Merge branch 'master' of github.com:jamesagnew/hapi-fhir

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

@@ -24,6 +24,7 @@ import java.lang.reflect.Method;
 import java.lang.reflect.Modifier;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
@@ -47,6 +48,7 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
 import ca.uhn.fhir.rest.param.CollectionBinder;
+import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.ResourceParameter;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -66,6 +68,7 @@ public class OperationParameter implements IParameter {
 	private Class<?> myParameterType;
 	private String myParamType;
 	private FhirContext myContext;
+	private boolean myAllowGet;
 
 	public OperationParameter(FhirContext theCtx, String theOperationName, OperationParam theOperationParam) {
 		this(theCtx, theOperationName, theOperationParam.name(), theOperationParam.min(), theOperationParam.max());
@@ -107,6 +110,8 @@ public class OperationParameter implements IParameter {
 			myMax = 1;
 		}
 		
+		myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType);
+		
 		/*
 		 * The parameter can be of type string for validation methods - This is a bit
 		 * weird. See ValidateDstu2Test. We should probably clean this up..
@@ -114,6 +119,10 @@ public class OperationParameter implements IParameter {
 		if (!myParameterType.equals(IBase.class) && !myParameterType.equals(String.class)) {
 			if (IBaseResource.class.isAssignableFrom(myParameterType) && myParameterType.isInterface()) {
 				myParamType = "Resource";
+			} else if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
+				myParamType = "date";
+				myMax = 2;
+				myAllowGet = true;
 			} else if (!IBase.class.isAssignableFrom(myParameterType) || myParameterType.isInterface() || Modifier.isAbstract(myParameterType.getModifiers())) {
 				throw new ConfigurationException("Invalid type for @OperationParam: " + myParameterType.getName());
 			} else if (myParameterType.equals(ValidationModeEnum.class)) {
@@ -153,13 +162,25 @@ public class OperationParameter implements IParameter {
 		if (theRequest.getRequestType() == RequestTypeEnum.GET) {
 			String[] paramValues = theRequest.getParameters().get(myName);
 			if (paramValues != null && paramValues.length > 0) {
-				if (IPrimitiveType.class.isAssignableFrom(myParameterType)) {
+				if (myAllowGet) {
-					for (String nextValue : paramValues) {
+					
-						FhirContext ctx = theRequest.getServer().getFhirContext();
+					if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
-						RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
+						List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
-						IPrimitiveType<?> instance = def.newInstance();
+						parameters.add(QualifiedParamList.singleton(paramValues[0]));
-						instance.setValueAsString(nextValue);
+						if (paramValues.length > 1) {
-						matchingParamValues.add(instance);
+							parameters.add(QualifiedParamList.singleton(paramValues[1]));
+						}
+						DateRangeParam dateRangeParam = new DateRangeParam();
+						dateRangeParam.setValuesAsQueryTokens(parameters);
+						matchingParamValues.add(dateRangeParam);
+					} else {
+						for (String nextValue : paramValues) {
+							FhirContext ctx = theRequest.getServer().getFhirContext();
+							RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
+							IPrimitiveType<?> instance = def.newInstance();
+							instance.setValueAsString(nextValue);
+							matchingParamValues.add(instance);
+						}
 					}
 				} else {
 					HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();

hapi-fhir-base/src/main/resources/ca/uhn/fhir/narrative/Medication.html

@@ -11,7 +11,14 @@ a browser.
 <!--*/-->
 
 <div>
-	<div class="hapiHeaderText" th:if="${not resource.nameElement.empty}" th:narrative="${resource.name}"></div>	
+	<th:block th:switch="${fhirVersion}">
+		<th:block th:case="'DSTU1'">
+			<div class="hapiHeaderText" th:if="${not resource.nameElement.empty}" th:narrative="${resource.name}"></div>	
+		</th:block>
+		<th:block th:case="*">
+			<div class="hapiHeaderText" th:if="${not resource.code.empty}" th:narrative="${resource.code}"></div>	
+		</th:block>
+	</th:block>
 </div>
 
 <!--/*-->

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

@@ -1227,11 +1227,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 			} else {
 				theOrders.add(theBuilder.desc(theFrom.get("myUpdated")));
 			}
-			
+
 			createSort(theBuilder, theFrom, theSort.getChain(), theOrders, thePredicates);
 			return;
 		}
-		
+
 		RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceType);
 		RuntimeSearchParam param = resourceDef.getSearchParam(theSort.getParamName());
 		if (param == null) {
@@ -1615,7 +1615,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 	/**
 	 * THIS SHOULD RETURN HASHSET and not jsut Set because we add to it later (so it can't be Collections.emptySet())
 	 */
-	private HashSet<Long> loadReverseIncludes(List<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode) {
+	private HashSet<Long> loadReverseIncludes(Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode) {
 		if (theMatches.size() == 0) {
 			return new HashSet<Long>();
 		}
@@ -1902,7 +1902,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 
 		Long pid = translateForcedIdToPid(theId);
 		BaseHasResource entity = myEntityManager.find(ResourceTable.class, pid);
-		
+
 		if (entity == null) {
 			throw new ResourceNotFoundException(theId);
 		}
@@ -2023,6 +2023,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 			}
 		}
 
+		// Load _include and _revinclude before filter and sort in everything mode
+		if (theParams.isEverythingMode() == true) {
+			if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
+				loadPids.addAll(loadReverseIncludes(loadPids, theParams.getRevIncludes(), true));
+				loadPids.addAll(loadReverseIncludes(loadPids, theParams.getIncludes(), false));
+			}
+		}
+
 		// Handle _lastUpdated
 		DateRangeParam lu = theParams.getLastUpdated();
 		if (lu != null && (lu.getLowerBoundAsInstant() != null || lu.getUpperBoundAsInstant() != null)) {
@@ -2047,59 +2055,22 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 			for (Long next : query.getResultList()) {
 				loadPids.add(next);
 			}
-			
+
 			if (loadPids.isEmpty()) {
 				return new SimpleBundleProvider();
 			}
 		}
 
 		// Handle sorting if any was provided
-		final List<Long> pids;
+		final List<Long> pids = processSort(theParams, loadPids);
-		if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
-			List<Order> orders = new ArrayList<Order>();
-			List<Predicate> predicates = new ArrayList<Predicate>();
-			CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-			CriteriaQuery<Tuple> cq = builder.createTupleQuery();
-			Root<ResourceTable> from = cq.from(ResourceTable.class);
-			predicates.add(from.get("myId").in(loadPids));
-			createSort(builder, from, theParams.getSort(), orders, predicates);
-			if (orders.size() > 0) {
-				Set<Long> originalPids = loadPids;
-				loadPids = new LinkedHashSet<Long>();
-				cq.multiselect(from.get("myId").as(Long.class));
-				cq.where(predicates.toArray(new Predicate[0]));
-				cq.orderBy(orders);
-
-				TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
-
-				for (Tuple next : query.getResultList()) {
-					loadPids.add(next.get(0, Long.class));
-				}
-
-				ourLog.debug("Sort PID order is now: {}", loadPids);
-
-				pids = new ArrayList<Long>(loadPids);
-
-				// Any ressources which weren't matched by the sort get added to the bottom
-				for (Long next : originalPids) {
-					if (loadPids.contains(next) == false) {
-						pids.add(next);
-					}
-				}
-
-			} else {
-				pids = new ArrayList<Long>(loadPids);
-			}
-		} else {
-			pids = new ArrayList<Long>(loadPids);
-		}
 
