		return myIsContainedResource;
+	}
+
 	public boolean isParamsCoordsPopulated() {
 		return myParamsCoordsPopulated;
 	}
@@ -376,6 +390,10 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		myContentText = theContentText;
 	}
 
+	public void setHasContainedResource(boolean theHasContainedResource) {
+		myHasContainedResource = theHasContainedResource;
+	}
+
 	public void setHasLinks(boolean theHasLinks) {
 		myHasLinks = theHasLinks;
 	}
@@ -388,6 +406,10 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		myIndexStatus = theIndexStatus;
 	}
 
+	public void setIsContainedResource(boolean theIsContainedResource) {
+		myIsContainedResource = theIsContainedResource;
+	}
+
 	public void setLanguage(String theLanguage) {
 		if (defaultString(theLanguage).length() > MAX_LANGUAGE_LENGTH) {
 			throw new UnprocessableEntityException("Language exceeds maximum length of " + MAX_LANGUAGE_LENGTH + " chars: " + theLanguage);

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

@@ -1,8 +1,9 @@
 package ca.uhn.fhir.jpa.dao;
 
+import static org.mockito.Mockito.mock;
+
 import java.io.IOException;
 import java.io.InputStream;
-import java.sql.DriverManager;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
@@ -12,21 +13,29 @@ import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
+import org.junit.Before;
 
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 
 public class BaseJpaTest {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaTest.class);
+	protected ServletRequestDetails mySrd;
 
 	@SuppressWarnings({ "rawtypes" })
 	protected List toList(IBundleProvider theSearch) {
 		return theSearch.getResources(0, theSearch.size());
 	}
 
+	@Before
+	public void beforeCreateSrd() {
+		mySrd = mock(ServletRequestDetails.class);
+	}
+	
 	protected List<IIdType> toUnqualifiedVersionlessIds(Bundle theFound) {
 		List<IIdType> retVal = new ArrayList<IIdType>();
 		for (Entry next : theFound.getEntry()) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -47,6 +47,7 @@ import org.springframework.context.ApplicationContext;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionCallback;
@@ -239,14 +240,14 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 
 	public TransactionTemplate newTxTemplate() {
 		TransactionTemplate retVal = new TransactionTemplate(myTxManager);
-		retVal.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
+		retVal.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 		retVal.afterPropertiesSet();
 		return retVal;
 	}
 
 	public static void purgeDatabase(final EntityManager entityManager, PlatformTransactionManager theTxManager) {
 		TransactionTemplate txTemplate = new TransactionTemplate(theTxManager);
-		txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
+		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
 		txTemplate.execute(new TransactionCallback<Void>() {
 			@Override
 			public Void doInTransaction(TransactionStatus theStatus) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ContainedTest.java

@@ -0,0 +1,59 @@
+package ca.uhn.fhir.jpa.dao.dstu3;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertThat;
+
+import org.hl7.fhir.dstu3.model.Observation;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.Reference;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.Test;
+
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.TokenParamModifier;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+
+public class FhirResourceDaoDstu3ContainedTest extends BaseJpaDstu3Test {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ContainedTest.class);
+	
+	@Test
+	public void before() {
+		myDaoConfig.setIndexContainedResources(true);
+	}
+	
+	@Test
+	public void testIndexContained() {
+		Patient p = new Patient();
+		p.setId("#some_patient");
+		p.addName().addFamily("MYFAMILY").addGiven("MYGIVEN");
+		
+		Observation o1 = new Observation();
+		o1.getCode().setText("Some Observation");
+		o1.setSubject(new Reference(p));
+		IIdType oid1 = myObservationDao.create(o1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		
+		Observation o2 = new Observation();
+		o2.getCode().setText("Some Observation");
+		o2.setSubject(new Reference(p));
+		IIdType oid2 = myObservationDao.create(o2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+
+		Patient p2 = new Patient();
+		p2.addName().addFamily("MYFAMILY").addGiven("MYGIVEN");
+		IIdType pid2 = myPatientDao.create(p2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(o2));
+		
+		
+		SearchParameterMap map;
+		
+//		map = new SearchParameterMap();
+//		map.add(Observation.SP_CODE, new TokenParam(null, "some observation").setModifier(TokenParamModifier.TEXT));
+//		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1, id2)));
+
+	}
+
+	
+	// TODO: make sure match URLs don't delete
+	
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchFtTest.java

@@ -31,6 +31,7 @@ import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 
@@ -46,31 +47,35 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		obs1.setStatus(ObservationStatus.FINAL);
 		obs1.setValue(new Quantity(123));
 		obs1.setComments("obs1");
-		IIdType id1 = myObservationDao.create(obs1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
 		
 		Observation obs2 = new Observation();
 		obs2.getCode().setText("Diastolic Blood Pressure");
 		obs2.setStatus(ObservationStatus.FINAL);
 		obs2.setValue(new Quantity(81));
-		IIdType id2 = myObservationDao.create(obs2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
 		
 		SearchParameterMap map;
 		
 		map = new SearchParameterMap();
-		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setText(true));
+		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
 		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1, id2)));
 
 		map = new SearchParameterMap();
-		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setText(true));
+		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
 		assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(map)), empty());
 
 		map = new SearchParameterMap();
-		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setText(true));
+		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
 		map.add(Constants.PARAM_CONTENT, new StringParam("obs1"));
 		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1)));
 
 	}
 
+	private ServletRequestDetails mockSrd() {
+		return new ServletRequestDetails();
+	}
+
 	@Test
 	@Ignore
 	public void testStringTextSearch() {
@@ -78,13 +83,13 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		obs1.getCode().setText("AAAAA");
 		obs1.setValue(new StringType("Systolic Blood Pressure"));
 		obs1.setStatus(ObservationStatus.FINAL);
-		IIdType id1 = myObservationDao.create(obs1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType id1 = myObservationDao.create(obs1, mockSrd()).getId().toUnqualifiedVersionless();
 		
 		Observation obs2 = new Observation();
 		obs1.getCode().setText("AAAAA");
 		obs1.setValue(new StringType("Diastolic Blood Pressure"));
 		obs2.setStatus(ObservationStatus.FINAL);
-		IIdType id2 = myObservationDao.create(obs2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType id2 = myObservationDao.create(obs2, mockSrd()).getId().toUnqualifiedVersionless();
 		
 		SearchParameterMap map;
 		
@@ -99,7 +104,7 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 	public void testSuggestIgnoresBase64Content() {
 		Patient patient = new Patient();
 		patient.addName().addFamily("testSuggest");
-		IIdType ptId = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType ptId = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Media med = new Media();
 		med.getSubject().setReferenceElement(ptId);
@@ -107,7 +112,7 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		med.getContent().setContentType("LCws");
 		med.getContent().setDataElement(new Base64BinaryType(new byte[] {44,44,44,44,44,44,44,44}));
 		med.getContent().setTitle("bbbb syst");
-		myMediaDao.create(med, new ServletRequestDetails());
+		myMediaDao.create(med, mockSrd());
 		ourLog.info(myFhirCtx.newJsonParser().encodeResourceToString(med));
 		
 		List<Suggestion> output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "press");
@@ -139,35 +144,35 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 	public void testSuggest() {
 		Patient patient = new Patient();
 		patient.addName().addFamily("testSuggest");
-		IIdType ptId = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType ptId = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Observation obs = new Observation();
 		obs.getSubject().setReferenceElement(ptId);
 		obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
-		myObservationDao.create(obs, new ServletRequestDetails());
+		myObservationDao.create(obs, mockSrd());
 
 		obs = new Observation();
 		obs.getSubject().setReferenceElement(ptId);
 		obs.getCode().setText("MNBVCXZ");
-		myObservationDao.create(obs, new ServletRequestDetails());
+		myObservationDao.create(obs, mockSrd());
 
 		obs = new Observation();
 		obs.getSubject().setReferenceElement(ptId);
 		obs.getCode().setText("ZXC HELLO");
 		obs.addComponent().getCode().setText("HHHHHHHHHH");
-		myObservationDao.create(obs, new ServletRequestDetails());
+		myObservationDao.create(obs, mockSrd());
 
