JPA server transactions sometimes created an incorrect resource reference if a resource being saved contained references that had a display value but not an actual reference. Thanks to David Hay for reporting!

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

@@ -42,6 +42,10 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetai
 
 public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {
 
+	public FhirResourceDaoPatientDstu2() {
+		super();
+	}
+	
 	private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative) {
 		SearchParameterMap paramMap = new SearchParameterMap();
 		if (theCount != null) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -460,6 +460,9 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 			List<BaseResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
 			for (BaseResourceReferenceDt nextRef : allRefs) {
 				IdDt nextId = nextRef.getReference();
+				if (!nextId.hasIdPart()) {
+					continue;
+				}
 				if (idSubstitutions.containsKey(nextId)) {
 					IdDt newId = idSubstitutions.get(nextId);
 					ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);

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

@@ -470,6 +470,9 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 			List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class);
 			for (IBaseReference nextRef : allRefs) {
 				IIdType nextId = nextRef.getReferenceElement();
+				if (!nextId.hasIdPart()) {
+					continue;
+				}
 				if (idSubstitutions.containsKey(nextId)) {
 					IdType newId = idSubstitutions.get(nextId);
 					ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -18,7 +18,6 @@ import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.ApplicationContext;
-import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.PlatformTransactionManager;
@@ -41,6 +40,7 @@ import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
+import ca.uhn.fhir.model.dstu2.resource.Appointment;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.ConceptMap;
 import ca.uhn.fhir.model.dstu2.resource.Device;
@@ -87,6 +87,9 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myConceptMapDaoDstu2")
 	protected IFhirResourceDao<ConceptMap> myConceptMapDao;
 	@Autowired
+	@Qualifier("myAppointmentDaoDstu2")
+	protected IFhirResourceDao<Appointment> myAppointmentDao;
+	@Autowired
 	@Qualifier("myBundleDaoDstu2")
 	protected IFhirResourceDao<Bundle> myBundleDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java

@@ -43,6 +43,7 @@ import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
+import ca.uhn.fhir.model.dstu2.resource.Appointment;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.EntryRequest;
@@ -66,19 +67,12 @@ import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu2Test.class);
 
-	@AfterClass
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-
 	@Test
 	public void testReindexing() {
 		Patient p = new Patient();
@@ -151,7 +145,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		assertEquals(Long.valueOf(2), entity.getIndexStatus());
 
 	}
-	
+
 	@Test
 	public void testSystemMetaOperation() {
 
@@ -240,7 +234,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		assertEquals("http://profile/2", profiles.get(0).getValue());
 
 	}
-
+	
 	@Test
 	public void testTransactionBatchWithFailingRead() {
 		String methodName = "testTransactionBatchWithFailingRead";
@@ -287,6 +281,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		assertThat(respEntry.getStatus(), startsWith("404"));
 
 	}
+	
 
 	@Test
 	public void testTransactionCreateMatchUrlWithOneMatch() {
@@ -329,7 +324,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		assertEquals("1", o.getId().getVersionIdPart());
 
 	}
-
+	
 	@Test
 	public void testTransactionCreateMatchUrlWithTwoMatch() {
 		String methodName = "testTransactionCreateMatchUrlWithTwoMatch";
@@ -929,6 +924,25 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 	}
 
+	private Bundle testTransactionOrderingCreateBundle(String methodName, int pass, IdDt patientPlaceholderId) {
+		Bundle req = new Bundle();
+		req.addEntry().getRequest().setMethod(HTTPVerbEnum.GET).setUrl("Patient?identifier=" + methodName);
+		
+		Observation obs = new Observation();
+		obs.getSubject().setReference(patientPlaceholderId);
+		obs.addIdentifier().setValue(methodName);
+		obs.getCode().setText(methodName + pass);
+		req.addEntry().setResource(obs).getRequest().setMethod(HTTPVerbEnum.PUT).setUrl("Observation?identifier=" + methodName);
+		
+		Patient pat = new Patient();
+		pat.addIdentifier().setValue(methodName);
+		pat.addName().addFamily(methodName + pass);
+		req.addEntry().setResource(pat).setFullUrl(patientPlaceholderId.getValue()).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
+		
+		req.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=" + methodName);
+		return req;
+	}
+
 	private void testTransactionOrderingValidateResponse(int pass, Bundle resp) {
 		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
 		assertEquals(4, resp.getEntry().size());
@@ -957,25 +971,6 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		assertThat(respGetBundle.getLink("self").getUrl(), endsWith("/Patient?identifier=testTransactionOrdering"));
 	}
 