 		// Load _revinclude resources
 		final Set<Long> revIncludedPids;
-		if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
+		if (theParams.isEverythingMode() == false) {
-			revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
+			if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
-			if (theParams.isEverythingMode()) {
+				revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
-				revIncludedPids.addAll(loadReverseIncludes(pids, theParams.getIncludes(), false));
+			} else {
+				revIncludedPids = new HashSet<Long>();
 			}
 		} else {
 			revIncludedPids = new HashSet<Long>();
@@ -2155,6 +2126,49 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		return retVal;
 	}
 
+	private List<Long> processSort(final SearchParameterMap theParams, Set<Long> loadPids) {
+		final List<Long> pids;
+		if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
+			List<Order> orders = new ArrayList<Order>();
+			List<Predicate> predicates = new ArrayList<Predicate>();
+			CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
+			CriteriaQuery<Tuple> cq = builder.createTupleQuery();
+			Root<ResourceTable> from = cq.from(ResourceTable.class);
+			predicates.add(from.get("myId").in(loadPids));
+			createSort(builder, from, theParams.getSort(), orders, predicates);
+			if (orders.size() > 0) {
+				Set<Long> originalPids = loadPids;
+				loadPids = new LinkedHashSet<Long>();
+				cq.multiselect(from.get("myId").as(Long.class));
+				cq.where(predicates.toArray(new Predicate[0]));
+				cq.orderBy(orders);
+
+				TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
+
+				for (Tuple next : query.getResultList()) {
+					loadPids.add(next.get(0, Long.class));
+				}
+
+				ourLog.debug("Sort PID order is now: {}", loadPids);
+
+				pids = new ArrayList<Long>(loadPids);
+
+				// Any ressources which weren't matched by the sort get added to the bottom
+				for (Long next : originalPids) {
+					if (loadPids.contains(next) == false) {
+						pids.add(next);
+					}
+				}
+
+			} else {
+				pids = new ArrayList<Long>(loadPids);
+			}
+		} else {
+			pids = new ArrayList<Long>(loadPids);
+		}
+		return pids;
+	}
+
 	@Override
 	public IBundleProvider search(String theParameterName, IQueryParameterType theValue) {
 		return search(Collections.singletonMap(theParameterName, theValue));

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java

@@ -8,13 +8,15 @@ import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.UnsignedIntDt;
+import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 
 public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {
 
 	@Override
-	public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount) {
+	public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount, DateRangeParam theLastUpdated, SortSpec theSort) {
 		SearchParameterMap paramMap = new SearchParameterMap();
 		if (theCount != null) {
 			paramMap.setCount(theCount.getValue());
@@ -23,6 +25,8 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
 		paramMap.setRevIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
 		paramMap.setIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
 		paramMap.setEverythingMode(true);
+		paramMap.setSort(theSort);
+		paramMap.setLastUpdated(theLastUpdated);
 		paramMap.add("_id", new StringParam(theId.getIdPart()));
 		ca.uhn.fhir.rest.server.IBundleProvider retVal = search(paramMap);
 		return retVal;

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

@@ -26,10 +26,12 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.UnsignedIntDt;
+import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 
 public interface IFhirResourceDaoPatient<T extends IBaseResource> extends IFhirResourceDao<T> {
 
-	IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount);
+	IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount, DateRangeParam theLastUpdate, SortSpec theSort);
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaValidationSupportDstu2.java

@@ -51,12 +51,12 @@ public class JpaValidationSupportDstu2 implements IValidationSupport {
 	private FhirContext myDstu2Ctx;
 
 	@Override
-	public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
+	public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
 		return null;
 	}
 
 	@Override
-	public ValueSet fetchCodeSystem(String theSystem) {
+	public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
 		return null;
 	}
 
@@ -85,20 +85,19 @@ public class JpaValidationSupportDstu2 implements IValidationSupport {
 		/*
 		 * Validator wants RI structures and not HAPI ones, so convert
 		 * 
-		 * TODO: we really need a more efficient way of converting.. Or maybe this will
+		 * TODO: we really need a more efficient way of converting.. Or maybe this will just go away when we move to RI structures
-		 * just go away when we move to RI structures 
 		 */
 		String encoded = myDstu2Ctx.newJsonParser().encodeResourceToString(res);
 		return myRiCtx.newJsonParser().parseResource(theClass, encoded);
 	}
 
 	@Override
-	public boolean isCodeSystemSupported(String theSystem) {
+	public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
 		return false;
 	}
 
 	@Override
-	public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
+	public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
 		return null;
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderPatientDstu2.java

@@ -6,6 +6,10 @@ import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.Sort;
+import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.server.Constants;
 
 public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu2<Patient> {
 
@@ -18,12 +22,21 @@ public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu
 			ca.uhn.fhir.model.primitive.IdDt theId,
 			
 			@Description(formalDefinition="Results from this method are returned across multiple pages. This parameter controls the size of those pages.") 
-			@OperationParam(name = "_count") 
+			@OperationParam(name = Constants.PARAM_COUNT) 
-			ca.uhn.fhir.model.primitive.UnsignedIntDt theCount) {
+			ca.uhn.fhir.model.primitive.UnsignedIntDt theCount,
+			
+			@Description(shortDefinition="Only return resources which were last updated as specified by the given range")
+			@OperationParam(name = Constants.PARAM_LASTUPDATED, min=0, max=1) 
+			DateRangeParam theLastUpdated,
+			
+//			@OperationParam(name = Constants.PARAM_SORT, min=0, max=1)
+			@Sort
+			SortSpec theSortSpec
+			) {
 
 		startRequest(theServletRequest);
 		try {
-			return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount);
+			return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount, theLastUpdated, theSortSpec);
 		} finally {
 			endRequest(theServletRequest);
 		}

hapi-fhir-jpaserver-base/src/main/resources/fhir-spring-subscription-config-dstu2.xml

@@ -13,7 +13,7 @@
 	<context:annotation-config />
 
 	<websocket:handlers>
-		<websocket:mapping path="/baseDstu2/websocket" handler="mySubscriptionWebsocketHandler" />
+		<websocket:mapping path="/websocket/dstu2" handler="mySubscriptionWebsocketHandler" />
 	</websocket:handlers>
 
 	<!-- 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -602,6 +602,96 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		}
 	}
 