 		/*
 		 * These shouldn't match since they're for another patient
 		 */
 		patient = new Patient();
 		patient.addName().addFamily("testSuggest2");
-		IIdType ptId2 = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType ptId2 = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Observation obs2 = new Observation();
 		obs2.getSubject().setReferenceElement(ptId2);
 		obs2.getCode().setText("ZXCVBNMZZ");
-		myObservationDao.create(obs2, new ServletRequestDetails());
+		myObservationDao.create(obs2, mockSrd());
 
 		List<Suggestion> output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "ZXCVBNM");
 		ourLog.info("Found: " + output);
@@ -212,7 +217,7 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		patient = new Patient();
 		patient.getText().setDivAsString("<div>DIVAAA</div>");
 		patient.addName().addGiven("NAMEAAA");
-		IIdType pId1 = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType pId1 = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
 
 		map = new SearchParameterMap();
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));
@@ -230,7 +235,7 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		patient.setId(pId1);
 		patient.getText().setDivAsString("<div>DIVBBB</div>");
 		patient.addName().addGiven("NAMEBBB");
-		myPatientDao.update(patient, new ServletRequestDetails());
+		myPatientDao.update(patient, mockSrd());
 
 		map = new SearchParameterMap();
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));
@@ -254,19 +259,19 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 	public void testEverythingInstanceWithContentFilter() {
 		Patient pt1 = new Patient();
 		pt1.addName().addFamily("Everything").addGiven("Arthur");
-		IIdType ptId1 = myPatientDao.create(pt1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType ptId1 = myPatientDao.create(pt1, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Patient pt2 = new Patient();
 		pt2.addName().addFamily("Everything").addGiven("Arthur");
-		IIdType ptId2 = myPatientDao.create(pt2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType ptId2 = myPatientDao.create(pt2, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Device dev1 = new Device();
 		dev1.setManufacturer("Some Manufacturer");
-		IIdType devId1 = myDeviceDao.create(dev1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType devId1 = myDeviceDao.create(dev1, mockSrd()).getId().toUnqualifiedVersionless();
 		
 		Device dev2 = new Device();
 		dev2.setManufacturer("Some Manufacturer 2");
-		myDeviceDao.create(dev2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		myDeviceDao.create(dev2, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Observation obs1 = new Observation();
 		obs1.getText().setDivAsString("<div>OBSTEXT1</div>");
@@ -274,19 +279,19 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		obs1.getCode().addCoding().setCode("CODE1");
 		obs1.setValue(new StringType("obsvalue1"));
 		obs1.getDevice().setReferenceElement(devId1);
-		IIdType obsId1 = myObservationDao.create(obs1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType obsId1 = myObservationDao.create(obs1, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Observation obs2 = new Observation();
 		obs2.getSubject().setReferenceElement(ptId1);
 		obs2.getCode().addCoding().setCode("CODE2");
 		obs2.setValue(new StringType("obsvalue2"));
-		IIdType obsId2 = myObservationDao.create(obs2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType obsId2 = myObservationDao.create(obs2, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Observation obs3 = new Observation();
 		obs3.getSubject().setReferenceElement(ptId2);
 		obs3.getCode().addCoding().setCode("CODE3");
 		obs3.setValue(new StringType("obsvalue3"));
-		IIdType obsId3 = myObservationDao.create(obs3, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType obsId3 = myObservationDao.create(obs3, mockSrd()).getId().toUnqualifiedVersionless();
 		
 		HttpServletRequest request;
 		List<String> actual;
@@ -297,16 +302,16 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, devId1)));
 
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obstext1")));
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, param, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, param, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, devId1)));
 
 		request = mock(HttpServletRequest.class);
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, null, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, null, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId2, devId1)));
 
 		/*
@@ -317,12 +322,12 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		obs4.getSubject().setReferenceElement(ptId1);
 		obs4.getCode().addCoding().setCode("CODE1");
 		obs4.setValue(new StringType("obsvalue1"));
-		IIdType obsId4 = myObservationDao.create(obs4, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType obsId4 = myObservationDao.create(obs4, mockSrd()).getId().toUnqualifiedVersionless();
 		assertNotEquals(obsId1.getIdPart(), obsId4.getIdPart(), devId1);
 
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId4, devId1)));
 
 		/*
@@ -334,11 +339,11 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		obs1.getSubject().setReferenceElement(ptId1);
 		obs1.getCode().addCoding().setCode("CODE2");
 		obs1.setValue(new StringType("obsvalue2"));
-		myObservationDao.update(obs1, new ServletRequestDetails());
+		myObservationDao.update(obs1, mockSrd());
 
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId4)));
 
 	}
@@ -347,38 +352,38 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 	public void testEverythingTypeWithContentFilter() {
 		Patient pt1 = new Patient();
 		pt1.addName().addFamily("Everything").addGiven("Arthur");
-		IIdType ptId1 = myPatientDao.create(pt1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType ptId1 = myPatientDao.create(pt1, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Patient pt2 = new Patient();
 		pt2.addName().addFamily("Everything").addGiven("Arthur");
-		IIdType ptId2 = myPatientDao.create(pt2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType ptId2 = myPatientDao.create(pt2, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Device dev1 = new Device();
 		dev1.setManufacturer("Some Manufacturer");
-		IIdType devId1 = myDeviceDao.create(dev1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType devId1 = myDeviceDao.create(dev1, mockSrd()).getId().toUnqualifiedVersionless();
 		
 		Device dev2 = new Device();
 		dev2.setManufacturer("Some Manufacturer 2");
-		IIdType devId2 = myDeviceDao.create(dev2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		myDeviceDao.create(dev2, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Observation obs1 = new Observation();
 		obs1.getSubject().setReferenceElement(ptId1);
 		obs1.getCode().addCoding().setCode("CODE1");
 		obs1.setValue(new StringType("obsvalue1"));
 		obs1.getDevice().setReferenceElement(devId1);
-		IIdType obsId1 = myObservationDao.create(obs1, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType obsId1 = myObservationDao.create(obs1, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Observation obs2 = new Observation();
 		obs2.getSubject().setReferenceElement(ptId1);
 		obs2.getCode().addCoding().setCode("CODE2");
 		obs2.setValue(new StringType("obsvalue2"));
-		IIdType obsId2 = myObservationDao.create(obs2, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType obsId2 = myObservationDao.create(obs2, mockSrd()).getId().toUnqualifiedVersionless();
 
 		Observation obs3 = new Observation();
 		obs3.getSubject().setReferenceElement(ptId2);
 		obs3.getCode().addCoding().setCode("CODE3");
 		obs3.setValue(new StringType("obsvalue3"));
-		IIdType obsId3 = myObservationDao.create(obs3, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType obsId3 = myObservationDao.create(obs3, mockSrd()).getId().toUnqualifiedVersionless();
 		
 		HttpServletRequest request;
 		List<String> actual;
@@ -389,11 +394,11 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, param, null, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, param, null, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, devId1)));
 
 		request = mock(HttpServletRequest.class);
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, null, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, null, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId2, devId1, ptId2, obsId3)));
 
 		/*
@@ -404,12 +409,12 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		obs4.getSubject().setReferenceElement(ptId1);
 		obs4.getCode().addCoding().setCode("CODE1");
 		obs4.setValue(new StringType("obsvalue1"));
-		IIdType obsId4 = myObservationDao.create(obs4, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType obsId4 = myObservationDao.create(obs4, mockSrd()).getId().toUnqualifiedVersionless();
 		assertNotEquals(obsId1.getIdPart(), obsId4.getIdPart(), devId1);
 
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, param, null, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, param, null, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId4, devId1)));
 
