Add support for bundle entry states

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

@@ -40,6 +40,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.model.valueset.BundleEntryStatusEnum;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.util.UrlUtil;
@@ -175,6 +176,12 @@ public class Bundle extends BaseBundle /* implements IElement */{
 					entry.getLinkAlternate().setValue(linkSearch);
 				}
 				
+				BundleEntryStatusEnum entryStatus = ResourceMetadataKeyEnum.ENTRY_STATUS.get(theResource);
+				if (entryStatus != null) {
+					entry.getStatus().setValueAsEnum(entryStatus);
+				}
+
+
 			}
 		}
 

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

@@ -29,6 +29,7 @@ import org.apache.commons.lang3.StringUtils;
 
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.valueset.BundleEntryStatusEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 
 /**
@@ -264,6 +265,31 @@ public abstract class ResourceMetadataKeyEnum<T> {
 		}
 	};
 
+	/**
+	 * If present and populated with a {@link BundleEntryStatusEnum}, contains the "bundle entry status",
+	 * which is the value of the status field in the Bundle.entry containing this resource. This value can be
+	 * set to provide a status value of "include" for included resources being returned by a server, or to 
+	 * set the value on a transaction, etc.
+	 * <p>
+	 * Note that status is only used in FHIR DSTU2 and later.
+	 * </p>
+	 * <p>
+	 * Values for this key are of type <b>{@link BundleEntryStatusEnum}</b>
+	 * </p>
+	 */
+	public static final ResourceMetadataKeyEnum<BundleEntryStatusEnum> ENTRY_STATUS = new ResourceMetadataKeyEnum<BundleEntryStatusEnum>("ENTRY_STATUS") {
+		@Override
+		public BundleEntryStatusEnum get(IResource theResource) {
+			return getEnumFromMetadataOrNullIfNone(theResource.getResourceMetadata(), ENTRY_STATUS, BundleEntryStatusEnum.class, BundleEntryStatusEnum.VALUESET_BINDER);
+		}
+
+		@Override
+		public void put(IResource theResource, BundleEntryStatusEnum theObject) {
+			theResource.getResourceMetadata().put(ENTRY_STATUS, theObject);
+		}
+	};
+
+	
 	private final String myValue;
 
 	public ResourceMetadataKeyEnum(String theValue) {
@@ -348,6 +374,20 @@ public abstract class ResourceMetadataKeyEnum<T> {
 				+ InstantDt.class.getCanonicalName());
 	}
 
+	@SuppressWarnings("unchecked")
+	private static <T extends Enum<?>> T getEnumFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<T> theKey, Class<T> theEnumType, IValueSetEnumBinder<T> theBinder) {
+		Object retValObj = theResourceMetadata.get(theKey);
+		if (retValObj == null) {
+			return null;
+		} else if (theEnumType.equals(retValObj.getClass())) {
+			return (T) retValObj;
+		} else if (retValObj instanceof String) {
+			return theBinder.fromCodeString((String) retValObj);
+		}
+		throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
+				+ InstantDt.class.getCanonicalName());
+	}
+
 	private static String getStringFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<String> theKey) {
 		Object retValObj = theResourceMetadata.get(theKey);
 		if (retValObj == null) {

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

@@ -1009,7 +1009,9 @@ class ParserState<T> {
 			if (!myEntry.getLinkSearch().isEmpty()) {
 				ResourceMetadataKeyEnum.LINK_SEARCH.put(myEntry.getResource(), myEntry.getLinkSearch().getValue());
 			}
-
+			if (!myEntry.getStatus().isEmpty()) {
+				ResourceMetadataKeyEnum.ENTRY_STATUS.put(myEntry.getResource(), myEntry.getStatus().getValueAsEnum());
+			}
 		}
 
 	}
@@ -1115,13 +1117,18 @@ class ParserState<T> {
 				String baseUrl = myInstance.getLinkBase().getValue();
 				String version = ResourceMetadataKeyEnum.VERSION.get(nextResource);
 				String resourceName = myContext.getResourceDefinition(nextResource).getName();
-				nextResource.setId(new IdDt(baseUrl, resourceName, nextResource.getId().getIdPart(), version));
+				String idPart = nextResource.getId().getIdPart();
+				if (isNotBlank(idPart)) {
+					nextResource.setId(new IdDt(baseUrl, resourceName, idPart, version));
+				}
 			}
 			
 			String bundleVersion = (String) myInstance.getResourceMetadata().get(ResourceMetadataKeyEnum.VERSION);
 			String baseUrl = myInstance.getLinkBase().getValue();
 			String id = myInstance.getId().getIdPart();
+			if (isNotBlank(id)) {
 				myInstance.setId(new IdDt(baseUrl, "Bundle", id, bundleVersion));
+			}
 			
 		}
 

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

@@ -1188,9 +1188,11 @@ public class RestfulServer extends HttpServlet {
 		for (IResource next : includedResources) {
 			BundleEntry entry = bundle.addResource(next, theContext, theServerBase);
 			if (theContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
+				if (entry.getStatus().isEmpty()) {
 					entry.getStatus().setValueAsEnum(BundleEntryStatusEnum.INCLUDE);
 				}
 			}
+		}
 
 		bundle.getTotalResults().setValue(theTotalResults);
 		return bundle;

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

@@ -75,6 +75,7 @@ import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
 import ca.uhn.fhir.model.dstu.valueset.SearchParamTypeEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.valueset.BundleEntryStatusEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.param.CompositeParam;
@@ -533,6 +534,9 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
 								if (!includePids.isEmpty()) {
 									ourLog.info("Loading {} included resources", includePids.size());
 									resources = loadResourcesById(includePids);
+									for (IResource next : resources) {
+										ResourceMetadataKeyEnum.ENTRY_STATUS.put(next, BundleEntryStatusEnum.INCLUDE);
+									}
 									retVal.addAll(resources);
 								}
 							} while (includePids.size() > 0 && previouslyLoadedPids.size() < getConfig().getIncludeLimit());

hapi-fhir-jpaserver-test/pom.xml

@@ -19,6 +19,11 @@
 			<artifactId>hapi-fhir-jpaserver-base</artifactId>
 			<version>0.9-SNAPSHOT</version>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dev</artifactId>
+			<version>0.9-SNAPSHOT</version>
+		</dependency>
 		<dependency>
 			<groupId>org.thymeleaf</groupId>
 			<artifactId>thymeleaf</artifactId>

hapi-fhir-jpaserver-test/src/test/java/ca/uhn/fhir/jpa/test/CompleteResourceProviderTest.java

@@ -24,20 +24,22 @@ import ca.uhn.fhir.jpa.provider.JpaSystemProvider;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.dstu.composite.PeriodDt;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.dev.composite.PeriodDt;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
-import ca.uhn.fhir.model.dstu.resource.DiagnosticOrder;
+import ca.uhn.fhir.model.dev.resource.DiagnosticOrder;
-import ca.uhn.fhir.model.dstu.resource.DocumentManifest;
+import ca.uhn.fhir.model.dev.resource.DocumentManifest;
-import ca.uhn.fhir.model.dstu.resource.DocumentReference;
+import ca.uhn.fhir.model.dev.resource.DocumentReference;
-import ca.uhn.fhir.model.dstu.resource.Encounter;
+import ca.uhn.fhir.model.dev.resource.Encounter;
-import ca.uhn.fhir.model.dstu.resource.ImagingStudy;
+import ca.uhn.fhir.model.dev.resource.ImagingStudy;
-import ca.uhn.fhir.model.dstu.resource.Location;
+import ca.uhn.fhir.model.dev.resource.Location;
-import ca.uhn.fhir.model.dstu.resource.Organization;
+import ca.uhn.fhir.model.dev.resource.Organization;
-import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dev.resource.Patient;
-import ca.uhn.fhir.model.dstu.valueset.EncounterClassEnum;
+import ca.uhn.fhir.model.dev.valueset.EncounterClassEnum;
-import ca.uhn.fhir.model.dstu.valueset.EncounterStateEnum;
+import ca.uhn.fhir.model.dev.valueset.EncounterStateEnum;
 import ca.uhn.fhir.model.dstu.valueset.NarrativeStatusEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.valueset.BundleEntryStatusEnum;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.IGenericClient;
@@ -72,7 +74,7 @@ public class CompleteResourceProviderTest {
 	public void testStoreUtf8Characters() throws Exception {
 		Organization org = new Organization();
 		org.setName("測試醫院");
-		org.addIdentifier("urn:system", "testStoreUtf8Characters_01");
+		org.addIdentifier().setSystem("urn:system").setValue("testStoreUtf8Characters_01");
 		IdDt orgId = ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId();
 