+	@Test
+	public void testEverythingWithLastUpdatedAndSort() throws Exception {
+		String methodName = "testEverythingWithLastUpdatedAndSort";
+
+		long time0 = System.currentTimeMillis();
+		Thread.sleep(10);
+		
+		Organization org = new Organization();
+		org.setName(methodName);
+		IIdType oId = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
+		
+		long time1 = System.currentTimeMillis();
+		Thread.sleep(10);
+		
+		Patient p = new Patient();
+		p.addName().addFamily(methodName);
+		p.getManagingOrganization().setReference(oId);
+		IIdType pId = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
+	
+		long time2 = System.currentTimeMillis();
+		Thread.sleep(10);
+		
+		Condition c = new Condition();
+		c.getCode().setText(methodName);
+		c.getPatient().setReference(pId);
+		IIdType cId = ourClient.create().resource(c).execute().getId().toUnqualifiedVersionless();
+
+		Thread.sleep(10);
+		long time3 = System.currentTimeMillis();
+		
+		// %3E=>   %3C=<
+
+		HttpGet get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time1)).getValueAsString());
+		CloseableHttpResponse response = ourHttpClient.execute(get);
+		try {
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			String output = IOUtils.toString(response.getEntity().getContent());
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			ourLog.info(output);
+			List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
+			ourLog.info(ids.toString());
+			assertThat(ids, containsInAnyOrder(pId, cId));
+		} finally {
+			response.close();
+		}
+
+		get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time2)).getValueAsString() + "&_lastUpdated=%3C" + new InstantDt(new Date(time3)).getValueAsString());
+		response = ourHttpClient.execute(get);
+		try {
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			String output = IOUtils.toString(response.getEntity().getContent());
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			ourLog.info(output);
+			List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
+			ourLog.info(ids.toString());
+			assertThat(ids, containsInAnyOrder(cId));
+		} finally {
+			response.close();
+		}
+
+		get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time1)).getValueAsString() + "&_sort=_lastUpdated");
+		response = ourHttpClient.execute(get);
+		try {
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			String output = IOUtils.toString(response.getEntity().getContent());
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			ourLog.info(output);
+			List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
+			ourLog.info(ids.toString());
+			assertThat(ids, contains(pId, cId));
+		} finally {
+			response.close();
+		}
+
+		get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_sort:desc=_lastUpdated");
+		response = ourHttpClient.execute(get);
+		try {
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			String output = IOUtils.toString(response.getEntity().getContent());
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			ourLog.info(output);
+			List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
+			ourLog.info(ids.toString());
+			assertThat(ids, contains(cId, pId, oId));
+		} finally {
+			response.close();
+		}
+		
+	}
+	
 	/**
 	 * See #148
 	 */

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SubscriptionsDstu2Test.java

@@ -324,7 +324,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
 		SimpleEchoSocket socket = new SimpleEchoSocket(subsId);
 		try {
 			client.start();
-			URI echoUri = new URI("ws://localhost:" + ourPort + "/baseDstu2/websocket");
+			URI echoUri = new URI("ws://localhost:" + ourPort + "/websocket/dstu2");
 			ClientUpgradeRequest request = new ClientUpgradeRequest();
 			client.connect(socket, echoUri, request);
 			ourLog.info("Connecting to : {}", echoUri);

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

@@ -1,5 +1,9 @@
 package ca.uhn.fhirtest;
 
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.Writer;
+
 import org.apache.derby.drda.NetworkServerControl;
 import org.springframework.beans.factory.DisposableBean;
 import org.springframework.beans.factory.InitializingBean;
@@ -22,7 +26,30 @@ public class DerbyNetworkServer implements InitializingBean, DisposableBean {
 	@Override
 	public void afterPropertiesSet() throws Exception {
 		server = new NetworkServerControl();
-		server.start (null);
+		Writer w = new Writer() {
+
+			@Override
+			public void write(char[] theCbuf, int theOff, int theLen) throws IOException {
+				ourLog.info("[DERBY] " + new String(theCbuf, theOff, theLen));
+			}
+
+			@Override
+			public void flush() throws IOException {
+				// nothing
+			}
+
+			@Override
+			public void close() throws IOException {
+				// nothing
+			}};
+		server.start (new PrintWriter(w));
 	}
 
+	
+	public static void main(String[] args) throws Exception {
+		DerbyNetworkServer s = new DerbyNetworkServer();
+		s.afterPropertiesSet();
+		s.destroy();
+	}
+	
 }

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

@@ -8,6 +8,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 
 import org.apache.commons.lang3.StringUtils;
+import org.springframework.context.ApplicationContext;
 import org.springframework.context.support.ClassPathXmlApplicationContext;
 import org.springframework.web.context.ContextLoaderListener;
 import org.springframework.web.context.WebApplicationContext;
@@ -35,7 +36,7 @@ public class TestRestfulServer extends RestfulServer {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestRestfulServer.class);
 
-	private ClassPathXmlApplicationContext myAppCtx;
+	private ApplicationContext myAppCtx;
 
 	@SuppressWarnings("unchecked")
 	@Override
@@ -44,6 +45,7 @@ public class TestRestfulServer extends RestfulServer {
 
 		// Get the spring context from the web container (it's declared in web.xml)
 		WebApplicationContext parentAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
+		myAppCtx = (parentAppCtx);
 
 		// These two parmeters are also declared in web.xml
 		String implDesc = getInitParameter("ImplementationDescription");
@@ -64,9 +66,6 @@ public class TestRestfulServer extends RestfulServer {
 		String baseUrlProperty;
 		switch (fhirVersionParam.trim().toUpperCase()) {
 		case "DSTU1": {
-			myAppCtx = new ClassPathXmlApplicationContext(new String[] { 
-					"hapi-fhir-server-database-config-dstu1.xml", 
-					"hapi-fhir-server-resourceproviders-dstu1.xml"}, parentAppCtx);
 			setFhirContext(FhirContext.forDstu1());
 			beans = myAppCtx.getBean("myResourceProvidersDstu1", List.class);
 			systemProviderDstu1 = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
@@ -79,11 +78,6 @@ public class TestRestfulServer extends RestfulServer {
 			break;
 		}
 		case "DSTU2": {
-			myAppCtx = new ClassPathXmlApplicationContext(new String[] {
-					"hapi-fhir-server-database-config-dstu2.xml", 
-					"hapi-fhir-server-resourceproviders-dstu2.xml", 
-					"fhir-spring-subscription-config-dstu2.xml"
-					}, parentAppCtx);
 			setFhirContext(FhirContext.forDstu2());
 			beans = myAppCtx.getBean("myResourceProvidersDstu2", List.class);
 			systemProviderDstu2 = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);

hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/web.xml

@@ -12,6 +12,11 @@
 			/WEB-INF/hapi-fhir-server-config.xml
 			/WEB-INF/hapi-fhir-tester-application-context.xml
 			/WEB-INF/hapi-fhir-tester-config.xml
+			classpath:/hapi-fhir-server-database-config-dstu1.xml 
+			classpath:/hapi-fhir-server-database-config-dstu2.xml 
+			classpath:hapi-fhir-server-resourceproviders-dstu1.xml
+			classpath:hapi-fhir-server-resourceproviders-dstu2.xml
+			classpath:fhir-spring-subscription-config-dstu2.xml
 		</param-value>
 	</context-param>
 
@@ -25,6 +30,7 @@
 			<param-value>
 				/WEB-INF/hapi-fhir-tester-application-context.xml
 				/WEB-INF/hapi-fhir-tester-config.xml
+				classpath:fhir-spring-subscription-config-dstu2.xml
 			</param-value>
 		</init-param>
 		<load-on-startup>2</load-on-startup>

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.narrative;
 
+import static org.hamcrest.Matchers.containsString;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
@@ -53,7 +54,7 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 		Patient value = new Patient();
 
 		value.addIdentifier().setSystem("urn:names").setValue("123456");
-		value.addName().addFamily("blow").addGiven("joe").addGiven((String)null).addGiven("john");
+		value.addName().addFamily("blow").addGiven("joe").addGiven((String) null).addGiven("john");
 		value.getAddressFirstRep().addLine("123 Fake Street").addLine("Unit 1");
 		value.getAddressFirstRep().setCity("Toronto").setState("ON").setCountry("Canada");
 