 		/*
@@ -421,11 +426,11 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		obs1.getSubject().setReferenceElement(ptId1);
 		obs1.getCode().addCoding().setCode("CODE2");
 		obs1.setValue(new StringType("obsvalue2"));
-		myObservationDao.update(obs1, new ServletRequestDetails());
+		myObservationDao.update(obs1, mockSrd());
 
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
-		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, param, null, new ServletRequestDetails()));
+		actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, param, null, mockSrd()));
 		assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId4)));
 
 	}
@@ -443,7 +448,7 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		patient = new Patient();
 		patient.getText().setDivAsString("<div>DIVAAA</div>");
 		patient.addName().addGiven("NAMEAAA");
-		IIdType pId1 = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType pId1 = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
 
 		map = new SearchParameterMap();
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));
@@ -461,7 +466,7 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		patient.setId(pId1);
 		patient.getText().setDivAsString("<div>DIVBBB</div>");
 		patient.addName().addGiven("NAMEBBB");
-		myPatientDao.update(patient, null, false, new ServletRequestDetails());
+		myPatientDao.update(patient, null, false, mockSrd());
 
 		map = new SearchParameterMap();
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));
@@ -470,7 +475,7 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEBBB"));
 		assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(map)), not(contains(toValues(pId1))));
 
-		myPatientDao.update(patient, null, true, new ServletRequestDetails());
+		myPatientDao.update(patient, null, true, mockSrd());
 
 		map = new SearchParameterMap();
 		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));
@@ -498,18 +503,18 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 			Patient patient = new Patient();
 			patient.addName().addGiven(methodName);
 			patient.addAddress().addLine("My fulltext address");
-			pId1 = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+			pId1 = myPatientDao.create(patient, mockSrd()).getId().toUnqualifiedVersionless();
 		}
 
 		Observation obs = new Observation();
 		obs.getSubject().setReferenceElement(pId1);
 		obs.setValue(new StringType("This is the FULLtext of the observation"));
-		IIdType oId1 = myObservationDao.create(obs, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType oId1 = myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless();
 
 		obs = new Observation();
 		obs.getSubject().setReferenceElement(pId1);
 		obs.setValue(new StringType("Another fullText"));
-		IIdType oId2 = myObservationDao.create(obs, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		IIdType oId2 = myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless();
 
 		List<String> patients;
 		SearchParameterMap params;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java

@@ -23,7 +23,6 @@ import java.util.Set;
 import javax.servlet.http.HttpServletRequest;
 
 import org.apache.commons.lang3.StringUtils;
-import org.hl7.fhir.dstu3.model.BaseResource;
 import org.hl7.fhir.dstu3.model.CodeType;
 import org.hl7.fhir.dstu3.model.ConceptMap;
 import org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem;
@@ -52,6 +51,7 @@ import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
 import org.hl7.fhir.dstu3.model.Substance;
 import org.hl7.fhir.dstu3.model.TemporalPrecisionEnum;
 import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Ignore;
@@ -586,21 +586,21 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		}
 		{
 			Map<String, IQueryParameterType> params = new HashMap<String, IQueryParameterType>();
-			params.put(BaseResource.SP_RES_LANGUAGE, new StringParam("en_CA"));
+			params.put(IAnyResource.SP_RES_LANGUAGE, new StringParam("en_CA"));
 			List<IBaseResource> patients = toList(myPatientDao.search(params));
 			assertEquals(1, patients.size());
 			assertEquals(id1.toUnqualifiedVersionless(), patients.get(0).getIdElement().toUnqualifiedVersionless());
 		}
 		{
 			Map<String, IQueryParameterType> params = new HashMap<String, IQueryParameterType>();
-			params.put(BaseResource.SP_RES_LANGUAGE, new StringParam("en_US"));
+			params.put(IAnyResource.SP_RES_LANGUAGE, new StringParam("en_US"));
 			List<Patient> patients = toList(myPatientDao.search(params));
 			assertEquals(1, patients.size());
 			assertEquals(id2.toUnqualifiedVersionless(), patients.get(0).getIdElement().toUnqualifiedVersionless());
 		}
 		{
 			Map<String, IQueryParameterType> params = new HashMap<String, IQueryParameterType>();
-			params.put(BaseResource.SP_RES_LANGUAGE, new StringParam("en_GB"));
+			params.put(IAnyResource.SP_RES_LANGUAGE, new StringParam("en_GB"));
 			List<Patient> patients = toList(myPatientDao.search(params));
 			assertEquals(0, patients.size());
 		}
@@ -629,18 +629,18 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		}
 		{
 			SearchParameterMap params = new SearchParameterMap();
-			params.add(BaseResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("en_US")));
+			params.add(IAnyResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("en_US")));
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1, id2));
 		}
 		{
 			SearchParameterMap params = new SearchParameterMap();
-			params.add(BaseResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("en_US")));
+			params.add(IAnyResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("en_US")));
 			params.setLastUpdated(new DateRangeParam(betweenTime, null));
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id2));
 		}
 		{
 			SearchParameterMap params = new SearchParameterMap();
-			params.add(BaseResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
+			params.add(IAnyResource.SP_RES_LANGUAGE, new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
 		}
 		{
@@ -648,7 +648,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			StringAndListParam and = new StringAndListParam();
 			and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
 			and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")));
-			params.add(BaseResource.SP_RES_LANGUAGE, and);
+			params.add(IAnyResource.SP_RES_LANGUAGE, and);
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
 		}
 		{
@@ -656,7 +656,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			StringAndListParam and = new StringAndListParam();
 			and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
 			and.addAnd(new StringOrListParam().addOr(new StringParam("ZZZZZ")));
-			params.add(BaseResource.SP_RES_LANGUAGE, and);
+			params.add(IAnyResource.SP_RES_LANGUAGE, and);
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty());
 		}
 		{
@@ -664,7 +664,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			StringAndListParam and = new StringAndListParam();
 			and.addAnd(new StringOrListParam().addOr(new StringParam("ZZZZZ")));
 			and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
-			params.add(BaseResource.SP_RES_LANGUAGE, and);
+			params.add(IAnyResource.SP_RES_LANGUAGE, and);
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty());
 		}
 		{
@@ -672,7 +672,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			StringAndListParam and = new StringAndListParam();
 			and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
 			and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
-			params.add(BaseResource.SP_RES_LANGUAGE, and);
+			params.add(IAnyResource.SP_RES_LANGUAGE, and);
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
 		}
 		{
@@ -681,7 +681,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			StringAndListParam and = new StringAndListParam();
 			and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
 			and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
-			params.add(BaseResource.SP_RES_LANGUAGE, and);
+			params.add(IAnyResource.SP_RES_LANGUAGE, and);
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
 		}
 		{
@@ -689,7 +689,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 			StringAndListParam and = new StringAndListParam();
 			and.addAnd(new StringOrListParam().addOr(new StringParam("en_CA")).addOr(new StringParam("ZZZZ")));
 			and.addAnd(new StringOrListParam().addOr(new StringParam("")).addOr(new StringParam(null)));
-			params.add(BaseResource.SP_RES_LANGUAGE, and);
+			params.add(IAnyResource.SP_RES_LANGUAGE, and);
 			params.add("_id", new StringParam(id1.getIdPart()));
 			assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1));
 		}
@@ -767,8 +767,6 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 
 	@Test
 	public void testSearchLastUpdatedParamWithComparator() throws InterruptedException {
-		String methodName = "testSearchLastUpdatedParamWithComparator";
-
 		IIdType id0;
 		{
 			Patient patient = new Patient();
@@ -781,7 +779,6 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		long start = System.currentTimeMillis();
 		Thread.sleep(sleep);
 