 		// Read back directly from the DAO
@@ -91,6 +93,36 @@ public class CompleteResourceProviderTest {
 		}
 	}
 
+	@Test
+	public void testSearchWithInclude() throws Exception {
+		Organization org = new Organization();
+		org.addIdentifier().setSystem("urn:system").setValue( "testSearchWithInclude01");
+		IdDt orgId = ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId();
+
+		Patient pat = new Patient();
+		pat.addIdentifier().setSystem("urn:system").setValue("testSearchWithInclude02");
+		pat.getManagingOrganization().setReference(orgId);
+		ourClient.create().resource(pat).prettyPrint().encodedXml().execute().getId();
+
+		//@formatter:off
+		Bundle found = ourClient
+				.search()
+				.forResource(Patient.class)
+				.where(Patient.IDENTIFIER.exactly().systemAndIdentifier("urn:system","testSearchWithInclude02"))
+				.include(Patient.INCLUDE_MANAGINGORGANIZATION)
+				.execute();
+		//@formatter:on
+		
+		assertEquals(2, found.size());
+		assertEquals(Patient.class, found.getEntries().get(0).getResource().getClass());
+		assertEquals(null, found.getEntries().get(0).getStatus().getValueAsEnum());
+		assertEquals(null, found.getEntries().get(0).getResource().getResourceMetadata().get(ResourceMetadataKeyEnum.ENTRY_STATUS));
+		assertEquals(Organization.class, found.getEntries().get(1).getResource().getClass());
+		assertEquals(BundleEntryStatusEnum.INCLUDE, found.getEntries().get(1).getStatus().getValueAsEnum());
+		assertEquals(BundleEntryStatusEnum.INCLUDE, found.getEntries().get(1).getResource().getResourceMetadata().get(ResourceMetadataKeyEnum.ENTRY_STATUS));
+	}
+
+	
 	@Test
 	public void testCountParam() throws Exception {
 		// NB this does not get used- The paging provider has its own limits built in
@@ -178,7 +210,7 @@ public class CompleteResourceProviderTest {
 		int initialSize = client.search().forResource(DiagnosticOrder.class).execute().size();
 
 		DiagnosticOrder res = new DiagnosticOrder();
-		res.addIdentifier("urn:foo", "123");
+		res.addIdentifier().setSystem("urn:foo").setValue( "123");
 
 		client.create().resource(res).execute();
 
@@ -241,19 +273,19 @@ public class CompleteResourceProviderTest {
 		deleteToken("Encounter", Encounter.SP_IDENTIFIER, "urn:foo", "testDeepChainingE1");
 
 		Location l1 = new Location();
-		l1.getName().setValue("testDeepChainingL1");
+		l1.getNameElement().setValue("testDeepChainingL1");
 		IdDt l1id = ourClient.create().resource(l1).execute().getId();
 
 		Location l2 = new Location();
-		l2.getName().setValue("testDeepChainingL2");
+		l2.getNameElement().setValue("testDeepChainingL2");
 		l2.getPartOf().setReference(l1id.toVersionless().toUnqualified());
 		IdDt l2id = ourClient.create().resource(l2).execute().getId();
 
 		Encounter e1 = new Encounter();
 		e1.addIdentifier().setSystem("urn:foo").setValue("testDeepChainingE1");
-		e1.getStatus().setValueAsEnum(EncounterStateEnum.IN_PROGRESS);
+		e1.getStatusElement().setValueAsEnum(EncounterStateEnum.IN_PROGRESS);
-		e1.getClassElement().setValueAsEnum(EncounterClassEnum.HOME);
+		e1.getClassElementElement().setValueAsEnum(EncounterClassEnum.HOME);
-		ca.uhn.fhir.model.dstu.resource.Encounter.Location location = e1.addLocation();
+		ca.uhn.fhir.model.dev.resource.Encounter.Location location = e1.addLocation();
 		location.getLocation().setReference(l2id.toUnqualifiedVersionless());
 		location.setPeriod(new PeriodDt().setStartWithSecondsPrecision(new Date()).setEndWithSecondsPrecision(new Date()));
 		IdDt e1id = ourClient.create().resource(e1).execute().getId();
@@ -372,7 +404,7 @@ public class CompleteResourceProviderTest {
 		//@formatter:off
 		Bundle actual = ourClient.search()
 				.forResource(Patient.class)
-				.where(Patient.PROVIDER.hasId(o1id.getIdPart()))
+				.where(Patient.ORGANIZATION.hasId(o1id.getIdPart()))
 				.encodedJson().prettyPrint().execute();
 		//@formatter:on
 		assertEquals(1, actual.size());
@@ -381,7 +413,7 @@ public class CompleteResourceProviderTest {
 		//@formatter:off
 		actual = ourClient.search()
 				.forResource(Patient.class)
-				.where(Patient.PROVIDER.hasId(o1id.getValue()))
+				.where(Patient.ORGANIZATION.hasId(o1id.getValue()))
 				.encodedJson().prettyPrint().execute();
 		//@formatter:on
 		assertEquals(1, actual.size());
@@ -412,12 +444,12 @@ public class CompleteResourceProviderTest {
 		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testUpdateRejectsInvalidTypes");
 
 		Patient p1 = new Patient();
-		p1.addIdentifier("urn:system", "testUpdateRejectsInvalidTypes");
+		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsInvalidTypes");
 		p1.addName().addFamily("Tester").addGiven("testUpdateRejectsInvalidTypes");
 		IdDt p1id = ourClient.create().resource(p1).execute().getId();
 
 		Organization p2 = new Organization();
-		p2.getName().setValue("testUpdateRejectsInvalidTypes");
+		p2.getNameElement().setValue("testUpdateRejectsInvalidTypes");
 		try {
 			ourClient.update().resource(p2).withId("Organization/" + p1id.getIdPart()).execute();
 			fail();
@@ -462,21 +494,25 @@ public class CompleteResourceProviderTest {
 	@BeforeClass
 	public static void beforeClass() throws Exception {
 		int port = RandomServerPortProvider.findFreePort();
+
 		RestfulServer restServer = new RestfulServer();
+		ourFhirCtx = FhirContext.forDev();
+		restServer.setFhirContext(ourFhirCtx);
+		
 		String serverBase = "http://localhost:" + port + "/fhir/context";
 
-		ourAppCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dstu1.xml", "fhir-spring-test-config.xml");
+		ourAppCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dev.xml", "fhir-spring-test-config.xml");
 
 		ourDaoConfig = (DaoConfig) ourAppCtx.getBean(DaoConfig.class);
 