@@ -67,12 +68,12 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 
 		String title = myGen.generateTitle(value);
 		assertEquals("joe john BLOW (123456)", title);
-//		ourLog.info(title);
+		// ourLog.info(title);
 
 		value.getIdentifierFirstRep().setValue("FOO MRN 123");
 		title = myGen.generateTitle(value);
 		assertEquals("joe john BLOW (FOO MRN 123)", title);
-//		ourLog.info(title);
+		// ourLog.info(title);
 
 	}
 
@@ -80,7 +81,7 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 	public void testGenerateEncounter() throws DataFormatException {
 		Encounter enc = new Encounter();
 
-		enc.addIdentifier().setSystem("urn:visits").setValue( "1234567");
+		enc.addIdentifier().setSystem("urn:visits").setValue("1234567");
 		enc.setClassElement(EncounterClassEnum.AMBULATORY);
 		enc.setPeriod(new PeriodDt().setStart(new DateTimeDt("2001-01-02T11:11:00")));
 		enc.setType(ca.uhn.fhir.model.dstu2.valueset.EncounterTypeEnum.ANNUAL_DIABETES_MELLITUS_SCREENING);
@@ -92,7 +93,6 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 
 	}
 
-
 	@Test
 	public void testGenerateDiagnosticReport() throws DataFormatException {
 		DiagnosticReport value = new DiagnosticReport();
@@ -127,9 +127,9 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 
 		OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, parse);
 
-//		String output = gen.generateTitle(oo);
+		// String output = gen.generateTitle(oo);
-//		ourLog.info(output);
+		// ourLog.info(output);
-//		assertEquals("Operation Outcome (2 issues)", output);
+		// assertEquals("Operation Outcome (2 issues)", output);
 
 		NarrativeDt narrative = new NarrativeDt();
 		myGen.generateNarrative(null, oo, narrative);
@@ -137,11 +137,11 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 
 		ourLog.info(output);
 
-//		oo = new OperationOutcome();
+		// oo = new OperationOutcome();
-//		oo.addIssue().setSeverity(IssueSeverityEnum.FATAL).setDetails("AA");
+		// oo.addIssue().setSeverity(IssueSeverityEnum.FATAL).setDetails("AA");
-//		output = gen.generateTitle(oo);
+		// output = gen.generateTitle(oo);
-//		ourLog.info(output);
+		// ourLog.info(output);
-//		assertEquals("Operation Outcome (fatal)", output);
+		// assertEquals("Operation Outcome (fatal)", output);
 
 	}
 
@@ -193,27 +193,43 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 		assertThat(output, StringContains.containsString("<div class=\"hapiHeaderText\"> Some &amp; Diagnostic Report </div>"));
 
 	}
-	
+
 	@Test
-	public void testGenerateMedicationPrescription(){
+	public void testGenerateMedicationPrescription() {
 		MedicationOrder mp = new MedicationOrder();
 		mp.setId("12345");
 		Medication med = new Medication();
 		med.getCode().setText("ciproflaxin");
 		ResourceReferenceDt medRef = new ResourceReferenceDt(med);
-		mp.setMedication(medRef );
+		mp.setMedication(medRef);
 		mp.setStatus(MedicationOrderStatusEnum.ACTIVE);
 		mp.setDateWritten(new DateTimeDt("2014-09-01"));
-		
+
 		NarrativeDt narrative = new NarrativeDt();
 		myGen.generateNarrative(mp, narrative);
-		
+
-		assertTrue("Expected medication name of ciprofloaxin within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ciprofloaxin")>-1);
+		assertTrue("Expected medication name of ciprofloaxin within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ciprofloaxin") > -1);
-		assertTrue("Expected string status of ACTIVE within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ACTIVE")>-1);
+		assertTrue("Expected string status of ACTIVE within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ACTIVE") > -1);
-		
+
 		String title = myGen.generateTitle(mp);
 		assertEquals("ciprofloaxin", title);
-		
+
+	}
+
+	@Test
+	public void testGenerateMedication() {
+		Medication med = new Medication();
+		med.getCode().setText("ciproflaxin");
+
+		NarrativeDt narrative = new NarrativeDt();
+		myGen.generateNarrative(med, narrative);
+
+		String string = narrative.getDiv().toString();
+		assertThat(string, containsString("ciproflaxin"));
+
+		String title = myGen.generateTitle(med);
+		assertEquals("ciproflaxin", title);
+
 	}
 
 }

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

@@ -92,63 +92,6 @@ public class XmlParserDstu2Test {
 	private static final FhirContext ourCtx = FhirContext.forDstu2();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu2Test.class);
 
-	@Test
-	public void testParseBundleWithResourceId() {
-		//@formatter:off
-		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
-				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
-				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
-				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
-				+ "</Bundle>\n";
-		//@formatter:on
-		
-		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
-		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getId().getValue());
-		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getId().getValue());
-		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getId().getValue());
-	}
-	
-	@Test
-	public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
-		
-		Patient patient = new Patient();
-		patient.setId("phitcc_pat_normal");
-		patient.addName().addGiven("Patty").setUse(NameUseEnum.NICKNAME);
-		patient.addTelecom().setSystem(ContactPointSystemEnum.EMAIL).setValue("patpain@ehealthinnovation.org");
-		patient.setGender(AdministrativeGenderEnum.FEMALE);
-		patient.setBirthDate(new DateDt("2001-10-13"));
-
-		DateTimeDt obsEffectiveTime = new DateTimeDt("2015-04-11T12:22:01-04:00");
-
-		Observation obsParent = new Observation();
-		obsParent.setId("phitcc_obs_bp_parent");
-		obsParent.getSubject().setResource(patient);
-		obsParent.setStatus(ObservationStatusEnum.FINAL);
-		obsParent.setEffective(obsEffectiveTime);
-
-		Observation obsSystolic = new Observation();
-		obsSystolic.setId("phitcc_obs_bp_dia");
-		obsSystolic.getSubject().setResource(patient);
-		obsSystolic.setEffective(obsEffectiveTime);
-		obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsSystolic));
-
-		Observation obsDiastolic = new Observation();
-		obsDiastolic.setId("phitcc_obs_bp_dia");
-		obsDiastolic.getSubject().setResource(patient);
-		obsDiastolic.setEffective(obsEffectiveTime);
-		obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsDiastolic));
-		
-		String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
-		ourLog.info(str);
-		
-		assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
-		assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
-	}
-	
-	
-	
-	
-	
 	@Test
 	public void testBundleWithBinary() {
 		//@formatter:off
@@ -231,86 +174,6 @@ public class XmlParserDstu2Test {
 		assertTrue(parsed.getEntries().get(0).getResource().getId().isEmpty());
 	}
 