-		DateTimeType beforeAny = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
 		IIdType id1a;
 		{
 			Patient patient = new Patient();
@@ -815,12 +812,12 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), containsInAnyOrder(id1a, id1b));
 		
 		map = new SearchParameterMap();
-		map.setLastUpdated(new DateRangeParam(new DateParam(QuantityCompararatorEnum.GREATERTHAN_OR_EQUALS, startDateTime), new DateParam(QuantityCompararatorEnum.LESSTHAN_OR_EQUALS, endDateTime)));
+		map.setLastUpdated(new DateRangeParam(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, startDateTime), new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, endDateTime)));
 		ourLog.info("Searching: {}", map.getLastUpdated());
 		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), containsInAnyOrder(id1a, id1b));
 		
 		map = new SearchParameterMap();
-		map.setLastUpdated(new DateRangeParam(new DateParam(QuantityCompararatorEnum.GREATERTHAN, startDateTime), new DateParam(QuantityCompararatorEnum.LESSTHAN, endDateTime)));
+		map.setLastUpdated(new DateRangeParam(new DateParam(ParamPrefixEnum.GREATERTHAN, startDateTime), new DateParam(ParamPrefixEnum.LESSTHAN, endDateTime)));
 		ourLog.info("Searching: {}", map.getLastUpdated());
 		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), containsInAnyOrder(id1a, id1b));
 
@@ -1373,7 +1370,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 
 		QuantityParam param;
 		Set<Long> found;
-		param = new QuantityParam(QuantityCompararatorEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null);
+		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null);
 		found = myObservationDao.searchForIds("value-quantity", param);
 		int initialSize = found.size();
 
@@ -1384,19 +1381,19 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 
 		myObservationDao.create(o, new ServletRequestDetails());
 
-		param = new QuantityParam(QuantityCompararatorEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null);
+		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null);
 		found = myObservationDao.searchForIds("value-quantity", param);
 		assertEquals(1 + initialSize, found.size());
 
-		param = new QuantityParam(QuantityCompararatorEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, methodName + "units");
+		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, methodName + "units");
 		found = myObservationDao.searchForIds("value-quantity", param);
 		assertEquals(1, found.size());
 
-		param = new QuantityParam(QuantityCompararatorEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), "urn:bar:" + methodName, null);
+		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), "urn:bar:" + methodName, null);
 		found = myObservationDao.searchForIds("value-quantity", param);
 		assertEquals(1, found.size());
 
-		param = new QuantityParam(QuantityCompararatorEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), "urn:bar:" + methodName, methodName + "units");
+		param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), "urn:bar:" + methodName, methodName + "units");
 		found = myObservationDao.searchForIds("value-quantity", param);
 		assertEquals(1, found.size());
 
@@ -1406,8 +1403,8 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 	public void testSearchWithEmptySort() {
 		SearchParameterMap criteriaUrl = new SearchParameterMap();
 		DateRangeParam range = new DateRangeParam();
-		range.setLowerBound(new DateParam(QuantityCompararatorEnum.GREATERTHAN, 1000000));
+		range.setLowerBound(new DateParam(ParamPrefixEnum.GREATERTHAN, 1000000));
-		range.setUpperBound(new DateParam(QuantityCompararatorEnum.LESSTHAN, 2000000));
+		range.setUpperBound(new DateParam(ParamPrefixEnum.LESSTHAN, 2000000));
 		criteriaUrl.setLastUpdated(range);
 		criteriaUrl.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC));
 		IBundleProvider results = myObservationDao.search(criteriaUrl);
@@ -1555,7 +1552,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 
 		{
 			SearchParameterMap params = new SearchParameterMap();
-			params.add(BaseResource.SP_RES_ID, new StringParam(orgId.getIdPart()));
+			params.add(IAnyResource.SP_RES_ID, new StringParam(orgId.getIdPart()));
 			params.addInclude(Organization.INCLUDE_PARTOF.asNonRecursive());
 			List<IIdType> resources = toUnqualifiedVersionlessIds(myOrganizationDao.search(params));
 			assertThat(resources, contains(orgId, parentOrgId));
@@ -1597,7 +1594,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 
 		{
 			SearchParameterMap params = new SearchParameterMap();
-			params.add(Organization.SP_RES_ID, new StringParam(orgId.getIdPart()));
+			params.add(IAnyResource.SP_RES_ID, new StringParam(orgId.getIdPart()));
 			params.addInclude(Organization.INCLUDE_PARTOF.asRecursive());
 			List<IIdType> resources = toUnqualifiedVersionlessIds(myOrganizationDao.search(params));
 			ourLog.info(resources.toString());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java

@@ -42,8 +42,10 @@ import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.After;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
+import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
@@ -112,7 +114,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		// Try making the resource unparseable
 
 		TransactionTemplate template = new TransactionTemplate(myTxManager);
-		template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
+		template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 		template.execute(new TransactionCallback<ResourceTable>() {
 			@Override
 			public ResourceTable doInTransaction(TransactionStatus theStatus) {
@@ -305,6 +307,100 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 
 	}
 
+	@After
+	public void after() {
+		myDaoConfig.setAllowInlineMatchUrlReferences(false);
+	}
+	
+	@Test
+	public void testTransactionCreateInlineMatchUrlWithOneMatch() {
+		String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch";
+		Bundle request = new Bundle();
+
+		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IIdType id = myPatientDao.update(p, mySrd).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference("Patient?identifier=urn%3Asystem%7C" + methodName);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(myRequestDetails, request);
+		assertEquals(1, resp.getEntry().size());
+
+		BundleEntryComponent respEntry = resp.getEntry().get(0);
+		assertEquals(Constants.STATUS_HTTP_201_CREATED + " Created", respEntry.getResponse().getStatus());
+		assertThat(respEntry.getResponse().getLocation(), containsString("Observation/"));
+		assertThat(respEntry.getResponse().getLocation(), endsWith("/_history/1"));
+		assertEquals("1", respEntry.getResponse().getEtag());
+
+		o = myObservationDao.read(new IdType(respEntry.getResponse().getLocationElement()), mySrd);
+		assertEquals(id.toVersionless().getValue(), o.getSubject().getReference());
+		assertEquals("1", o.getIdElement().getVersionIdPart());
+
+	}
+
+	@Test
+	public void testTransactionCreateInlineMatchUrlWithNoMatches() {
+		String methodName = "testTransactionCreateInlineMatchUrlWithNoMatches";
+		Bundle request = new Bundle();
+
+		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		myPatientDao.create(p, mySrd).getId();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		myPatientDao.create(p, mySrd).getId();
+
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference("Patient?identifier=urn%3Asystem%7C" + methodName);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		try {
+			mySystemDao.transaction(myRequestDetails, request);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid match URL \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateInlineMatchUrlWithNoMatches\" - Multiple resources match this search", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testTransactionCreateInlineMatchUrlWithTwoMatches() {
+		String methodName = "testTransactionCreateInlineMatchUrlWithTwoMatches";
+		Bundle request = new Bundle();
+
+		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		myPatientDao.create(p, mySrd).getId();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		myPatientDao.create(p, mySrd).getId();
+
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference("Patient?identifier=urn%3Asystem%7C" + methodName);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		try {
+			mySystemDao.transaction(myRequestDetails, request);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid match URL \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateInlineMatchUrlWithTwoMatches\" - Multiple resources match this search", e.getMessage());
+		}
+	}
+
 	@Test
 	public void testTransactionCreateMatchUrlWithTwoMatch() {
 		String methodName = "testTransactionCreateMatchUrlWithTwoMatch";

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -50,6 +50,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.setSubscriptionPollDelay(5000);
 		retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
 		retVal.setAllowMultipleDelete(true);
+		retVal.setAllowInlineMatchUrlReferences(true);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -46,6 +46,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.setSubscriptionPollDelay(5000);
 		retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
 		retVal.setAllowMultipleDelete(true);
+		retVal.setAllowInlineMatchUrlReferences(true);
 		return retVal;
 	}
 

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

@@ -1,7 +1,9 @@
 package ca.uhn.fhir.rest.client;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertArrayEquals;
-import static org.mockito.Mockito.*;
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 import java.io.ByteArrayInputStream;
 