-		ourOrganizationDao = (IFhirResourceDao<Organization>) ourAppCtx.getBean("myOrganizationDaoDstu1", IFhirResourceDao.class);
+		ourOrganizationDao = (IFhirResourceDao<Organization>) ourAppCtx.getBean("myOrganizationDaoDev", IFhirResourceDao.class);
 
-		List<IResourceProvider> rpsDstu1 = (List<IResourceProvider>) ourAppCtx.getBean("myResourceProvidersDstu1", List.class);
+		List<IResourceProvider> rpsDev = (List<IResourceProvider>) ourAppCtx.getBean("myResourceProvidersDev", List.class);
-		restServer.setResourceProviders(rpsDstu1);
+		restServer.setResourceProviders(rpsDev);
 
 		restServer.getFhirContext().setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
 
-		IFhirSystemDao systemDao = (IFhirSystemDao) ourAppCtx.getBean("mySystemDaoDstu1", IFhirSystemDao.class);
+		IFhirSystemDao systemDao = (IFhirSystemDao) ourAppCtx.getBean("mySystemDaoDev", IFhirSystemDao.class);
 		JpaSystemProvider systemProv = new JpaSystemProvider(systemDao);
 		restServer.setPlainProviders(systemProv);
 
@@ -494,8 +530,6 @@ public class CompleteResourceProviderTest {
 		ourServer.setHandler(proxyHandler);
 		ourServer.start();
 
-		ourFhirCtx = restServer.getFhirContext();
-
 		ourClient = ourFhirCtx.newRestfulGenericClient(serverBase);
 		ourClient.registerInterceptor(new LoggingInterceptor(true));
 

hapi-fhir-jpaserver-test/src/test/java/ca/uhn/fhir/jpa/test/CompleteResourceProviderTestDstu1.java