-	private Bundle testTransactionOrderingCreateBundle(String methodName, int pass, IdDt patientPlaceholderId) {
-		Bundle req = new Bundle();
-		req.addEntry().getRequest().setMethod(HTTPVerbEnum.GET).setUrl("Patient?identifier=" + methodName);
-		
-		Observation obs = new Observation();
-		obs.getSubject().setReference(patientPlaceholderId);
-		obs.addIdentifier().setValue(methodName);
-		obs.getCode().setText(methodName + pass);
-		req.addEntry().setResource(obs).getRequest().setMethod(HTTPVerbEnum.PUT).setUrl("Observation?identifier=" + methodName);
-		
-		Patient pat = new Patient();
-		pat.addIdentifier().setValue(methodName);
-		pat.addName().addFamily(methodName + pass);
-		req.addEntry().setResource(pat).setFullUrl(patientPlaceholderId.getValue()).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
-		
-		req.addEntry().getRequest().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient?identifier=" + methodName);
-		return req;
-	}
-
 	@Test
 	public void testTransactionReadAndSearch() {
 		String methodName = "testTransactionReadAndSearch";
@@ -1308,6 +1303,87 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 	}
 
+	/**
+	 * From a message from David Hay
+	 */
+	@Test
+	public void testTransactionWithAppointments() {
+		Patient p = new Patient();
+		p.addName().addFamily("family");
+		final IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+
+		//@formatter:on
+		String input = "{\n" + 
+				"    \"resourceType\": \"Bundle\",\n" + 
+				"    \"type\": \"transaction\",\n" + 
+				"    \"entry\": [\n" + 
+				"        {\n" + 
+				"            \"resource\": {\n" + 
+				"                \"resourceType\": \"Appointment\",\n" + 
+				"                \"status\": \"pending\",\n" + 
+				"                \"type\": {\"text\": \"Cardiology\"},\n" + 
+				"                \"description\": \"Investigate Angina\",\n" + 
+				"                \"start\": \"2016-04-30T18:48:29+12:00\",\n" + 
+				"                \"end\": \"2016-04-30T19:03:29+12:00\",\n" + 
+				"                \"minutesDuration\": 15,\n" + 
+				"                \"participant\": [\n" + 
+				"                    {\n" + 
+				"                        \"actor\": {\"display\": \"Clarence cardiology clinic\"},\n" + 
+				"                        \"status\": \"accepted\"\n" + 
+				"                    },\n" + 
+				"                    {\n" + 
+				"                        \"actor\": {\"reference\": \"Patient/" + id.getIdPart() + "\"},\n" + 
+				"                        \"status\": \"accepted\"\n" + 
+				"                    }\n" + 
+				"                ],\n" + 
+				"                \"text\": {\n" + 
+				"                    \"status\": \"generated\",\n" + 
+				"                    \"div\": \"<div><div>Investigate Angina<\\/div><div>Clarence cardiology clinic<\\/div><\\/div>\"\n" + 
+				"                }\n" + 
+				"            },\n" + 
+				"            \"request\": {\n" + 
+				"                \"method\": \"POST\",\n" + 
+				"                \"url\": \"Appointment\"\n" + 
+				"            }\n" + 
+				"        },\n" + 
+				"        {\n" + 
+				"            \"resource\": {\n" + 
+				"                \"resourceType\": \"Appointment\",\n" + 
+				"                \"status\": \"pending\",\n" + 
+				"                \"type\": {\"text\": \"GP Visit\"},\n" + 
+				"                \"description\": \"Routine checkup\",\n" + 
+				"                \"start\": \"2016-05-03T18:48:29+12:00\",\n" + 
+				"                \"end\": \"2016-05-03T19:03:29+12:00\",\n" + 
+				"                \"minutesDuration\": 15,\n" + 
+				"                \"participant\": [\n" + 
+				"                    {\n" + 
+				"                        \"actor\": {\"display\": \"Dr Dave\"},\n" + 
+				"                        \"status\": \"accepted\"\n" + 
+				"                    },\n" + 
+				"                    {\n" + 
+				"                        \"actor\": {\"reference\": \"Patient/" + id.getIdPart() + "\"},\n" + 
+				"                        \"status\": \"accepted\"\n" + 
+				"                    }\n" + 
+				"                ],\n" + 
+				"                \"text\": {\n" + 
+				"                    \"status\": \"generated\",\n" + 
+				"                    \"div\": \"<div><div>Routine checkup<\\/div><div>Dr Dave<\\/div><\\/div>\"\n" + 
+				"                }\n" + 
+				"            },\n" + 
+				"            \"request\": {\n" + 
+				"                \"method\": \"POST\",\n" + 
+				"                \"url\": \"Appointment\"\n" + 
+				"            }\n" + 
+				"        }\n" + 
+				"    ]\n" + 
+				"}";
+		//@formatter:on
+		
+		Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
+		Bundle outputBundle = mySystemDao.transaction(mySrd, inputBundle);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
+	}
+
 	@Test
 	public void testTransactionWithInvalidType() {
 		Bundle request = new Bundle();
@@ -1324,6 +1400,65 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 	}
 