@@ -17,11 +19,9 @@ import org.apache.http.message.BasicStatusLine;
 import org.junit.Before;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
-import org.mockito.Mockito;
 import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.dstu.resource.Binary;
 import ca.uhn.fhir.model.dstu.resource.Conformance;
 import ca.uhn.fhir.model.dstu.resource.Patient;
@@ -48,7 +48,7 @@ public class BinaryClientTest {
 
 		httpClient = mock(HttpClient.class, new ReturnsDeepStubs());
 		ctx.getRestfulClientFactory().setHttpClient(httpClient);
-		ctx.getRestfulClientFactory().setServerValidationModeEnum(ServerValidationModeEnum.NEVER);
+		ctx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
 
 		httpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
 	}
@@ -59,7 +59,7 @@ public class BinaryClientTest {
 		when(httpClient.execute(capt.capture())).thenReturn(httpResponse);
 		when(httpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(httpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", "foo/bar"));
-		when(httpResponse.getEntity().getContent()).thenReturn(new ByteArrayInputStream(new byte[] {1,2,3,4}));
+		when(httpResponse.getEntity().getContent()).thenReturn(new ByteArrayInputStream(new byte[] { 1, 2, 3, 4 }));
 
 		IClient client = ctx.newRestfulClient(IClient.class, "http://foo");
 		Binary resp = client.read(new IdDt("http://foo/Patient/123"));
@@ -72,13 +72,6 @@ public class BinaryClientTest {
 		assertArrayEquals(new byte[] { 1, 2, 3, 4 }, resp.getContent());
 	}
 
-	public static void main(String[] args) {
-		
-		IClient c = Mockito.mock(IClient.class, new ReturnsDeepStubs());
-		
-	}
-	
-	
 	@Test
 	public void testCreate() throws Exception {
 		Binary res = new Binary();
@@ -92,29 +85,23 @@ public class BinaryClientTest {
 		when(httpResponse.getEntity().getContent()).thenReturn(new ByteArrayInputStream(new byte[] {}));
 
 		IClient client = ctx.newRestfulClient(IClient.class, "http://foo");
-		MethodOutcome resp = client.create(res);
+		client.create(res);
 
 		assertEquals(HttpPost.class, capt.getValue().getClass());
 		HttpPost post = (HttpPost) capt.getValue();
 		assertEquals("http://foo/Binary", post.getURI().toString());
 
-		assertEquals("text/plain", post.getEntity().getContentType().getValue());
+		assertEquals("text/plain", capt.getValue().getFirstHeader("Content-Type").getValue());
 		assertArrayEquals(new byte[] { 1, 2, 3, 4 }, IOUtils.toByteArray(post.getEntity().getContent()));
 
 	}
 
-
-	private String createBundle() {
-		return ctx.newXmlParser().encodeBundleToString(new Bundle());
-	}
-
-
 	private interface IClient extends IBasicClient {
 
-		@Read(type=Binary.class)
+		@Read(type = Binary.class)
 		public Binary read(@IdParam IdDt theBinary);
 
-		@Create(type=Binary.class)
+		@Create(type = Binary.class)
 		public MethodOutcome create(@ResourceParam Binary theBinary);
 
 	}

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

@@ -173,8 +173,8 @@ public class DynamicSearchTest {
 		@Override
 		public List<RuntimeSearchParam> getSearchParameters() {
 			ArrayList<RuntimeSearchParam> retVal = new ArrayList<RuntimeSearchParam>();
-			retVal.add(new RuntimeSearchParam("param1", "This is the first parameter", "Patient.param1", RestSearchParameterTypeEnum.STRING));
+			retVal.add(new RuntimeSearchParam("param1", "This is the first parameter", "Patient.param1", RestSearchParameterTypeEnum.STRING, null));
-			retVal.add(new RuntimeSearchParam("param2", "This is the second parameter", "Patient.param2", RestSearchParameterTypeEnum.DATE));
+			retVal.add(new RuntimeSearchParam("param2", "This is the second parameter", "Patient.param2", RestSearchParameterTypeEnum.DATE, null));
 			return retVal;
 		}
 

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

@@ -143,7 +143,7 @@ public class GenericClientDstu2Test {
 		client.fetchConformance().ofType(Conformance.class).execute();
 		assertEquals("http://example.com/fhir/metadata", capt.getAllValues().get(idx).getURI().toASCIIString());
 		assertEquals(1, capt.getAllValues().get(idx).getHeaders("Accept").length);
-		assertThat(capt.getAllValues().get(idx).getHeaders("Accept")[0].getValue(), containsString(Constants.HEADER_ACCEPT_VALUE_ALL));
+		assertThat(capt.getAllValues().get(idx).getHeaders("Accept")[0].getValue(), containsString(Constants.HEADER_ACCEPT_VALUE_XML_OR_JSON));
 		idx++;
 
 		client.fetchConformance().ofType(Conformance.class).encodedJson().execute();
@@ -192,12 +192,12 @@ public class GenericClientDstu2Test {
 		assertEquals("FAMILY", resp.getName().get(0).getFamily().get(0).getValue());
 		assertEquals("http://" + methodName + ".example.com/fhir/metadata", capt.getAllValues().get(0).getURI().toASCIIString());
 		assertEquals(1, capt.getAllValues().get(0).getHeaders("Accept").length);
-		assertThat(capt.getAllValues().get(0).getHeaders("Accept")[0].getValue(), containsString(Constants.HEADER_ACCEPT_VALUE_ALL));
+		assertThat(capt.getAllValues().get(0).getHeaders("Accept")[0].getValue(), containsString(Constants.HEADER_ACCEPT_VALUE_XML_OR_JSON));
 		assertThat(capt.getAllValues().get(0).getHeaders("Accept")[0].getValue(), containsString(Constants.CT_FHIR_XML));
 		assertThat(capt.getAllValues().get(0).getHeaders("Accept")[0].getValue(), containsString(Constants.CT_FHIR_JSON));
 		assertEquals("http://" + methodName + ".example.com/fhir/Patient/123", capt.getAllValues().get(1).getURI().toASCIIString());
 		assertEquals(1, capt.getAllValues().get(1).getHeaders("Accept").length);
-		assertThat(capt.getAllValues().get(1).getHeaders("Accept")[0].getValue(), containsString(Constants.HEADER_ACCEPT_VALUE_ALL));
+		assertThat(capt.getAllValues().get(1).getHeaders("Accept")[0].getValue(), containsString(Constants.HEADER_ACCEPT_VALUE_XML_OR_JSON));
 		assertThat(capt.getAllValues().get(1).getHeaders("Accept")[0].getValue(), containsString(Constants.CT_FHIR_XML));
 		assertThat(capt.getAllValues().get(1).getHeaders("Accept")[0].getValue(), containsString(Constants.CT_FHIR_JSON));
 	}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu3Test.java