@@ -0,0 +1,538 @@
+package ca.uhn.fhir.jpa.test;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.provider.JpaSystemProvider;
+import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.dstu.composite.PeriodDt;
+import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu.resource.DiagnosticOrder;
+import ca.uhn.fhir.model.dstu.resource.DocumentManifest;
+import ca.uhn.fhir.model.dstu.resource.DocumentReference;
+import ca.uhn.fhir.model.dstu.resource.Encounter;
+import ca.uhn.fhir.model.dstu.resource.ImagingStudy;
+import ca.uhn.fhir.model.dstu.resource.Location;
+import ca.uhn.fhir.model.dstu.resource.Organization;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu.valueset.EncounterClassEnum;
+import ca.uhn.fhir.model.dstu.valueset.EncounterStateEnum;
+import ca.uhn.fhir.model.dstu.valueset.NarrativeStatusEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.valueset.BundleEntryStatusEnum;
+import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.gclient.StringClientParam;
+import ca.uhn.fhir.rest.gclient.TokenClientParam;
+import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+
+public class CompleteResourceProviderTestDstu1 {
+
+	private static ClassPathXmlApplicationContext ourAppCtx;
+	private static IGenericClient ourClient;
+	private static FhirContext ourFhirCtx;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CompleteResourceProviderTestDstu1.class);
+	// private static IFhirResourceDao<Observation> ourObservationDao;
+	// private static IFhirResourceDao<Patient> ourPatientDao;
+	// private static IFhirResourceDao<Questionnaire> ourQuestionnaireDao;
+	private static Server ourServer;
+	private static IFhirResourceDao<Organization> ourOrganizationDao;
+	private static DaoConfig ourDaoConfig;
+
+	// private static JpaConformanceProvider ourConfProvider;
+
+	/**
+	 * Test for issue #60
+	 */
+	@Test
+	public void testStoreUtf8Characters() throws Exception {
+		Organization org = new Organization();
+		org.setName("測試醫院");
+		org.addIdentifier().setSystem("urn:system").setValue("testStoreUtf8Characters_01");
+		IdDt orgId = ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId();
+
+		// Read back directly from the DAO
+		{
+			Organization returned = ourOrganizationDao.read(orgId);
+			String val = ourFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
+			ourLog.info(val);
+			assertThat(val, containsString("<name value=\"測試醫院\"/>"));
+		}
+		// Read back through the HTTP API
+		{
+			Organization returned = ourClient.read(Organization.class, orgId);
+			String val = ourFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
+			ourLog.info(val);
+			assertThat(val, containsString("<name value=\"測試醫院\"/>"));
+		}
+	}
+
+	@Test
+	public void testSearchWithInclude() throws Exception {
+		Organization org = new Organization();
+		org.addIdentifier().setSystem("urn:system").setValue( "testSearchWithInclude01");
+		IdDt orgId = ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId();
+
+		Patient pat = new Patient();
+		pat.addIdentifier().setSystem("urn:system").setValue("testSearchWithInclude02");
+		pat.getManagingOrganization().setReference(orgId);
+		ourClient.create().resource(pat).prettyPrint().encodedXml().execute().getId();
+
+		//@formatter:off
+		Bundle found = ourClient
+				.search()
+				.forResource(Patient.class)
+				.where(Patient.IDENTIFIER.exactly().systemAndIdentifier("urn:system","testSearchWithInclude02"))
+				.include(Patient.INCLUDE_MANAGINGORGANIZATION)
+				.execute();
+		//@formatter:on
+		
+		assertEquals(2, found.size());
+		assertEquals(Patient.class, found.getEntries().get(0).getResource().getClass());
+		assertEquals(null, found.getEntries().get(0).getStatus().getValueAsEnum());
+		assertEquals(null, found.getEntries().get(0).getResource().getResourceMetadata().get(ResourceMetadataKeyEnum.ENTRY_STATUS));
+		assertEquals(Organization.class, found.getEntries().get(1).getResource().getClass());
+		assertEquals(BundleEntryStatusEnum.INCLUDE, found.getEntries().get(1).getStatus().getValueAsEnum());
+		assertEquals(BundleEntryStatusEnum.INCLUDE, found.getEntries().get(1).getResource().getResourceMetadata().get(ResourceMetadataKeyEnum.ENTRY_STATUS));
+	}
+
+	
+	@Test
+	public void testCountParam() throws Exception {
+		// NB this does not get used- The paging provider has its own limits built in
+		ourDaoConfig.setHardSearchLimit(100);
+
+		List<IResource> resources = new ArrayList<>();
+		for (int i = 0; i < 100; i++) {
+			Organization org = new Organization();
+			org.setName("testCountParam_01");
+			resources.add(org);
+		}
+		ourClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
+
+		Bundle found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).limitTo(10).execute();
+		assertEquals(100, found.getTotalResults().getValue().intValue());
+		assertEquals(10, found.getEntries().size());
+
+		found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).limitTo(999).execute();
+		assertEquals(100, found.getTotalResults().getValue().intValue());
+		assertEquals(50, found.getEntries().size());
+
+	}
+
+	/**
+	 * See issue #52
+	 */
+	@Test
+	public void testImagingStudyResources() throws Exception {
+		IGenericClient client = ourClient;
+
+		int initialSize = client.search().forResource(ImagingStudy.class).execute().size();
+
+		String resBody = IOUtils.toString(CompleteResourceProviderTestDstu1.class.getResource("/imagingstudy.json"));
+		client.create().resource(resBody).execute();
+
+		int newSize = client.search().forResource(ImagingStudy.class).execute().size();
+
+		assertEquals(1, newSize - initialSize);
+
+	}
+
+	/**
+	 * See issue #52
+	 */
+	@Test
+	public void testDocumentManifestResources() throws Exception {
+		IGenericClient client = ourClient;
+
+		int initialSize = client.search().forResource(DocumentManifest.class).execute().size();
+
+		String resBody = IOUtils.toString(CompleteResourceProviderTestDstu1.class.getResource("/documentmanifest.json"));
+		client.create().resource(resBody).execute();
+
+		int newSize = client.search().forResource(DocumentManifest.class).execute().size();
+
+		assertEquals(1, newSize - initialSize);
+
+	}
+
+	/**
+	 * See issue #52
+	 */
+	@Test
+	public void testDocumentReferenceResources() throws Exception {
+		IGenericClient client = ourClient;
+
+		int initialSize = client.search().forResource(DocumentReference.class).execute().size();
+
+		String resBody = IOUtils.toString(CompleteResourceProviderTestDstu1.class.getResource("/documentreference.json"));
+		client.create().resource(resBody).execute();
+
+		int newSize = client.search().forResource(DocumentReference.class).execute().size();
+
+		assertEquals(1, newSize - initialSize);
+
+	}
+
+	/**
+	 * See issue #52
+	 */
+	@Test
+	public void testDiagnosticOrderResources() throws Exception {
+		IGenericClient client = ourClient;
+
+		int initialSize = client.search().forResource(DiagnosticOrder.class).execute().size();
+
+		DiagnosticOrder res = new DiagnosticOrder();
+		res.addIdentifier().setSystem("urn:foo").setValue( "123");
+
+		client.create().resource(res).execute();
+
+		int newSize = client.search().forResource(DiagnosticOrder.class).execute().size();
+
+		assertEquals(1, newSize - initialSize);
+
+	}
+
+	private void delete(String theResourceType, String theParamName, String theParamValue) {
+		Bundle resources = ourClient.search().forResource(theResourceType).where(new StringClientParam(theParamName).matches().value(theParamValue)).execute();
+		for (IResource next : resources.toListOfResources()) {
+			ourLog.info("Deleting resource: {}", next.getId());
+			ourClient.delete().resource(next).execute();
+		}
+	}
+
+	private void deleteToken(String theResourceType, String theParamName, String theParamSystem, String theParamValue) {
+		Bundle resources = ourClient.search().forResource(theResourceType).where(new TokenClientParam(theParamName).exactly().systemAndCode(theParamSystem, theParamValue)).execute();
+		for (IResource next : resources.toListOfResources()) {
+			ourLog.info("Deleting resource: {}", next.getId());
+			ourClient.delete().resource(next).execute();
+		}
+	}
+
+	@Test
+	public void testCreateWithClientSuppliedId() {
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testCreateWithId01");
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testCreateWithId01");
+		IdDt p1Id = ourClient.create().resource(p1).withId("testCreateWithId").execute().getId();
+
+		assertThat(p1Id.getValue(), containsString("Patient/testCreateWithId/_history"));
+
+		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testCreateWithId01")).encodedJson().prettyPrint().execute();
+		assertEquals(1, actual.size());
+		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getId().getIdPart());
+
+		/*
+		 * ensure that trying to create the same ID again fails appropriately
+		 */
+		try {
+			ourClient.create().resource(p1).withId("testCreateWithId").execute().getId();
+			fail();
+		} catch (UnprocessableEntityException e) {
+			// good
+		}
+
+		Bundle history = ourClient.history(null, (String) null, null, null);
+
+		assertEquals("Expected[" + p1Id.getIdPart() + "] but was " + history.getEntries().get(0).getId(), p1Id.getIdPart(), history.getEntries().get(0).getId().getIdPart());
+		assertNotNull(history.getEntries().get(0).getResource());
+	}
+
+	@Test
+	public void testDeepChaining() {
+		delete("Location", Location.SP_NAME, "testDeepChainingL1");
+		delete("Location", Location.SP_NAME, "testDeepChainingL2");
+		deleteToken("Encounter", Encounter.SP_IDENTIFIER, "urn:foo", "testDeepChainingE1");
+
+		Location l1 = new Location();
+		l1.getNameElement().setValue("testDeepChainingL1");
+		IdDt l1id = ourClient.create().resource(l1).execute().getId();
+
+		Location l2 = new Location();
+		l2.getNameElement().setValue("testDeepChainingL2");
+		l2.getPartOf().setReference(l1id.toVersionless().toUnqualified());
+		IdDt l2id = ourClient.create().resource(l2).execute().getId();
+
+		Encounter e1 = new Encounter();
+		e1.addIdentifier().setSystem("urn:foo").setValue("testDeepChainingE1");
+		e1.getStatusElement().setValueAsEnum(EncounterStateEnum.IN_PROGRESS);