-	/**
-	 * See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
-	 */
-	@Test
-	public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
-		IParser xmlParser = ourCtx.newXmlParser();
-
-		String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
-		MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
-		SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
-		assertEquals("1", q.getValueElement().getValueAsString());
-		
-		String output = xmlParser.encodeResourceToString(ms);
-		assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
-	}
-	
-	/**
-	 * See #216
-	 */
-	@Test
-	public void testEncodeAndParseIdentifierDstu2() {
-		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
-
-		Patient patient = new Patient();
-		patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(IdentifierTypeCodesEnum.MR);
-		
-		String out = xmlParser.encodeResourceToString(patient);
-		ourLog.info(out);
-		
-		//@formatter:off
-		assertThat(out, stringContainsInOrder("<identifier>", 
-				"<type>",
-				"<coding>",
-				"<system value=\"http://hl7.org/fhir/v2/0203\"/>", 
-				"<code value=\"MR\"/>", 
-				"</coding>", 
-				"</type>",
-				"<system value=\"SYS\"/>", 
-				"<value value=\"VAL\"/>", 
-				"</identifier>"));
-		//@formatter:on
-		
-		patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
-		assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), contains(IdentifierTypeCodesEnum.MR));
-		assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());		
-		assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());		
-	}
-
-	/**
-	 * See #216
-	 */
-	@Test
-	public void testParseMalformedIdentifierDstu2() {
-
-		// This was changed from 0.5 to 1.0.0
-		
-		//@formatter:off
-		String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
-				"   <identifier>\n" + 
-				"      <type value=\"MRN\"/>\n" + 
-				"      <system value=\"SYS\"/>\n" + 
-				"      <value value=\"VAL\"/>\n" + 
-				"   </identifier>\n" + 
-				"</Patient>";
-		//@formatter:on
-		
-		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
-		
-		IParser p = ourCtx.newXmlParser();
-		p.setParserErrorHandler(errorHandler);
-		
-		Patient patient = p.parseResource(Patient.class, out);
-		assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), IsEmptyCollection.empty());
-		
-		ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
-		verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
-		
-		assertEquals("value", capt.getValue());
-	}
-
 	@Test
 	public void testEncodeAndParseContained() {
 		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
@@ -448,9 +311,11 @@ public class XmlParserDstu2Test {
 		String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
 		assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
 		assertThat(enc, containsString("<modifierExtension url=\"http://example.com/extensions#modext\"><valueDate value=\"1995-01-02\"/></modifierExtension>"));
-		assertThat(enc, containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
+		assertThat(enc, containsString(
+				"<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
 		assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
-		assertThat(enc, containsString("<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
+		assertThat(enc, containsString(
+				"<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
 
 		/*
 		 * Now parse this back
@@ -490,6 +355,38 @@ public class XmlParserDstu2Test {
 
 	}
 
+	/**
+	 * See #216
+	 */
+	@Test
+	public void testEncodeAndParseIdentifierDstu2() {
+		IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
+
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(IdentifierTypeCodesEnum.MR);
+
+		String out = xmlParser.encodeResourceToString(patient);
+		ourLog.info(out);
+
+		//@formatter:off
+		assertThat(out, stringContainsInOrder("<identifier>", 
+				"<type>",
+				"<coding>",
+				"<system value=\"http://hl7.org/fhir/v2/0203\"/>", 
+				"<code value=\"MR\"/>", 
+				"</coding>", 
+				"</type>",
+				"<system value=\"SYS\"/>", 
+				"<value value=\"VAL\"/>", 
+				"</identifier>"));
+		//@formatter:on
+
+		patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
+		assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), contains(IdentifierTypeCodesEnum.MR));
+		assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
+		assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
+	}
+
 	@Test
 	public void testEncodeAndParseMetaProfileAndTags() {
 		Patient p = new Patient();
@@ -595,6 +492,38 @@ public class XmlParserDstu2Test {
 		assertEquals(new Tag("scheme2", "term2", "label2"), tagList.get(1));
 	}
 
+	/**
+	 * Test for #233
+	 */
+	@Test
+	public void testEncodeAndParseProfiledDatatype() {
+		MedicationOrder mo = new MedicationOrder();
+		mo.addDosageInstruction().getTiming().getRepeat().setBounds(new DurationDt().setCode("code"));
+		String out = ourCtx.newXmlParser().encodeResourceToString(mo);
+		ourLog.info(out);
+		assertThat(out, containsString("</boundsQuantity>"));
+
+		mo = ourCtx.newXmlParser().parseResource(MedicationOrder.class, out);
+		DurationDt duration = (DurationDt) mo.getDosageInstruction().get(0).getTiming().getRepeat().getBounds();
+		assertEquals("code", duration.getCode());
+	}
+
+	/**
+	 * See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
+	 */
+	@Test
+	public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
+		IParser xmlParser = ourCtx.newXmlParser();
+
+		String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
+		MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
+		SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
+		assertEquals("1", q.getValueElement().getValueAsString());
+
+		String output = xmlParser.encodeResourceToString(ms);
+		assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
+	}
+
 	@Test
 	public void testEncodeAndParseSecurityLabels() {
 		Patient p = new Patient();
@@ -791,12 +720,14 @@ public class XmlParserDstu2Test {
 		ourLog.info(encoded);
 
 		// @formatter:on
-		assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
+		assertThat(encoded,
-				"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
+				stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
+						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
+						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
 		//@formatter:off
 
 	}
-	
+
 	/**
 	 * See #113
 	 */
@@ -824,12 +755,13 @@ public class XmlParserDstu2Test {
 		ourLog.info(encoded);
 		
 		//@formatter:on
-		assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
+		assertThat(encoded,
-				"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
+				stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>",
+						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>",
+						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
 		//@formatter:off
 	}
 
-	
 	/**
 	 * See #113
 	 */
@@ -861,8 +793,10 @@ public class XmlParserDstu2Test {
 		ourLog.info(encoded);
 		
 		//@formatter:on
-		assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
+		assertThat(encoded,
-				"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
+				stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
+						"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
+						"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
 		//@formatter:off
 
 	}
@@ -893,7 +827,6 @@ public class XmlParserDstu2Test {
 		assertThat(encoded, (containsString("BARFOO")));
 
 	}
-
 	
 	/**
 	 * #158
@@ -911,6 +844,7 @@ public class XmlParserDstu2Test {
 		assertThat(encoded, not(containsString("tag")));
 	}
 
+	
 	/**
 	 * #158
 	 */
@@ -929,7 +863,6 @@ public class XmlParserDstu2Test {
 		assertThat(encoded, not(containsString("Label")));
 	}
 
-
 	@Test
 	public void testEncodeExtensionWithResourceContent() {
 		IParser parser = ourCtx.newXmlParser();
@@ -951,6 +884,7 @@ public class XmlParserDstu2Test {
 
 	}
 
+	
 	@Test
 	public void testEncodeNarrativeSuppressed() {
 		Patient patient = new Patient();
@@ -1010,7 +944,44 @@ public class XmlParserDstu2Test {
 		