@@ -0,0 +1,219 @@
+package ca.uhn.fhir.rest.client;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.nio.charset.Charset;
+import java.util.Arrays;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.input.ReaderInputStream;
+import org.apache.http.HttpResponse;
+import org.apache.http.ProtocolVersion;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpEntityEnclosingRequestBase;
+import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.message.BasicHeader;
+import org.apache.http.message.BasicStatusLine;
+import org.hl7.fhir.dstu3.model.Binary;
+import org.hl7.fhir.dstu3.model.Conformance;
+import org.hl7.fhir.dstu3.model.OperationOutcome;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.util.VersionUtil;
+
+public class GenericClientDstu3Test {
+	private static FhirContext ourCtx;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(GenericClientDstu3Test.class);
+	private HttpClient myHttpClient;
+	private HttpResponse myHttpResponse;
+
+	@Before
+	public void before() {
+		myHttpClient = mock(HttpClient.class, new ReturnsDeepStubs());
+		ourCtx.getRestfulClientFactory().setHttpClient(myHttpClient);
+		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+		myHttpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
+	}
+
+	private byte[] extractBodyAsByteArray(ArgumentCaptor<HttpUriRequest> capt) throws IOException {
+		byte[] body = IOUtils.toByteArray(((HttpEntityEnclosingRequestBase) capt.getAllValues().get(0)).getEntity().getContent());
+		return body;
+	}
+
+	private String extractBodyAsString(ArgumentCaptor<HttpUriRequest> capt) throws IOException {
+		String body = IOUtils.toString(((HttpEntityEnclosingRequestBase) capt.getAllValues().get(0)).getEntity().getContent(), "UTF-8");
+		return body;
+	}
+
+	@Test
+	public void testUserAgentForConformance() throws Exception {
+		IParser p = ourCtx.newXmlParser();
+
+		Conformance conf = new Conformance();
+		conf.setCopyright("COPY");
+
+		final String respString = p.encodeResourceToString(conf);
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
+			@Override
+			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
+			}
+		});
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		client.fetchConformance().ofType(Conformance.class).execute();
+		assertEquals("http://example.com/fhir/metadata", capt.getAllValues().get(0).getURI().toASCIIString());
+		validateUserAgent(capt);
+	}
+
+	@Test
+	public void testUserAgentForBinary() throws Exception {
+		IParser p = ourCtx.newXmlParser();
+
+		Conformance conf = new Conformance();
+		conf.setCopyright("COPY");
+
+		final String respString = p.encodeResourceToString(conf);
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
+			@Override
+			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
+			}
+		});
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		Binary bin = new Binary();
+		bin.setContentType("application/foo");
+		bin.setContent(new byte[] { 0, 1, 2, 3, 4 });
+		client.create().resource(bin).execute();
+
+		ourLog.info(Arrays.asList(capt.getAllValues().get(0).getAllHeaders()).toString());
+
+		assertEquals("http://example.com/fhir/Binary", capt.getAllValues().get(0).getURI().toASCIIString());
+		validateUserAgent(capt);
+
+		assertEquals("application/foo", capt.getAllValues().get(0).getHeaders("Content-Type")[0].getValue());
+		assertEquals(Constants.HEADER_ACCEPT_VALUE_XML_OR_JSON, capt.getAllValues().get(0).getHeaders("Accept")[0].getValue());
+		assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, extractBodyAsByteArray(capt));
+
+	}
+
+	@Test
+	public void testBinaryCreateWithNoContentType() throws Exception {
+		IParser p = ourCtx.newXmlParser();
+
+		OperationOutcome conf = new OperationOutcome();
+		conf.getText().setDivAsString("OK!");
+
+		final String respString = p.encodeResourceToString(conf);
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
+			@Override
+			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
+			}
+		});
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		Binary bin = new Binary();
+		bin.setContent(new byte[] { 0, 1, 2, 3, 4 });
+		client.create().resource(bin).execute();
+
+		ourLog.info(Arrays.asList(capt.getAllValues().get(0).getAllHeaders()).toString());
+
+		assertEquals("http://example.com/fhir/Binary", capt.getAllValues().get(0).getURI().toASCIIString());
+		validateUserAgent(capt);
+
+		assertEquals("application/xml+fhir;charset=utf-8", capt.getAllValues().get(0).getHeaders("Content-Type")[0].getValue().toLowerCase().replace(" ", ""));
+		assertEquals(Constants.CT_FHIR_XML, capt.getAllValues().get(0).getHeaders("Accept")[0].getValue());
+		assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourCtx.newXmlParser().parseResource(Binary.class, extractBodyAsString(capt)).getContent());
+
+	}
+
+	@Test
+	public void testBinaryCreateWithFhirContentType() throws Exception {
+		IParser p = ourCtx.newXmlParser();
+
+		OperationOutcome conf = new OperationOutcome();
+		conf.getText().setDivAsString("OK!");
+
+		final String respString = p.encodeResourceToString(conf);
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
+			@Override
+			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
+			}
+		});
+
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		Patient pt = new Patient();
+		pt.getText().setDivAsString("A PATIENT");
+
+		Binary bin = new Binary();
+		bin.setContent(ourCtx.newJsonParser().encodeResourceToString(pt).getBytes("UTF-8"));
+		bin.setContentType(Constants.CT_FHIR_JSON);
+		client.create().resource(bin).execute();
+
+		ourLog.info(Arrays.asList(capt.getAllValues().get(0).getAllHeaders()).toString());
+
+		assertEquals("http://example.com/fhir/Binary", capt.getAllValues().get(0).getURI().toASCIIString());
+		validateUserAgent(capt);
+
+		assertEquals("application/xml+fhir;charset=utf-8", capt.getAllValues().get(0).getHeaders("Content-Type")[0].getValue().toLowerCase().replace(" ", ""));
+		assertEquals(Constants.CT_FHIR_XML, capt.getAllValues().get(0).getHeaders("Accept")[0].getValue());
+		Binary output = ourCtx.newXmlParser().parseResource(Binary.class, extractBodyAsString(capt));
+		assertEquals(Constants.CT_FHIR_JSON, output.getContentType());
+
+		Patient outputPt = (Patient) ourCtx.newJsonParser().parseResource(new String(output.getContent(), "UTF-8"));
+		assertEquals("<div>A PATIENT</div>", outputPt.getText().getDivAsString());
+	}
+
+	private void validateUserAgent(ArgumentCaptor<HttpUriRequest> capt) {
+		assertEquals(1, capt.getAllValues().get(0).getHeaders("User-Agent").length);
+		assertEquals(expectedUserAgent(), capt.getAllValues().get(0).getHeaders("User-Agent")[0].getValue());
+	}
+
+	private String expectedUserAgent() {
+		return "HAPI-FHIR/" + VersionUtil.getVersion() + " (FHIR Client)";
+	}
+
+	@BeforeClass
+	public static void beforeClass() {
+		ourCtx = FhirContext.forDstu3();
+	}
+
+}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/CreateBinaryDstu3Test.java

@@ -0,0 +1,161 @@
+package ca.uhn.fhir.rest.server;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import java.util.concurrent.TimeUnit;
+
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ByteArrayEntity;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.dstu3.model.Binary;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.annotation.Create;
+import ca.uhn.fhir.rest.annotation.ResourceParam;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.util.PortUtil;
+
+public class CreateBinaryDstu3Test {
+	private static CloseableHttpClient ourClient;
+	private static int ourPort;
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+	private static Server ourServer;
+	private static Binary ourLastBinary;
+	private static String ourLastBinaryString;
+	private static byte[] ourLastBinaryBytes;
+	
+	
+	
+	@Before
+	public void before() {
+		ourLastBinary = null;
+		ourLastBinaryBytes = null;
+		ourLastBinaryString = null;
+	}
+
+
+	@Test
+	public void testRawBytesNoContentType() throws Exception {
+		HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
+		post.setEntity(new ByteArrayEntity(new byte[] {0,1,2,3,4}));
+		ourClient.execute(post);
+		
+		assertNull(ourLastBinary.getContentType());
+		assertArrayEquals(new byte[] {0,1,2,3,4}, ourLastBinary.getContent());
+	}
+
+	@Test
+	public void testRawBytesBinaryContentType() throws Exception {
+		HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
+		post.setEntity(new ByteArrayEntity(new byte[] {0,1,2,3,4}));
+		post.addHeader("Content-Type", "application/foo");
+		ourClient.execute(post);
+		
+		assertEquals("application/foo", ourLastBinary.getContentType());
+		assertArrayEquals(new byte[] {0,1,2,3,4}, ourLastBinary.getContent());
+		assertArrayEquals(new byte[] {0,1,2,3,4}, ourLastBinaryBytes);
+	}
+	
+	/**
+	 * Technically the client shouldn't be doing it this way,
+	 * but we'll be accepting
+	 */
+	@Test
+	public void testRawBytesFhirContentType() throws Exception {
+		
+		Binary b = new Binary();
+		b.setContentType("application/foo");
+		b.setContent(new byte[] {0,1,2,3,4});
+		String encoded = ourCtx.newJsonParser().encodeResourceToString(b);
+		
+		HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
+		post.setEntity(new StringEntity(encoded));
+		post.addHeader("Content-Type", Constants.CT_FHIR_JSON);
+		ourClient.execute(post);
+		
+		assertEquals("application/foo", ourLastBinary.getContentType());
+		assertArrayEquals(new byte[] {0,1,2,3,4}, ourLastBinary.getContent());
+	}
+
+	@Test
+	public void testRawBytesFhirContentTypeContainingFhir() throws Exception {
+		
+		Patient p = new Patient();
+		p.getText().setDivAsString("A PATIENT");
+		
+		Binary b = new Binary();
+		b.setContentType("application/xml+fhir");
+		b.setContent(ourCtx.newXmlParser().encodeResourceToString(p).getBytes("UTF-8"));
+		String encoded = ourCtx.newJsonParser().encodeResourceToString(b);
+		
+		HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
+		post.setEntity(new StringEntity(encoded));
+		post.addHeader("Content-Type", Constants.CT_FHIR_JSON);
+		ourClient.execute(post);
+		
+		assertEquals("application/xml+fhir", ourLastBinary.getContentType());
+		assertArrayEquals(b.getContent(), ourLastBinary.getContent());
+		assertEquals(encoded, ourLastBinaryString);
+		assertArrayEquals(encoded.getBytes("UTF-8"), ourLastBinaryBytes);
+	}
+
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+	}
+		
+	
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		BinaryProvider binaryProvider = new BinaryProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(ourCtx);
+		servlet.setResourceProviders(binaryProvider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+	}
+	
+	public static class BinaryProvider implements IResourceProvider {
+
+		@Override
+		public Class<? extends IBaseResource> getResourceType() {
+			return Binary.class;
+		}
+		
+		@Create()
+		public MethodOutcome createBinary(@ResourceParam Binary theBinary, @ResourceParam String theBinaryString, @ResourceParam byte[] theBinaryBytes) {
+			ourLastBinary = theBinary;
+			ourLastBinaryString = theBinaryString;
+			ourLastBinaryBytes = theBinaryBytes;
+			return new MethodOutcome(new IdType("Binary/001/_history/002"));
+		}
+
+	}
+
+}