+		e1.getClassElementElement().setValueAsEnum(EncounterClassEnum.HOME);
+		ca.uhn.fhir.model.dstu.resource.Encounter.Location location = e1.addLocation();
+		location.getLocation().setReference(l2id.toUnqualifiedVersionless());
+		location.setPeriod(new PeriodDt().setStartWithSecondsPrecision(new Date()).setEndWithSecondsPrecision(new Date()));
+		IdDt e1id = ourClient.create().resource(e1).execute().getId();
+
+		//@formatter:off
+		Bundle res = ourClient.search()
+			.forResource(Encounter.class)
+			.where(Encounter.IDENTIFIER.exactly().systemAndCode("urn:foo", "testDeepChainingE1"))
+			.include(Encounter.INCLUDE_LOCATION_LOCATION)
+			.include(Location.INCLUDE_PARTOF)
+			.execute();
+		//@formatter:on
+
+		assertEquals(3, res.size());
+		assertEquals(1, res.getResources(Encounter.class).size());
+		assertEquals(e1id.toUnqualifiedVersionless(), res.getResources(Encounter.class).get(0).getId().toUnqualifiedVersionless());
+
+	}
+
+	@Test
+	public void testSaveAndRetrieveExistingNarrative() {
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testSaveAndRetrieveExistingNarrative01");
+
+		Patient p1 = new Patient();
+		p1.getText().setStatus(NarrativeStatusEnum.GENERATED);
+		p1.getText().getDiv().setValueAsString("<div>HELLO WORLD</div>");
+		p1.addIdentifier().setSystem("urn:system").setValue("testSaveAndRetrieveExistingNarrative01");
+
+		IdDt newId = ourClient.create().resource(p1).execute().getId();
+
+		Patient actual = ourClient.read(Patient.class, newId);
+		assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">HELLO WORLD</div>", actual.getText().getDiv().getValueAsString());
+	}
+
+	@Test
+	public void testSaveAndRetrieveWithContained() {
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testSaveAndRetrieveWithContained01");
+
+		Organization o1 = new Organization();
+		o1.addIdentifier().setSystem("urn:system").setValue("testSaveAndRetrieveWithContained02");
+
+		p1.getManagingOrganization().setResource(o1);
+
+		IdDt newId = ourClient.create().resource(p1).execute().getId();
+
+		Patient actual = ourClient.read(Patient.class, newId);
+		assertEquals(1, actual.getContained().getContainedResources().size());
+		assertThat(actual.getText().getDiv().getValueAsString(), containsString("<td>Identifier</td><td>testSaveAndRetrieveWithContained01</td>"));
+
+		Bundle b = ourClient.search().forResource("Patient").where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testSaveAndRetrieveWithContained01")).execute();
+		assertEquals(1, b.size());
+
+	}
+
+	@Test
+	public void testSaveAndRetrieveWithoutNarrative() {
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testSearchByResourceChain01");
+
+		IdDt newId = ourClient.create().resource(p1).execute().getId();
+
+		Patient actual = ourClient.read(Patient.class, newId);
+		assertThat(actual.getText().getDiv().getValueAsString(), containsString("<td>Identifier</td><td>testSearchByResourceChain01</td>"));
+	}
+
+	@Test
+	public void testSearchByIdentifier() {
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testSearchByIdentifier01");
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testSearchByIdentifier02");
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testSearchByIdentifier01");
+		p1.addName().addFamily("testSearchByIdentifierFamily01").addGiven("testSearchByIdentifierGiven01");
+		IdDt p1Id = ourClient.create().resource(p1).execute().getId();
+
+		Patient p2 = new Patient();
+		p2.addIdentifier().setSystem("urn:system").setValue("testSearchByIdentifier02");
+		p2.addName().addFamily("testSearchByIdentifierFamily01").addGiven("testSearchByIdentifierGiven02");
+		ourClient.create().resource(p2).execute().getId();
+
+		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testSearchByIdentifier01")).encodedJson().prettyPrint().execute();
+		assertEquals(1, actual.size());
+		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getId().getIdPart());
+	}
+
+	@Test
+	public void testSearchByIdentifierWithoutSystem() {
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "", "testSearchByIdentifierWithoutSystem01");
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setValue("testSearchByIdentifierWithoutSystem01");
+		IdDt p1Id = ourClient.create().resource(p1).execute().getId();
+
+		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode(null, "testSearchByIdentifierWithoutSystem01")).encodedJson().prettyPrint().execute();
+		assertEquals(1, actual.size());
+		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getId().getIdPart());
+
+	}
+
+	@Test
+	public void testSearchByResourceChain() {
+		delete("Organization", Organization.SP_NAME, "testSearchByResourceChainName01");
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testSearchByResourceChain01");
+
+		Organization o1 = new Organization();
+		o1.setName("testSearchByResourceChainName01");
+		IdDt o1id = ourClient.create().resource(o1).execute().getId();
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testSearchByResourceChain01");
+		p1.addName().addFamily("testSearchByResourceChainFamily01").addGiven("testSearchByResourceChainGiven01");
+		p1.setManagingOrganization(new ResourceReferenceDt(o1id));
+		IdDt p1Id = ourClient.create().resource(p1).execute().getId();
+
+		//@formatter:off
+		Bundle actual = ourClient.search()
+				.forResource(Patient.class)
+				.where(Patient.PROVIDER.hasId(o1id.getIdPart()))
+				.encodedJson().prettyPrint().execute();
+		//@formatter:on
+		assertEquals(1, actual.size());
+		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getId().getIdPart());
+
+		//@formatter:off
+		actual = ourClient.search()
+				.forResource(Patient.class)
+				.where(Patient.PROVIDER.hasId(o1id.getValue()))
+				.encodedJson().prettyPrint().execute();
+		//@formatter:on
+		assertEquals(1, actual.size());
+		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getId().getIdPart());
+
+	}
+
+	@Test
+	public void testTryToCreateResourceWithReferenceThatDoesntExist() {
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testTryToCreateResourceWithReferenceThatDoesntExist01");
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testTryToCreateResourceWithReferenceThatDoesntExist01");
+		p1.addName().addFamily("testTryToCreateResourceWithReferenceThatDoesntExistFamily01").addGiven("testTryToCreateResourceWithReferenceThatDoesntExistGiven01");
+		p1.setManagingOrganization(new ResourceReferenceDt("Organization/1323123232349875324987529835"));
+
+		try {
+			ourClient.create().resource(p1).execute().getId();
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("Organization/1323123232349875324987529835"));
+		}
+
+	}
+
+	@Test
+	public void testUpdateRejectsInvalidTypes() throws InterruptedException {
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testUpdateRejectsInvalidTypes");
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsInvalidTypes");
+		p1.addName().addFamily("Tester").addGiven("testUpdateRejectsInvalidTypes");
+		IdDt p1id = ourClient.create().resource(p1).execute().getId();
+
+		Organization p2 = new Organization();
+		p2.getNameElement().setValue("testUpdateRejectsInvalidTypes");
+		try {
+			ourClient.update().resource(p2).withId("Organization/" + p1id.getIdPart()).execute();
+			fail();
+		} catch (UnprocessableEntityException e) {
+			// good
+		}
+
+		try {
+			ourClient.update().resource(p2).withId("Patient/" + p1id.getIdPart()).execute();
+			fail();
+		} catch (UnprocessableEntityException e) {
+			// good
+		}
+
+	}
+
+	@Test
+	public void testUpdateWithClientSuppliedIdWhichDoesntExist() {
+		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testUpdateWithClientSuppliedIdWhichDoesntExist");
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateWithClientSuppliedIdWhichDoesntExist");
+		MethodOutcome outcome = ourClient.update().resource(p1).withId("testUpdateWithClientSuppliedIdWhichDoesntExist").execute();
+		assertEquals(true, outcome.getCreated().booleanValue());
+		IdDt p1Id = outcome.getId();
+
+		assertThat(p1Id.getValue(), containsString("Patient/testUpdateWithClientSuppliedIdWhichDoesntExist/_history"));
+
+		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testUpdateWithClientSuppliedIdWhichDoesntExist")).encodedJson().prettyPrint().execute();
+		assertEquals(1, actual.size());
+		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getId().getIdPart());
+
+	}
+
+	@AfterClass
+	public static void afterClass() throws Exception {
+		ourServer.stop();
+		ourAppCtx.stop();
+	}
+
+	@SuppressWarnings("unchecked")
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		int port = RandomServerPortProvider.findFreePort();
+
+		RestfulServer restServer = new RestfulServer();
+		ourFhirCtx = FhirContext.forDstu1();
+		restServer.setFhirContext(ourFhirCtx);
+		
+		String serverBase = "http://localhost:" + port + "/fhir/context";
+
+		ourAppCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dev.xml", "fhir-spring-test-config.xml");
+
+		ourDaoConfig = (DaoConfig) ourAppCtx.getBean(DaoConfig.class);
+
+		ourOrganizationDao = (IFhirResourceDao<Organization>) ourAppCtx.getBean("myOrganizationDaoDev", IFhirResourceDao.class);
+
+		List<IResourceProvider> rpsDev = (List<IResourceProvider>) ourAppCtx.getBean("myResourceProvidersDev", List.class);
+		restServer.setResourceProviders(rpsDev);
+
+		restServer.getFhirContext().setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
+
+		IFhirSystemDao systemDao = (IFhirSystemDao) ourAppCtx.getBean("mySystemDaoDev", IFhirSystemDao.class);
+		JpaSystemProvider systemProv = new JpaSystemProvider(systemDao);
+		restServer.setPlainProviders(systemProv);
+
+		restServer.setPagingProvider(new FifoMemoryPagingProvider(10));
+
+		ourServer = new Server(port);
+
+		ServletContextHandler proxyHandler = new ServletContextHandler();
+		proxyHandler.setContextPath("/");
+
+		ServletHolder servletHolder = new ServletHolder();
+		servletHolder.setServlet(restServer);
+		proxyHandler.addServlet(servletHolder, "/fhir/context/*");
+
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		ourClient = ourFhirCtx.newRestfulGenericClient(serverBase);
+		ourClient.registerInterceptor(new LoggingInterceptor(true));
+
+	}
+
+}