 	}
 
-	
+
+	@Test
+	public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
+		
+		Patient patient = new Patient();
+		patient.setId("phitcc_pat_normal");
+		patient.addName().addGiven("Patty").setUse(NameUseEnum.NICKNAME);
+		patient.addTelecom().setSystem(ContactPointSystemEnum.EMAIL).setValue("patpain@ehealthinnovation.org");
+		patient.setGender(AdministrativeGenderEnum.FEMALE);
+		patient.setBirthDate(new DateDt("2001-10-13"));
+
+		DateTimeDt obsEffectiveTime = new DateTimeDt("2015-04-11T12:22:01-04:00");
+
+		Observation obsParent = new Observation();
+		obsParent.setId("phitcc_obs_bp_parent");
+		obsParent.getSubject().setResource(patient);
+		obsParent.setStatus(ObservationStatusEnum.FINAL);
+		obsParent.setEffective(obsEffectiveTime);
+
+		Observation obsSystolic = new Observation();
+		obsSystolic.setId("phitcc_obs_bp_dia");
+		obsSystolic.getSubject().setResource(patient);
+		obsSystolic.setEffective(obsEffectiveTime);
+		obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsSystolic));
+
+		Observation obsDiastolic = new Observation();
+		obsDiastolic.setId("phitcc_obs_bp_dia");
+		obsDiastolic.getSubject().setResource(patient);
+		obsDiastolic.setEffective(obsEffectiveTime);
+		obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsDiastolic));
+		
+		String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
+		ourLog.info(str);
+		
+		assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
+		assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
+	}
+
 	@Test
 	public void testEncodeSummary() {
 		Patient patient = new Patient();
@@ -1052,6 +1023,57 @@ public class XmlParserDstu2Test {
 		assertThat(encoded, not(containsString("maritalStatus")));
 	}
 
+	
+	@Test
+	public void testEncodeWithEncodeElements() throws Exception {
+		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
+		
+		Patient patient = new Patient();
+		patient.addName().addFamily("FAMILY");
+		patient.addAddress().addLine("LINE1");
+		
+		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
+		bundle.setTotal(100);
+		bundle.addEntry().setResource(patient);
+
+		{
+		IParser p = ourCtx.newXmlParser();
+		p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
+		p.setPrettyPrint(true);
+		String out = p.encodeResourceToString(bundle);
+		ourLog.info(out);
+		assertThat(out, not(containsString("total")));
+		assertThat(out, (containsString("Patient")));
+		assertThat(out, (containsString("name")));
+		assertThat(out, not(containsString("address")));
+		}
+		{
+		IParser p = ourCtx.newXmlParser();
+		p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
+		p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
+		p.setPrettyPrint(true);
+		String out = p.encodeResourceToString(bundle);
+		ourLog.info(out);
+		assertThat(out, (containsString("total")));
+		assertThat(out, (containsString("Patient")));
+		assertThat(out, (containsString("name")));
+		assertThat(out, not(containsString("address")));
+		}
+		{
+		IParser p = ourCtx.newXmlParser();
+		p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
+		p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
+		p.setPrettyPrint(true);
+		String out = p.encodeResourceToString(bundle);
+		ourLog.info(out);
+		assertThat(out, (containsString("total")));
+		assertThat(out, (containsString("Patient")));
+		assertThat(out, (containsString("name")));
+		assertThat(out, (containsString("address")));
+		}
+		
+	}
+
 	@Test
 	public void testMoreExtensions() throws Exception {
 
@@ -1105,7 +1127,7 @@ public class XmlParserDstu2Test {
 		assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
 		assertThat(enc, containsString("<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
 	}
-	
+
 	@Test
 	public void testOmitResourceId() {
 		Patient p = new Patient();
@@ -1116,57 +1138,6 @@ public class XmlParserDstu2Test {
 		assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), containsString("ABC"));
 		assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), not(containsString("123")));
 	}
-
-	@Test
-	public void testEncodeWithEncodeElements() throws Exception {
-		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
-		
-		Patient patient = new Patient();
-		patient.addName().addFamily("FAMILY");
-		patient.addAddress().addLine("LINE1");
-		
-		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
-		bundle.setTotal(100);
-		bundle.addEntry().setResource(patient);
-
-		{
-		IParser p = ourCtx.newXmlParser();
-		p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
-		p.setPrettyPrint(true);
-		String out = p.encodeResourceToString(bundle);
-		ourLog.info(out);
-		assertThat(out, not(containsString("total")));
-		assertThat(out, (containsString("Patient")));
-		assertThat(out, (containsString("name")));
-		assertThat(out, not(containsString("address")));
-		}
-		{
-		IParser p = ourCtx.newXmlParser();
-		p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
-		p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
-		p.setPrettyPrint(true);
-		String out = p.encodeResourceToString(bundle);
-		ourLog.info(out);
-		assertThat(out, (containsString("total")));
-		assertThat(out, (containsString("Patient")));
-		assertThat(out, (containsString("name")));
-		assertThat(out, not(containsString("address")));
-		}
-		{
-		IParser p = ourCtx.newXmlParser();
-		p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
-		p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
-		p.setPrettyPrint(true);
-		String out = p.encodeResourceToString(bundle);
-		ourLog.info(out);
-		assertThat(out, (containsString("total")));
-		assertThat(out, (containsString("Patient")));
-		assertThat(out, (containsString("name")));
-		assertThat(out, (containsString("address")));
-		}
-		
-	}
-	
 	
 	@Test
 	public void testParseAndEncodeBundle() throws Exception {
@@ -1202,7 +1173,7 @@ public class XmlParserDstu2Test {
 		assertTrue(d.toString(), d.identical());
 
 	}
-	
+
 	@Test
 	public void testParseAndEncodeBundleNewStyle() throws Exception {
 		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
@@ -1239,7 +1210,8 @@ public class XmlParserDstu2Test {
 		assertTrue(d.toString(), d.identical());
 
 	}
-
+	
+	
 	@Test
 	public void testParseAndEncodeExtensionOnResourceReference() {
 		//@formatter:off
@@ -1642,6 +1614,22 @@ public class XmlParserDstu2Test {
 		assertEquals("Observation", link.getUrl());
 	}
 
+	@Test
+	public void testParseBundleWithResourceId() {
+		//@formatter:off
+		String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
+				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+				+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+				+ "</Bundle>\n";
+		//@formatter:on
+
+		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
+		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getId().getValue());
+		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getId().getValue());
+		assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getId().getValue());
+	}
+
 	/**
 	 * see #144 and #146
 	 */
@@ -1710,6 +1698,38 @@ public class XmlParserDstu2Test {
 
 	}
 
+	/**
+	 * See #216
+	 */
+	@Test
+	public void testParseMalformedIdentifierDstu2() {
+
+		// This was changed from 0.5 to 1.0.0
+
+		//@formatter:off
+		String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" + 
+				"   <identifier>\n" + 
+				"      <type value=\"MRN\"/>\n" + 
+				"      <system value=\"SYS\"/>\n" + 
+				"      <value value=\"VAL\"/>\n" + 
+				"   </identifier>\n" + 
+				"</Patient>";
+		//@formatter:on
+
+		IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
+
+		IParser p = ourCtx.newXmlParser();
+		p.setParserErrorHandler(errorHandler);
+
+		Patient patient = p.parseResource(Patient.class, out);
+		assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), IsEmptyCollection.empty());
+
+		ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
+		verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
+
+		assertEquals("value", capt.getValue());
+	}
+
 	@Test
 	public void testParseMetadata() throws Exception {
 		//@formatter:off

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/DefaultProfileValidationSupport.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.validation;
 
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.UnsupportedEncodingException;
@@ -20,67 +22,102 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 
 public class DefaultProfileValidationSupport implements IValidationSupport {
 