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

@@ -1,35 +0,0 @@
-package ca.uhn.fhir.tinder;
-
-import org.apache.maven.plugin.AbstractMojo;
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugin.MojoFailureException;
-import org.apache.maven.plugins.annotations.Parameter;
-
-import ca.uhn.fhir.tinder.parser.CompartmentParser;
-
-public class CompartmentGeneratorMojo extends AbstractMojo {
-
-	@Parameter(required = true)
-	private String fhirVersion;
-
-	@Override
-	public void execute() throws MojoExecutionException, MojoFailureException {
-		CompartmentParser p = new CompartmentParser(fhirVersion);
-		try {
-			p.parse();
-		} catch (MojoExecutionException e) {
-			throw e;
-		} catch (MojoFailureException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new MojoFailureException("Failure during parse", e);
-		}
-	}
-
-	public static void main(String[] args) throws MojoExecutionException, MojoFailureException {
-		CompartmentGeneratorMojo mojo = new CompartmentGeneratorMojo();
-		mojo.fhirVersion = "dstu2";
-		mojo.execute();
-	}
-	
-}

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

@@ -228,7 +228,7 @@ public class TinderStructuresMojo extends AbstractMojo {
 		String dtOutputDir = "target/generated-sources/tinder/ca/uhn/fhir/model/dev/composite";
 
 		ResourceGeneratorUsingSpreadsheet rp = new ResourceGeneratorUsingSpreadsheet("dstu2", ".");
-		rp.setBaseResourceNames(Arrays.asList( "supplyrequest"   
+		rp.setBaseResourceNames(Arrays.asList( "patient", "auditevent" , "observation"  
 //				//, "contract" 
 //				"valueset", "organization", "location" 
 //				, "observation", "conformance"

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

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.tinder.model;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public class Resource extends BaseRootType {
 
 	@Override
@@ -20,4 +23,20 @@ public class Resource extends BaseRootType {
 		return name;
 	}
 
+	public SearchParameter getSearchParameterByName(String theName) {
+		for (SearchParameter next : getSearchParameters()) {
+			if (next.getName().equalsIgnoreCase(theName)) {
+				return next;
+			}
+		}
+		return null;
+	}
+	public List<String> getSearchParameterNames() {
+		ArrayList<String> retVal = new ArrayList<String>();
+		for (SearchParameter next : getSearchParameters()) {
+			retVal.add(next.getName());
+		}
+		return retVal;
+	}
+
 }

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

@@ -10,6 +10,7 @@ import org.apache.commons.lang3.StringUtils;
 public class SearchParameter {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParameter.class);
+	private List<String> myCompartments = new ArrayList<String>();
 	private List<String> myCompositeOf;
 	private List<String> myCompositeTypes;
 	private String myDescription;
@@ -18,7 +19,6 @@ public class SearchParameter {
 	private String myResourceName;
 	private List<String> myTargetTypes;
 	private String myType;
-
 	private String myVersion;
 
 	public SearchParameter(String theVersion, String theResourceName) {
@@ -26,6 +26,14 @@ public class SearchParameter {
 		this.myResourceName = theResourceName;
 	}
 
+	public void addCompartment(String theCompartment) {
+		myCompartments.add(theCompartment);
+	}
+
+	public List<String> getCompartments() {
+		return myCompartments;
+	}
+
 	public List<String> getCompositeOf() {
 		if (myCompositeOf == null) {
 			myCompositeOf = new ArrayList<String>();

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

@@ -16,6 +16,7 @@ import java.util.Set;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.text.WordUtils;
 import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
@@ -404,7 +405,7 @@ public abstract class BaseStructureSpreadsheetParser extends BaseStructureParser
 	/**
 	 * Subclasses may override
 	 */
-	protected void postProcess(BaseElement theTarget) {
+	protected void postProcess(BaseElement theTarget) throws MojoFailureException {
 		// nothing
 	}
 

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

@@ -1,20 +1,31 @@
 package ca.uhn.fhir.tinder.parser;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
 import java.io.InputStream;
+import java.util.HashMap;
+import java.util.Map;
 
 import org.apache.maven.plugin.MojoFailureException;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
 
+import ca.uhn.fhir.tinder.model.BaseElement;
+import ca.uhn.fhir.tinder.model.Resource;
+import ca.uhn.fhir.tinder.model.SearchParameter;
 import ca.uhn.fhir.tinder.util.XMLUtils;
 
 public class CompartmentParser {
 
 	private String myVersion;
+	private Resource myResourceDef;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CompartmentParser.class);
 
-	public CompartmentParser(String theVersion) {
+	public CompartmentParser(String theVersion, Resource theResourceDef) {
 		myVersion = theVersion;
+		myResourceDef = theResourceDef;
 	}
 	
 	public void parse() throws Exception {
@@ -45,6 +56,67 @@ public class CompartmentParser {
 			throw new Exception("Failed to find worksheet with name 'Data Elements' in spreadsheet: " + resName);
 		}
 