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.parser;
 
+import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
 
 import java.io.StringReader;
@@ -14,8 +15,10 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.dev.resource.MedicationPrescription;
+import ca.uhn.fhir.model.dev.resource.Organization;
 import ca.uhn.fhir.model.dstu.resource.Binary;
 import ca.uhn.fhir.model.primitive.InstantDt;
+import ca.uhn.fhir.model.valueset.BundleEntryStatusEnum;
 
 public class XmlParserTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserTest.class);
@@ -50,6 +53,7 @@ public class XmlParserTest {
 
 		assertEquals(1, parsed.getEntries().size());
 		assertEquals("update", parsed.getEntries().get(0).getStatus().getValue());
+		assertEquals(BundleEntryStatusEnum.UPDATE, ResourceMetadataKeyEnum.ENTRY_STATUS.get(parsed.getEntries().get(0).getResource()));
 		assertEquals("http://foo?search", parsed.getEntries().get(0).getLinkSearch().getValue());
 
 		MedicationPrescription p = (MedicationPrescription) parsed.getEntries().get(0).getResource();
@@ -65,6 +69,20 @@ public class XmlParserTest {
 
 	}
 
+	@Test
+	public void testEncodeAndParseBundleWithoutResourceIds() {
+		Organization org = new Organization();
+		org.addIdentifier().setSystem("urn:system").setValue("someval");
+		
+		Bundle bundle = Bundle.withSingleResource(org);
+		String str = ourCtx.newXmlParser().encodeBundleToString(bundle);
+		ourLog.info(str);
+		
+		Bundle parsed = ourCtx.newXmlParser().parseBundle(str);
+		assertThat(parsed.getEntries().get(0).getResource().getId().getValue(), isEmptyOrNullString());
+		assertTrue(parsed.getEntries().get(0).getResource().getId().isEmpty());
+	}
+	
 	@Test
 	public void testBundleWithBinary() {
 		//@formatter:off