-	private Map<String, ValueSet> myDefaultValueSets;
+  private Map<String, ValueSet> myDefaultValueSets;
-	
+  private Map<String, ValueSet> myCodeSystems;
-	@Override
-	public boolean isCodeSystemSupported(String theSystem) {
-		return false;
-	}
-
-	@SuppressWarnings("unchecked")
-	@Override
-	public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
-		if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
-			return (T) FhirInstanceValidator.loadProfileOrReturnNull(null, FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext), theUri.substring("http://hl7.org/fhir/StructureDefinition/".length()));
-		}
-		if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
-			Map<String, ValueSet> defaultValueSets = myDefaultValueSets;
-			if (defaultValueSets == null) {
-				InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml");
-				if (valuesetText == null) {
-					return null;
-				}
-				InputStreamReader reader;
-				try {
-					reader = new InputStreamReader(valuesetText, "UTF-8");
-				} catch (UnsupportedEncodingException e) {
-					// Shouldn't happen!
-					throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
-				}
-				
-				defaultValueSets = new HashMap<String, ValueSet>();
-				
-				FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
-				Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
-				for (BundleEntryComponent next : bundle.getEntry()) {
-					IdType nextId = new IdType(next.getFullUrl());
-					if (nextId.isEmpty() || !nextId.getValue().startsWith("http://hl7.org/fhir/ValueSet/")) {
-						continue;
-					}
-					defaultValueSets.put(nextId.toVersionless().getValue(), (ValueSet) next.getResource());
-				}
-				
-				myDefaultValueSets = defaultValueSets;
-			}
-			
-			return (T) defaultValueSets.get(theUri);
-		}
-
-		return null;
-	}
 
   @Override
-  public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
+  public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
+    return false;
+  }
+
+  @SuppressWarnings("unchecked")
+  @Override
+  public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
+    if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
+      return (T) FhirInstanceValidator.loadProfileOrReturnNull(null, FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext), theUri.substring("http://hl7.org/fhir/StructureDefinition/".length()));
+    }
+    if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
+      Map<String, ValueSet> defaultValueSets = myDefaultValueSets;
+      if (defaultValueSets == null) {
+        InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml");
+        if (valuesetText == null) {
+          return null;
+        }
+        InputStreamReader reader;
+        try {
+          reader = new InputStreamReader(valuesetText, "UTF-8");
+        } catch (UnsupportedEncodingException e) {
+          // Shouldn't happen!
+          throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
+        }
+
+        defaultValueSets = new HashMap<String, ValueSet>();
+
+        FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
+        Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
+        for (BundleEntryComponent next : bundle.getEntry()) {
+          IdType nextId = new IdType(next.getFullUrl());
+          if (nextId.isEmpty() || !nextId.getValue().startsWith("http://hl7.org/fhir/ValueSet/")) {
+            continue;
+          }
+          defaultValueSets.put(nextId.toVersionless().getValue(), (ValueSet) next.getResource());
+        }
+
+        myDefaultValueSets = defaultValueSets;
+      }
+
+      return (T) defaultValueSets.get(theUri);
+    }
+
+    return null;
+  }
+
+  @Override
+  public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
     return new CodeValidationResult(IssueSeverity.INFORMATION, "Unknown code: " + theCodeSystem + " / " + theCode);
   }
 
   @Override
-  public ValueSet fetchCodeSystem(String theSystem) {
+  public ValueSet fetchCodeSystem(FhirContext theContext, String theSystem) {
-    return null;
+    Map<String, ValueSet> codeSystems = myCodeSystems;
+    if (codeSystems == null) {
+      codeSystems = new HashMap<String, ValueSet>();
+
+      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
+      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
+      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
+
+      myCodeSystems = codeSystems;
+    }
+
+    return codeSystems.get(theSystem);
+  }
+
+  private void loadCodeSystems(FhirContext theContext, Map<String, ValueSet> codeSystems, String file) {
+    InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(file);
+    if (valuesetText != null) {
+      InputStreamReader reader;
+      try {
+        reader = new InputStreamReader(valuesetText, "UTF-8");
+      } catch (UnsupportedEncodingException e) {
+        // Shouldn't happen!
+        throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
+      }
+
+      FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
+      Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
+      for (BundleEntryComponent next : bundle.getEntry()) {
+        ValueSet nextValueSet = (ValueSet) next.getResource();
+        String system = nextValueSet.getCodeSystem().getSystem();
+        if (isNotBlank(system)) {
+          codeSystems.put(system, nextValueSet);
+        }
+      }
+    }
   }
 
   @Override
-  public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
+  public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
     return null;
   }
 

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/FhirInstanceValidator.java

@@ -269,7 +269,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 
     @Override
     public ValueSetExpansionComponent expandVS(ConceptSetComponent theInc) {
-      return myValidationSupport.expandValueSet(theInc);
+      return myValidationSupport.expandValueSet(myCtx, theInc);
     }
 
     @Override
@@ -282,7 +282,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
       if (myValidationSupport == null) {
         return null;
       } else {
-        return myValidationSupport.fetchCodeSystem(theSystem);
+        return myValidationSupport.fetchCodeSystem(myCtx, theSystem);
       }
     }
 
@@ -335,13 +335,13 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
       if (myValidationSupport == null) {
         return false;
       } else {
-        return myValidationSupport.isCodeSystemSupported(theSystem);
+        return myValidationSupport.isCodeSystemSupported(myCtx, theSystem);
       }
     }
 
     @Override
     public ValidationResult validateCode(String theSystem, String theCode, String theDisplay) {
-      CodeValidationResult result = myValidationSupport.validateCode(theSystem, theCode, theDisplay);
+      CodeValidationResult result = myValidationSupport.validateCode(myCtx, theSystem, theCode, theDisplay);
       if (result == null) {
         return null;
       }

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/IValidationSupport.java

@@ -18,7 +18,7 @@ public interface IValidationSupport {
    *          The portion to include
    * @return The expansion
    */
-  ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude);
+  ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude);
 
   /**
    * Fetch a code system by ID
@@ -27,7 +27,7 @@ public interface IValidationSupport {
    *          The code system
    * @return The valueset (must not be null, but can be an empty ValueSet)
    */
-  ValueSet fetchCodeSystem(String theSystem);
+  ValueSet fetchCodeSystem(FhirContext theContext, String theSystem);
 
   /**
    * Loads a resource needed by the validation (a StructureDefinition, or a
@@ -53,7 +53,7 @@ public interface IValidationSupport {
    * @return Returns <code>true</code> if codes in the given code system can be
    *         validated
    */
-  boolean isCodeSystemSupported(String theSystem);
+  boolean isCodeSystemSupported(FhirContext theContext, String theSystem);
 
   /**
    * Validates that the given code exists and if possible returns a display
@@ -68,7 +68,7 @@ public interface IValidationSupport {
    *          The display name, if it should also be validated
    * @return Returns a validation result object
    */
-  CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay);
+  CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
 
   public class CodeValidationResult {
     private ConceptDefinitionComponent definition;

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/ValidationSupportChain.java

@@ -24,19 +24,19 @@ public class ValidationSupportChain implements IValidationSupport {
   }
 
   @Override
-  public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
+  public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
     for (IValidationSupport next : myChain) {
-      if (next.isCodeSystemSupported(theInclude.getSystem())) {
+      if (next.isCodeSystemSupported(theCtx, theInclude.getSystem())) {
-        return next.expandValueSet(theInclude);
+        return next.expandValueSet(theCtx, theInclude);
       }
     }
-    return myChain.get(0).expandValueSet(theInclude);
+    return myChain.get(0).expandValueSet(theCtx, theInclude);
   }
 
