Fix issue in calling JPA server transactions programmatically where

resources
            are linked by object reference and not by ID where indexes
				were not correctly
				            generated. This should not affect most users.

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

@@ -334,6 +334,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 						continue;
 					}
 					nextId = nextValue.getReferenceElement();
+
+					/*
+					 * This can only really happen if the DAO is being called
+					 * programatically with a Bundle (not through the FHIR REST API)
+					 * but Smile does this 
+					 */
+					if (nextId.isEmpty() && nextValue.getResource() != null) {
+						nextId = nextValue.getResource().getIdElement();
+					}
+					
 					if (nextId.isEmpty() || nextId.getValue().startsWith("#")) {
 						// This is a blank or contained resource reference
 						continue;

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

@@ -273,8 +273,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 			// Notify interceptors
 			IdDt idToDelete = entity.getIdDt();
-			ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
+			if (theRequestDetails != null) {
-			notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
+				ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
+				notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
+			}
 			
 			// Perform delete
 			Date updateTime = new Date();
@@ -282,10 +284,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 			// Notify JPA interceptors
 			T resourceToDelete = toResource(myResourceType, entity, false);
-			theRequestDetails.getRequestOperationCallback().resourceDeleted(resourceToDelete);
+			if (theRequestDetails != null) {
-			for (IServerInterceptor next : getConfig().getInterceptors()) {
+				theRequestDetails.getRequestOperationCallback().resourceDeleted(resourceToDelete);
-				if (next instanceof IJpaServerInterceptor) {
+				ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
-					((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity);
+				for (IServerInterceptor next : getConfig().getInterceptors()) {
+					if (next instanceof IJpaServerInterceptor) {
+						((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity);
+					}
 				}
 			}
 			for (IServerInterceptor next : getConfig().getInterceptors()) {

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

@@ -542,6 +542,60 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		}
 	}
 
+	@Test
+	public void testTransactionWithReferenceUuid() {
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.setActive(true);
+		p.setId(IdType.newRandomUuid());
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl(p.getId());
+		
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference(p.getId());
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+		
+		String patientId = new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualifiedVersionless().getValue();
+		assertThat(patientId, startsWith("Patient/"));
+		
+		SearchParameterMap params = new SearchParameterMap();
+		params.setLoadSynchronous(true);
+		params.add("subject", new ReferenceParam(patientId));
+		IBundleProvider found = myObservationDao.search(params);
+		assertEquals(1, found.size().intValue());
+	}
+
+	@Test
+	public void testTransactionWithReferenceResource() {
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.setActive(true);
+		p.setId(IdType.newRandomUuid());
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl(p.getId());
+		
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setResource(p);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+		
+		String patientId = new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualifiedVersionless().getValue();
+		assertThat(patientId, startsWith("Patient/"));
+		
+		SearchParameterMap params = new SearchParameterMap();
+		params.setLoadSynchronous(true);
+		params.add("subject", new ReferenceParam(patientId));
+		IBundleProvider found = myObservationDao.search(params);
+		assertEquals(1, found.size().intValue());
+	}
+
 	@Test
 	public void testTransactionCreateInlineMatchUrlWithOneMatch() {
 		String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch";

src/changes/changes.xml

@@ -52,6 +52,11 @@
 				Prevent duplicates in $everything query response in JPA server. Thanks to @vlad-ignatov 
 				for reporting!
 			</action>
+			<action type="fix">
+				Fix issue in calling JPA server transactions programmatically where resources
+				are linked by object reference and not by ID where indexes were not correctly
+				generated. This should not affect most users.
+			</action>
 		</release>
 		<release version="2.5" date="2017-06-08">
 			<action type="fix">