pom.xml.orig

@@ -1,694 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-
-	<parent>
-		<groupId>org.sonatype.oss</groupId>
-		<artifactId>oss-parent</artifactId>
-		<version>9</version>
-	</parent>
-
-	<modelVersion>4.0.0</modelVersion>
-	<groupId>ca.uhn.hapi.fhir</groupId>
-	<artifactId>hapi-fhir</artifactId>
-	<packaging>pom</packaging>
-	<version>0.9-SNAPSHOT</version>
-	<name>HAPI-FHIR</name>
-	<url>http://hl7api.sourceforge.net/hapi-fhir/</url>
-
-	<organization>
-		<name>University Health Network</name>
-		<url>http://www.uhn.ca</url>
-	</organization>
-
-	<inceptionYear>2014</inceptionYear>
-
-	<issueManagement>
-		<system>GitHub</system>
-		<url>https://github.com/jamesagnew/hapi-fhir/issues/</url>
-	</issueManagement>
-
-	<distributionManagement>
-		<site>
-			<id>git.server</id>
-			<url>scm:git:git@github.com:jamesagnew/hapi-fhir.git</url>
-		</site>
-	</distributionManagement>
-
-	<scm>
-		<connection>scm:git:git@github.com:jamesagnew/hapi-fhir.git</connection>
-		<url>scm:git:git@github.com:jamesagnew/hapi-fhir.git</url>
-		<developerConnection>scm:git:git@github.com:jamesagnew/hapi-fhir.git</developerConnection>
-	</scm>
-
-	<description>
-	</description>
-
-	<dependencies>
-	</dependencies>
-
-	<prerequisites>
-		<maven>3.0.1</maven>
-	</prerequisites>
-
-	<developers>
-		<developer>
-			<id>jamesagnew</id>
-			<name>James Agnew</name>
-			<organization>University Health Network</organization>
-		</developer>
-		<developer>
-			<name>Dmitri Sotnikov</name>
-			<organization>University Health Network</organization>
-		</developer>
-		<developer>
-			<name>Lisa Wong</name>
-			<organization>University Health Network</organization>
-		</developer>
-		<developer>
-			<name>Josh Mandel</name>
-			<organization>Boston Children's Hospital</organization>
-		</developer>
-		<developer>
-			<id>lmds</id>
-			<name>Laura MacDougall Sookraj</name>
-			<organization>University Health Network</organization>
-		</developer>
-		<developer>
-			<name>Neal Acharya</name>
-			<organization>University Health Network</organization>
-		</developer>
-		<developer>
-			<name>David Hay</name>
-			<organization>Orion Health</organization>
-		</developer>
-		<developer>
-			<id>suranga</id>
-			<name>Suranga Nath Kasthurirathne</name>
-			<organization>OpenMRS / Regenstrief Center for Biomedical Informatics</organization>
-		</developer>
-		<developer>
-			<id>dougmartin</id>
-			<name>Doug Martin</name>
-			<organization>Regenstrief Center for Biomedical Informatics</organization>
-		</developer>
-		<developer>
-			<id>akley</id>
-			<name>Alexander Kley</name>
-		</developer>
-		<developer>
-			<id>preston</id>
-			<name>Preston Lee</name>
-			<organization>Arizona State University</organization>
-		</developer>
-		<developer>
-			<id>jjathman</id>
-			<name>Joe Athman</name>
-		</developer>
-		<developer>
-			<id>petromykhailysyn</id>
-			<name>Petro Mykhailyshyn</name>
-		</developer>
-		<developer>
-			<id>tahurac</id>
-			<name>Tahura Chaudhry</name>
-			<organization>University Health Network</organization>
-		</developer>
-		<developer>
-			<id>b.debeaubien</id>
-			<name>Bill de Beaubien</name>
-			<organization>Systems Made Simple</organization>
-		</developer>
-	</developers>
-
-	<licenses>
-		<license>
-			<name>Apache Software License 2.0</name>
-			<url>https://www.apache.org/licenses/LICENSE-2.0.txt</url>
-		</license>
-	</licenses>
-
-	<properties>
-		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		
-		<!-- For site-deploy -->
-		<siteMainDirectory>${user.home}/sites/hapi-fhir</siteMainDirectory>
-		<scmPubCheckoutDirectory>${user.home}/sites/scm/hapi-fhir</scmPubCheckoutDirectory>
-
-		<!-- Plugin Versions -->
-		<apache_httpclient_version>4.3.6</apache_httpclient_version>
-		<apache_httpcore_version>4.4</apache_httpcore_version>
-		<commons_io_version>2.4</commons_io_version>
-		<commons_lang_version>3.3.2</commons_lang_version>
-		<commons_codec_version>1.10</commons_codec_version>
-		<derby_version>10.11.1.1</derby_version>
-		<guava_version>18.0</guava_version>
-		<hamcrest_version>1.3</hamcrest_version>
-		<hibernate_version>4.3.7.Final<!-- 4.2.12.Final --></hibernate_version>
-		<hibernate_validator_version>5.1.0.Final</hibernate_validator_version>
-		<jetty_version>9.2.6.v20141205</jetty_version>
-		<jscience_version>4.3.1</jscience_version>
-		<junit_version>4.12</junit_version>
-		<logback_version>1.1.2</logback_version>
-		<maven_assembly_plugin_version>2.4.1</maven_assembly_plugin_version>
-		<maven_javadoc_plugin_version>2.10.1</maven_javadoc_plugin_version>
-		<maven_license_plugin_version>1.7</maven_license_plugin_version>
-		<maven_surefire_plugin_version>2.18.1</maven_surefire_plugin_version>
-		<maven_site_plugin_version>3.4</maven_site_plugin_version>
-		<maven_source_plugin_version>2.3</maven_source_plugin_version>
-		<mitreid-connect-version>1.1.8</mitreid-connect-version>
-		<mockito_version>1.10.17</mockito_version>
-		<phloc_schematron_version>2.7.1</phloc_schematron_version>
-		<phloc_commons_version>4.3.5</phloc_commons_version>
-		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<servlet_api_version>3.1.0</servlet_api_version>
-		<slf4j_version>1.7.9</slf4j_version>
-		<spring_version>4.1.3.RELEASE</spring_version>
-		<spring_security_version>3.2.4.RELEASE</spring_security_version>
-		<thymeleaf-version>2.1.4.RELEASE</thymeleaf-version>
-		<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
-		<woodstox_version>4.4.0</woodstox_version>
-	</properties>
-
-	<build>
-		<pluginManagement>
-			<plugins>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.2</version>
-					<configuration>
-						<source>1.6</source>
-						<target>1.6</target>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-surefire-plugin</artifactId>
-					<version>${maven_surefire_plugin_version}</version>
-					<configuration>
-						<redirectTestOutputToFile>true</redirectTestOutputToFile>
-						<runOrder>random</runOrder>
-<<<<<<< HEAD
-=======
-						<!--<argLine>-Dfile.encoding=ISO-8859-1</argLine> -->
->>>>>>> 8c96bf7d9ef6d6c590c3c7420c293b815935b336
-						<argLine>-Dfile.encoding=UTF-8</argLine>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-site-plugin</artifactId>
-					<version>${maven_site_plugin_version}</version>
-					<dependencies>
-						<dependency>
-							<groupId>org.apache.maven.wagon</groupId>
-							<artifactId>wagon-ssh</artifactId>
-							<version>1.0</version>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.doxia</groupId>
-							<artifactId>doxia-module-markdown</artifactId>
-							<version>1.6</version>
-						</dependency>
-					</dependencies>
-					<configuration>
-						<skip>true</skip>
-						<skipDeploy>true</skipDeploy>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-deploy-plugin</artifactId>
-					<version>2.8.1</version>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-javadoc-plugin</artifactId>
-					<version>${maven_javadoc_plugin_version}</version>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-source-plugin</artifactId>
-					<version>${maven_source_plugin_version}</version>
-				</plugin>
-				<plugin>
-					<groupId>org.codehaus.mojo</groupId>
-					<artifactId>license-maven-plugin</artifactId>
-					<version>${maven_license_plugin_version}</version>
-					<configuration>
-						<verbose>true</verbose>
-						<addSvnKeyWords>false</addSvnKeyWords>
-					</configuration>
-				</plugin>
-				<plugin>
-					<artifactId>maven-site-plugin</artifactId>
-					<version>${maven_site_plugin_version}</version>
-					<configuration>
-						<skip>false</skip>
-						<skipDeploy>true</skipDeploy>
-					</configuration>
-					<dependencies>
-						<dependency>
-							<groupId>org.apache.maven.wagon</groupId>
-							<artifactId>wagon-scm</artifactId>
-							<version>2.2</version>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-manager-plexus</artifactId>
-							<version>1.9</version>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-provider-gitexe</artifactId>
-							<version>1.9</version>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-api</artifactId>
-							<version>1.9</version>
-						</dependency>
-					</dependencies>
-				</plugin>
-				<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
-				<plugin>
-					<groupId>org.eclipse.m2e</groupId>
-					<artifactId>lifecycle-mapping</artifactId>
-					<version>1.0.0</version>
-					<configuration>
-						<lifecycleMappingMetadata>
-							<pluginExecutions>
-								<pluginExecution>
-									<pluginExecutionFilter>
-										<groupId>
-											ca.uhn.hapi.fhir
-										</groupId>
-										<artifactId>
-											hapi-tinder-plugin
-										</artifactId>
-										<versionRange>
-											[0.8-SNAPSHOT,)
-										</versionRange>
-										<goals>
-											<goal>
-												generate-jparest-server
-											</goal>
-										</goals>
-									</pluginExecutionFilter>
-									<action>
-										<ignore></ignore>
-									</action>
-								</pluginExecution>
-								<pluginExecution>
-									<pluginExecutionFilter>
-										<groupId>
-											org.apache.maven.plugins
-										</groupId>
-										<artifactId>
-											maven-antrun-plugin
-										</artifactId>
-										<versionRange>
-											[1.7,)
-										</versionRange>
-										<goals>
-											<goal>run</goal>
-										</goals>
-									</pluginExecutionFilter>
-									<action>
-										<ignore></ignore>
-									</action>
-								</pluginExecution>
-							</pluginExecutions>
-						</lifecycleMappingMetadata>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
-		<plugins>
-			<plugin>
-				<artifactId>maven-antrun-plugin</artifactId>
-				<version>1.7</version>
-				<inherited>false</inherited>
-				<executions>
-					<execution>
-						<id>copySubProjects</id>
-						<phase>site</phase>
-						<goals>
-							<goal>run</goal>
-						</goals>
-						<configuration>
-							<target>
-								<copy todir="target/site/apidocs">
-									<fileset dir="hapi-fhir-base/target/site/apidocs"/>
-								</copy>
-								<copy todir="target/site/apidocs-dstu">
-									<fileset dir="hapi-fhir-structures-dstu/target/site/apidocs"/>
-								</copy>
-								<copy todir="target/site/apidocs-dev">