   @Override
-  public ValueSet fetchCodeSystem(String theSystem) {
+  public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
     for (IValidationSupport next : myChain) {
-      ValueSet retVal = next.fetchCodeSystem(theSystem);
+      ValueSet retVal = next.fetchCodeSystem(theCtx, theSystem);
       if (retVal != null) {
         return retVal;
       }
@@ -56,9 +56,9 @@ public class ValidationSupportChain implements IValidationSupport {
   }
 
   @Override
-  public boolean isCodeSystemSupported(String theSystem) {
+  public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
     for (IValidationSupport next : myChain) {
-      if (next.isCodeSystemSupported(theSystem)) {
+      if (next.isCodeSystemSupported(theCtx, theSystem)) {
         return true;
       }
     }
@@ -66,13 +66,13 @@ public class ValidationSupportChain implements IValidationSupport {
   }
 
   @Override
-  public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
+  public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
     for (IValidationSupport next : myChain) {
-      if (next.isCodeSystemSupported(theCodeSystem)) {
+      if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
-        return next.validateCode(theCodeSystem, theCode, theDisplay);
+        return next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
       }
     }
-    return myChain.get(0).validateCode(theCodeSystem, theCode, theDisplay);
+    return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);
   }
 
 }

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/validation/FhirInstanceValidatorTest.java

@@ -2,7 +2,9 @@ package ca.uhn.fhir.validation;
 
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.greaterThan;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 import static org.mockito.Matchers.any;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
@@ -16,6 +18,7 @@ import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.CodeType;
 import org.hl7.fhir.instance.model.Observation;
 import org.hl7.fhir.instance.model.Observation.ObservationStatus;
+import org.hl7.fhir.instance.model.Patient;
 import org.hl7.fhir.instance.model.StringType;
 import org.hl7.fhir.instance.model.ValueSet;
 import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
@@ -61,19 +64,19 @@ public class FhirInstanceValidatorTest {
     myValidConcepts = new ArrayList<String>();
 
     myMockSupport = mock(IValidationSupport.class);
-    when(myMockSupport.expandValueSet(any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
+    when(myMockSupport.expandValueSet(any(FhirContext.class), any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
       @Override
       public ValueSetExpansionComponent answer(InvocationOnMock theInvocation) throws Throwable {
         ConceptSetComponent arg = (ConceptSetComponent)theInvocation.getArguments()[0];
         ValueSetExpansionComponent retVal = mySupportedCodeSystemsForExpansion.get(arg.getSystem());
         if (retVal == null) {
-          retVal = myDefaultValidationSupport.expandValueSet(arg);
+          retVal = myDefaultValidationSupport.expandValueSet(any(FhirContext.class), arg);
         }
         ourLog.info("expandValueSet({}) : {}", new Object[] { theInvocation.getArguments()[0], retVal });
         return retVal;
       }
     });
-    when(myMockSupport.isCodeSystemSupported(any(String.class))).thenAnswer(new Answer<Boolean>() {
+    when(myMockSupport.isCodeSystemSupported(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<Boolean>() {
       @Override
       public Boolean answer(InvocationOnMock theInvocation) throws Throwable {
         boolean retVal = mySupportedCodeSystemsForExpansion.containsKey(theInvocation.getArguments()[0]);
@@ -93,28 +96,29 @@ public class FhirInstanceValidatorTest {
             return retVal;
           }
         });
-    when(myMockSupport.validateCode(any(String.class), any(String.class), any(String.class)))
+    when(myMockSupport.validateCode(any(FhirContext.class), any(String.class), any(String.class), any(String.class)))
         .thenAnswer(new Answer<CodeValidationResult>() {
           @Override
           public CodeValidationResult answer(InvocationOnMock theInvocation) throws Throwable {
-            String system = (String) theInvocation.getArguments()[0];
+            FhirContext ctx = (FhirContext) theInvocation.getArguments()[0];
-            String code = (String) theInvocation.getArguments()[1];
+            String system = (String) theInvocation.getArguments()[1];
+            String code = (String) theInvocation.getArguments()[2];
             CodeValidationResult retVal;
             if (myValidConcepts.contains(system + "___" + code)) {
               retVal = new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code)));
             } else {
-              retVal = myDefaultValidationSupport.validateCode(system, code, (String) theInvocation.getArguments()[2]);
+              retVal = myDefaultValidationSupport.validateCode(ctx, system, code, (String) theInvocation.getArguments()[2]);
             }
             ourLog.info("validateCode({}, {}, {}) : {}",
                 new Object[] { system, code, (String) theInvocation.getArguments()[2], retVal });
             return retVal;
           }
         });
-    when(myMockSupport.fetchCodeSystem(any(String.class))).thenAnswer(new Answer<ValueSet>() {
+    when(myMockSupport.fetchCodeSystem(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<ValueSet>() {
       @Override
       public ValueSet answer(InvocationOnMock theInvocation) throws Throwable {
-        ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((String) theInvocation.getArguments()[0]);
+        ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0],(String) theInvocation.getArguments()[1]);
-        ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[0], retVal });
+        ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[1], retVal });
         return retVal;
       }
     });
@@ -306,6 +310,29 @@ public class FhirInstanceValidatorTest {
         output.getMessages().get(0).getMessage());
   }
 
+  
+  @Test
+  public void testValidateResourceWithValuesetExpansion() {
+    
+    Patient patient = new Patient();
+    patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("foo").setCode("bar");
+
+    ValidationResult output = myVal.validateWithResult(patient);
+    List<SingleValidationMessage> all = logResultsAndReturnAll(output);
+    assertEquals(1, all.size());
+    assertEquals("/f:Patient/f:identifier/f:type", all.get(0).getLocationString());
+    assertEquals("None of the codes are in the expected value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type)", all.get(0).getMessage());
+    assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
+
+    patient = new Patient();
+    patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("http://hl7.org/fhir/v2/0203").setCode("MR");
+
+    output = myVal.validateWithResult(patient);
+    all = logResultsAndReturnAll(output);
+    assertEquals(0, all.size());
+  }
+
+  
   @Test
   public void testValidateResourceWithExampleBindingCodeValidationFailing() {
     Observation input = new Observation();
@@ -353,7 +380,11 @@ public class FhirInstanceValidatorTest {
 
     ValidationResult output = myVal.validateWithResult(input);
     List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
-    assertEquals(errors.toString(), 0, errors.size());
+    assertEquals(errors.toString(), 1, errors.size());
+    assertEquals("Unable to validate code \"1234\" in code system \"http://loinc.org\"", errors.get(0).getMessage());
+    assertEquals(ResultSeverityEnum.WARNING, errors.get(0).getSeverity());
+    
+    
   }
 
   @Test

src/changes/changes.xml

@@ -84,6 +84,17 @@
 				a more appropriate 400/404 in the JPA server (vread on invalid version,
 				delete with no ID, etc.)
 			</action>
+			<action type="fix">
+				Fix narrative generation for DSTU2 Medication resource
+			</action>
+			<action type="fix">
+				Profile validator now works for valuesets which use
+				v2 tables
+			</action>
+			<action type="add">
+				JPA server Patient/[id]/$everything operation now supports
+				_lastUpdated filtering and _sort'ing of results.
+			</action>
 		</release>
 		<release version="1.2" date="2015-09-18">
 			<action type="add">