+		Element table = (Element) resourcesSheet.getElementsByTagName("Table").item(0);
+		NodeList rows = table.getElementsByTagName("Row");
+		
+		Map<Integer, String> col2compartment = new HashMap<Integer, String>();
+		Element headerRow = (Element) rows.item(0);
+		for (int i = 1; i < headerRow.getElementsByTagName("Cell").getLength(); i++) {
+			Element cellElement = (Element) headerRow.getElementsByTagName("Cell").item(i);
+			Element dataElement = (Element) cellElement.getElementsByTagName("Data").item(0);
+			col2compartment.put(i, dataElement.getTextContent());
+		}
+		
+		Element row = null;
+		for (int i = 1; i < rows.getLength(); i++) {
+			Element nextRow = (Element) rows.item(i);
+			
+			NodeList cells = nextRow.getElementsByTagName("Cell");
+			Element cellElement = (Element) cells.item(0);
+			Element dataElement = (Element) cellElement.getElementsByTagName("Data").item(0);
+			if (dataElement.getTextContent().equals(myResourceDef.getName())) {
+				row = nextRow;
+				break;
+			}
+		}
+		
+		if (row == null) {
+			ourLog.debug("No compartments for resource {}", myResourceDef.getName());
+			return;
+		}
+		
+		NodeList cells = row.getElementsByTagName("Cell");
+		for (int i = 1; i < cells.getLength(); i++) {
+			Element cellElement = (Element) cells.item(i);
+			int index = i;
+			if (cellElement.hasAttribute("Index")) {
+				index = Integer.parseInt(cellElement.getAttribute("Index"));
+			}
+			
+			String compartment = col2compartment.get(index);
+			
+			Element dataElement = (Element) cellElement.getElementsByTagName("Data").item(0);
+			String namesUnsplit = dataElement.getTextContent();
+			String[] namesSplit = namesUnsplit.split("\\|");
+			for (String nextName : namesSplit) {
+				nextName = nextName.trim();
+				if (isBlank(nextName)) {
+					continue;
+				}
+				
+				String[] parts = nextName.split("\\.");
+				if (parts[0].equals("{def}")) {
+					continue;
+				}
+				Resource element = myResourceDef;
+				SearchParameter sp = element.getSearchParameterByName(parts[0]);
+				if (sp == null) {
+					throw new MojoFailureException("Can't find child named " + parts[0] + " - Valid names: " + element.getSearchParameterNames());
+				}
+				
+				sp.addCompartment(compartment);
+			}
+		}
 	}
 	
 }

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

@@ -22,7 +22,7 @@ import com.google.common.reflect.ClassPath.ClassInfo;
 public class DatatypeGeneratorUsingSpreadsheet extends BaseStructureSpreadsheetParser {
 
 	@Override
-	protected void postProcess(BaseElement theTarget) {
+	protected void postProcess(BaseElement theTarget) throws MojoFailureException {
 		super.postProcess(theTarget);
 
 		/*

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

@@ -26,12 +26,21 @@ public class ResourceGeneratorUsingSpreadsheet extends BaseStructureSpreadsheetP
 	}
 
 	@Override
-	protected void postProcess(BaseElement theTarget) {
+	protected void postProcess(BaseElement theTarget) throws MojoFailureException {
 		super.postProcess(theTarget);
 		
 		if ("Bundle".equals(theTarget.getName())) {
 			addEverythingToSummary(theTarget);
 		}
+		
+		if (getVersion().equals("dstu2") && theTarget instanceof Resource) {
+			try {
+				new CompartmentParser(getVersion(), (Resource) theTarget).parse();
+			} catch (Exception e) {
+				throw new MojoFailureException(e.toString(), e);
+			}
+		}
+		
 	}
 
 	private void addEverythingToSummary(BaseElement theTarget) {

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

@@ -56,6 +56,13 @@ public class ${className} extends ca.uhn.fhir.model.${version}.resource.BaseReso
 	 * </p>
 	 */
 	@SearchParamDefinition(name="${param.name}", path="${param.path}", description="${param.description}", type="${param.type}" #{if}($param.compositeOf.empty == false) , compositeOf={ #{foreach}($compositeOf in $param.compositeOf) "${compositeOf}"#{if}($foreach.hasNext), #{end}#{end} } #{end} )
+#if ($param.compartments.size() > 0)
+	@Compartments(providesMembershipIn={
+#foreach ($compartment in $param.compartments)
+		@Compartment(name="$compartment") #{if}($foreach.hasNext), #{end}
+#end
+	})
+#end
 	public static final String $param.constantName = "${param.name}";
 
 	/**

src/changes/changes.xml

@@ -59,6 +59,50 @@
 			<action type="add">
 				JPA server now supports :above and :below qualifiers on URI search params
 			</action>
+			<action type="add">
+				Add optional support (disabled by default for now) to JPA server to support
+				inline references containing search URLs. These URLs will be resolved when
+				a resource is being created/updated and replaced with the single matching
+				resource. This is being used as a part of the May 2016 Connectathon for
+				a testing scenario.
+			</action>
+			<action type="add">
+				The server no longer adds a 
+				<![CDATA[<code>WWW-Authenticate</code>]]>
+				header to the response if any resource provider code throws an
+				<![CDATA[<code>AuthenticationException</code>]]>. This header is 
+				used for interactive authentication, which isn't generally 
+				appropriate for FHIR. We added code to add this header a long time
+				ago for testing purposes and it never got removed. Please let us
+				know if you need the ability to add this header automatically. Thanks
+				to Lars Kristian Roland for pointing this out.
+			</action>
+			<action type="fix">
+				In the client, the create/update operations on a Binary resource 
+				(which use the raw binary's content type as opposed to the FHIR
+				content type) were not including any request headers (Content-Type, 
+				User-Agent, etc.) Thanks to Peter Van Houte of Agfa Healthcare for
+				reporting!
+			</action>
+			<action type="fix">
+				Handling of Binary resources containing embedded FHIR resources for
+				create/update/etc operations has been corrected per the FHIR rules
+				outlined at
+				<a href="http://hl7.org/fhir/binary.html">Binary Resource</a> in both
+				the client and server. 
+				<![CDATA[<br/><br/>]]>
+				Essentially, if the Binary contains something
+				that isn't FHIR (e.g. an image with an image content-type) the
+				client will send the raw data with the image content type to the server. The
+				server will place the content type and raw data into a Binary resource instance
+				and pass those to the resource provider. This part was already correct previous
+				to 1.5. 
+				<![CDATA[<br/><br/>]]>
+				On the other hand, if the Binary contains a FHIR content type, the Binary
+				is now sent by the client to the server as a Binary resource with a FHIR content-type,
+				and the embedded FHIR content is contained in the appropriate fields. The server
+				will pass this "outer" Binary resource to the resource provider code. 
+			</action>
 			<action type="add">
 				The RequestDetails and ActionRequestDetails objects which are passed to 
 				server interceptor methods and may also be used as server provider method

src/site/xdoc/doc_rest_operations.xml

@@ -115,8 +115,9 @@
 				Update methods must be annotated with the
 				<a href="./apidocs/ca/uhn/fhir/rest/annotation/Update.html">@Update</a>
 				annotation, and have a parameter annotated with the
-				<a href="./apidocs/ca/uhn/fhir/rest/annotation/ResourceParam.html">@Resource</a>
+				<a href="./apidocs/ca/uhn/fhir/rest/annotation/ResourceParam.html">@ResourceParam</a>
 				annotation. This parameter contains the resource instance to be created.
+				See the <a href="./apidocs/ca/uhn/fhir/rest/annotation/ResourceParam.html">@ResourceParam</a> for information on the types allowed for this parameter (resource types, String, byte[]).
 			</p>
 			<p>
 				In addition, the method may optionally have a parameter annotated with the
@@ -316,8 +317,9 @@
 				Create methods must be annotated with the
 				<a href="./apidocs/ca/uhn/fhir/rest/annotation/Create.html">@Create</a>
 				annotation, and have a single parameter annotated with the
-				<a href="./apidocs/ca/uhn/fhir/rest/annotation/ResourceParam.html">@Resource</a>
+				<a href="./apidocs/ca/uhn/fhir/rest/annotation/ResourceParam.html">@ResourceParam</a>
 				annotation. This parameter contains the resource instance to be created.
+				See the <a href="./apidocs/ca/uhn/fhir/rest/annotation/ResourceParam.html">@ResourceParam</a> for information on the types allowed for this parameter (resource types, String, byte[]).
 			</p>
 			<p>
 				Create methods must return an object of type
@@ -1104,7 +1106,7 @@
 				Validate methods must be annotated with the
 				<a href="./apidocs/ca/uhn/fhir/rest/annotation/Validate.html">@Validate</a>
 				annotation, and have a parameter annotated with the
-				<a href="./apidocs/ca/uhn/fhir/rest/annotation/ResourceParam.html">@Resource</a>
+				<a href="./apidocs/ca/uhn/fhir/rest/annotation/ResourceParam.html">@ResourceParam</a>
 				annotation. This parameter contains the resource instance to be created.
 			</p>
 			<p>