-									<fileset dir="hapi-fhir-structures-dev/target/site/apidocs"/>
-								</copy>
-							</target>
-						</configuration>
-					</execution>
-					<execution>
-						<id>addSyntaxHighlighter</id>
-						<phase>site</phase>
-						<goals>
-							<goal>run</goal>
-						</goals>
-						<configuration>
-							<target>
-								<echo>Adding Syntax Highlighter</echo>
-								<replace dir="target/site" summary="true">
-									<include name="*.html"></include>
-									<replacetoken><![CDATA[</body>]]></replacetoken>
-									<replacevalue><![CDATA[
-<script type="text/javascript">
-	var elements = document.getElementsByClassName("source");
-	for (var i=0; i < elements.length; i++) {
-		var pres = elements[i].getElementsByTagName("pre");
-		for (var j = 0; j < pres.length; j++) {
-			var pre = pres[j];
-			if (pre.innerHTML.match(/\/\*/)) {
-				pre.className = 'brush: java';
-			} else if (pre.innerHTML.match(/^\/\//)) {
-				pre.className = 'brush: java';
-			} else if (pre.innerHTML.match(/^\{/)) {
-				pre.className = 'brush: jscript';
-			} else if (pre.innerHTML.match(/^\#/)) {
-				pre.className = 'brush: bash';
-			} else if (pre.innerHTML.match(/\&lt\;\//)) {
-				pre.className = 'brush: xml';
-			} else {
-				pre.className = 'brush: java';
-			}
-		}
-	}
-
-	SyntaxHighlighter.all();
-</script>
-</body>
-									]]></replacevalue>
-								</replace>
-							</target>
-						</configuration>
-					</execution>
-					<execution>
-						<id>addAnalytics</id>
-						<phase>post-site</phase>
-						<configuration>
-							<target>
-								<echo>Adding Google analytics in target/site for &lt;body&gt;</echo>
-								<replace dir="target/site" summary="true">
-									<include name="**/*.html"></include>
-									<replacefilter token="#build#" value="${label}" />
-									<replacefilter token="#version#" value="${project.version}" />
-									<replacetoken><![CDATA[</body>]]></replacetoken>
-									<replacevalue><![CDATA[
-<script>
-  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-  })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-
-  ga('create', 'UA-1395874-5', 'auto');
-  ga('require', 'displayfeatures');
-  ga('require', 'linkid', 'linkid.js');
-  ga('send', 'pageview');
-
-</script>
-                </body >
-                ]]></replacevalue>
-								</replace>
-								<echo>Adding Google analytics in target/site for &lt;BODY&gt;</echo>
-								<replace dir="target/site" summary="true">
-									<include name="**/*.html"></include>
-									<replacetoken><![CDATA[</BODY>]]></replacetoken>
-									<replacevalue><![CDATA[
-<script>
-  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-  })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-
-  ga('create', 'UA-1395874-5', 'auto');
-  ga('require', 'displayfeatures');
-  ga('require', 'linkid', 'linkid.js');
-  ga('send', 'pageview');
-
-</script>
-                </BODY >
-                ]]></replacevalue>
-								</replace>
-								<echo>Adding social plugins for HAPI</echo>
-								<replace dir="target/site/" summary="true">
-									<include name="**/*.html"></include>
-									<replacetoken><![CDATA[SOCIALPLUGINSHEREFHIR]]></replacetoken>
-									<replacevalue><![CDATA[
-            	<table cellpadding="0" cellspacing="0" border="0"><tr>
-            	<td><div class="g-plusone" data-annotation="inline" data-width="300" data-href="http://hl7api.sourceforge.net/"></div></td>
-            	<td><div class="fb-like" data-href="http://hl7api.sourceforge.net/" data-send="false" data-layout="button_count" data-width="450" data-show-faces="true"></div></td>
-            	</tr></table>
-
-            	</p><p>
-            	<!-- Place this tag after the last +1 button tag. -->
-            	<script type="text/javascript">
-            	  (function() {
-            	    var po = document.createElement('script'); po.type = 'text/javascript'; po.async = true;
-            	    po.src = 'https://apis.google.com/js/plusone.js';
-            	    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(po, s);
-            	  })();
-            	</script>
-            	<div id="fb-root"></div>
-            	<script>(function(d, s, id) {
-            	  var js, fjs = d.getElementsByTagName(s)[0];
-            	  if (d.getElementById(id)) return;
-            	  js = d.createElement(s); js.id = id;
-            	  js.src = "//connect.facebook.net/en_US/all.js#xfbml=1";
-            	  fjs.parentNode.insertBefore(js, fjs);
-            	}(document, 'script', 'facebook-jssdk'));</script>
-				]]></replacevalue>
-								</replace>
-
-
-							</target>
-						</configuration>
-						<goals>
-							<goal>run</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>animal-sniffer-maven-plugin</artifactId>
-				<version>1.12</version>
-				<inherited>true</inherited>
-				<configuration>
-					<signature>
-						<groupId>org.codehaus.mojo.signature</groupId>
-						<artifactId>java16</artifactId>
-						<version>1.01</version>
-					</signature>
-				</configuration>
-			</plugin>
-			<plugin>
-				<artifactId>maven-site-plugin</artifactId>
-				<inherited>false</inherited>
-				<executions>
-					<execution>
-						<id>stage-for-scm-publish</id>
-						<phase>post-site</phase>
-						<goals>
-							<goal>stage</goal>
-						</goals>
-						<configuration>
-							<stagingDirectory>${siteMainDirectory}</stagingDirectory>
-						</configuration>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-scm-publish-plugin</artifactId>
-				<version>1.1</version>
-				<inherited>false</inherited>
-				<configuration>
-					<checkoutDirectory>${scmPubCheckoutDirectory}</checkoutDirectory>
-					<content>\${siteMainDirectory}</content>
-					<tryUpdate>true</tryUpdate>
-					<scmBranch>gh-pages</scmBranch>
-					<pubScmUrl>scm:git:git@github.com:jamesagnew/hapi-fhir.git</pubScmUrl>
-				</configuration>
-				<executions>
-					<execution>
-						<id>scm-publish</id>
-						<phase>site-deploy</phase>
-						<goals>
-							<goal>publish-scm</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-		</plugins>
-	</build>
-
-	<reporting>
-		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-changes-plugin</artifactId>
-				<version>2.11</version>
-				<inherited>false</inherited>
-				<reportSets>
-					<reportSet>
-						<reports>
-							<report>changes-report</report>
-						</reports>
-					</reportSet>
-				</reportSets>
-				<configuration>
-					<feedType>atom_1.0</feedType>
-					<issueLinkTemplatePerSystem>
-						<default>https://github.com/jamesagnew/hapi-fhir/issues/%ISSUE%</default>
-					</issueLinkTemplatePerSystem>
-					<escapeHTML>false</escapeHTML>
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-surefire-report-plugin</artifactId>
-				<version>${maven_surefire_plugin_version}</version>
-				<configuration>
-					<aggregate>true</aggregate>
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-project-info-reports-plugin</artifactId>
-				<version>2.7</version>
-				<inherited>false</inherited>
-				<reportSets>
-					<reportSet>
-						<reports>
-							<report>project-team</report>
-							<report>issue-tracking</report>
-							<report>license</report>
-							<report>scm</report>
-						</reports>
-					</reportSet>
-				</reportSets>
-			</plugin>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>findbugs-maven-plugin</artifactId>
-				<version>3.0.0</version>
-				<configuration>
-					<classFilesDirectory>./hapi-fhir-base/target/classes</classFilesDirectory>
-				</configuration>
-				<reportSets>
-					<reportSet>
-						<reports>
-							<report>findbugs</report>
-						</reports>
-					</reportSet>
-				</reportSets>
-			</plugin>
-	
-			<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-linkcheck-plugin</artifactId> 
-				<version>1.1</version> </plugin> -->
-		</plugins>
-	</reporting>
-
-	<profiles>
-		<profile>
-			<id>ROOT</id>
-			<modules>
-			</modules>
-			<build>
-				<plugins>
-					<!-- 
-					<plugin>
-						<artifactId>maven-assembly-plugin</artifactId>
-						<version>${maven_assembly_plugin_version}</version>
-						<executions>
-							<execution>
-								<phase>package</phase>
-								<goals>
-									<goal>single</goal>
-								</goals>
-								<configuration>
-									<attach>false</attach>
-									<descriptors>
-										<descriptor>${project.basedir}/src/assembly/hapi-fhir-sample-projects.xml</descriptor>
-									</descriptors>
-								</configuration>
-							</execution>
-						</executions>
-					</plugin>
-					 -->
-				</plugins>
-			</build>
-		</profile>
-		<profile>
-			<id>SIGN_ARTIFACTS</id>
-			<activation>
-				<property>
-					<name>gpg.passphrase</name>
-				</property>
-			</activation>
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.apache.maven.plugins</groupId>
-						<artifactId>maven-gpg-plugin</artifactId>
-						<version>1.5</version>
-						<executions>
-							<execution>
-								<id>sign-artifacts</id>
-								<phase>verify</phase>
-								<goals>
-									<goal>sign</goal>
-								</goals>
-							</execution>
-						</executions>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-		<profile>
-			<id>SITE</id>
-			<modules>
-				<module>hapi-fhir-base</module>
-				<module>hapi-fhir-structures-dstu</module>
-				<module>hapi-fhir-structures-dev</module>
-				<module>examples</module>
-			</modules>
-		</profile>
-		<profile>
-			<id>ALLMODULES</id>
-			<activation>
-				<activeByDefault>true</activeByDefault>
-			</activation>
-			<modules>
-				<module>hapi-deployable-pom</module>
-				<module>hapi-fhir-base</module>
-				<!--<module>hapi-fhir-oauth2</module>-->
-				<module>hapi-fhir-base/testmindeps</module>
-				<module>hapi-tinder-plugin</module>
-				<module>hapi-tinder-test</module>
-				<module>hapi-fhir-structures-dstu</module>
-				<module>hapi-fhir-structures-dev</module>
-				<module>hapi-fhir-jpaserver-base</module>
-				<module>hapi-fhir-jpaserver-test</module>
-				<module>restful-server-example</module>
-				<module>restful-server-example-test</module>
-				<module>hapi-fhir-testpage-overlay</module>
-				<module>hapi-fhir-jpaserver-uhnfhirtest</module>
-			<!--	<module>hapi-fhir-dist</module> -->
-			</modules>
-		</profile>
-	</profiles>
-
-</project>