+	@Test
+	public void testTransactionWithNullReference() {
+		Patient p = new Patient();
+		p.addName().addFamily("family");
+		final IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+		
+		Bundle inputBundle = new Bundle();
+
+		//@formatter:off
+		Patient app0 = new Patient();
+		app0.addName().addFamily("NEW PATIENT");
+		String placeholderId0 = IdDt.newRandomUuid().getValue();
+		inputBundle
+			.addEntry()
+				.setResource(app0)
+				.setFullUrl(placeholderId0)
+				.getRequest()
+					.setMethod(HTTPVerbEnum.POST)
+					.setUrl("Patient");
+		//@formatter:on
+		
+		//@formatter:off
+		Appointment app1 = new Appointment();
+		app1.addParticipant().getActor().setReference(id);
+		inputBundle
+			.addEntry()
+				.setResource(app1)
+				.getRequest()
+					.setMethod(HTTPVerbEnum.POST)
+					.setUrl("Appointment");
+		//@formatter:on
+
+		//@formatter:off
+		Appointment app2 = new Appointment();
+		app2.addParticipant().getActor().setDisplay("NO REF");
+		app2.addParticipant().getActor().setDisplay("YES REF").setReference(placeholderId0);
+		inputBundle
+			.addEntry()
+				.setResource(app2)
+				.getRequest()
+					.setMethod(HTTPVerbEnum.POST)
+					.setUrl("Appointment");
+		//@formatter:on
+
+		Bundle outputBundle = mySystemDao.transaction(mySrd, inputBundle);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
+		
+		assertEquals(3, outputBundle.getEntry().size());
+		IdDt id0 = new IdDt(outputBundle.getEntry().get(0).getResponse().getLocation());
+		IdDt id1 = new IdDt(outputBundle.getEntry().get(1).getResponse().getLocation());
+		IdDt id2 = new IdDt(outputBundle.getEntry().get(2).getResponse().getLocation());
+		
+		app2 = myAppointmentDao.read(id2, mySrd);
+		assertEquals("NO REF", app2.getParticipant().get(0).getActor().getDisplay().getValue());
+		assertEquals(null, app2.getParticipant().get(0).getActor().getReference().getValue());
+		assertEquals("YES REF", app2.getParticipant().get(1).getActor().getDisplay().getValue());
+		assertEquals(id0.toUnqualifiedVersionless().getValue(), app2.getParticipant().get(1).getActor().getReference().getValue());
+	}
+
 	@Test
 	public void testTransactionWithReferenceToCreateIfNoneExist() {
 		Bundle bundle = new Bundle();
@@ -1377,6 +1512,46 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		assertNotEquals(medOrderId1, medOrderId2);
 	}
 
+	@Test
+	public void testTransactionWithRelativeOidIds() throws Exception {
+		Bundle res = new Bundle();
+		res.setType(BundleTypeEnum.TRANSACTION);
+
+		Patient p1 = new Patient();
+		p1.setId("urn:oid:0.1.2.3");
+		p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01");
+		res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
+
+		Observation o1 = new Observation();
+		o1.setId("cid:observation1");
+		o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
+		o1.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
+		res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
+
+		Observation o2 = new Observation();
+		o2.setId("cid:observation2");
+		o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
+		o2.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
+		res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
+
+		Bundle resp = mySystemDao.transaction(mySrd, res);
+
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+
+		assertEquals(BundleTypeEnum.TRANSACTION_RESPONSE, resp.getTypeElement().getValueAsEnum());
+		assertEquals(3, resp.getEntry().size());
+
+		assertTrue(resp.getEntry().get(0).getResponse().getLocation(), new IdDt(resp.getEntry().get(0).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
+		assertTrue(resp.getEntry().get(1).getResponse().getLocation(), new IdDt(resp.getEntry().get(1).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
+		assertTrue(resp.getEntry().get(2).getResponse().getLocation(), new IdDt(resp.getEntry().get(2).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
+
+		o1 = myObservationDao.read(new IdDt(resp.getEntry().get(1).getResponse().getLocation()), mySrd);
+		o2 = myObservationDao.read(new IdDt(resp.getEntry().get(2).getResponse().getLocation()), mySrd);
+		assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
+		assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
+
+	}
+
 	//
 	//
 	// /**
@@ -1479,46 +1654,6 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 	//
 	// }
 
-	@Test
-	public void testTransactionWithRelativeOidIds() throws Exception {
-		Bundle res = new Bundle();
-		res.setType(BundleTypeEnum.TRANSACTION);
-
-		Patient p1 = new Patient();
-		p1.setId("urn:oid:0.1.2.3");
-		p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01");
-		res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
-
-		Observation o1 = new Observation();
-		o1.setId("cid:observation1");
-		o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
-		o1.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
-		res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
-
-		Observation o2 = new Observation();
-		o2.setId("cid:observation2");
-		o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
-		o2.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
-		res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
-
-		Bundle resp = mySystemDao.transaction(mySrd, res);
-
-		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
-
-		assertEquals(BundleTypeEnum.TRANSACTION_RESPONSE, resp.getTypeElement().getValueAsEnum());
-		assertEquals(3, resp.getEntry().size());
-
-		assertTrue(resp.getEntry().get(0).getResponse().getLocation(), new IdDt(resp.getEntry().get(0).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
-		assertTrue(resp.getEntry().get(1).getResponse().getLocation(), new IdDt(resp.getEntry().get(1).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
-		assertTrue(resp.getEntry().get(2).getResponse().getLocation(), new IdDt(resp.getEntry().get(2).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
-
-		o1 = myObservationDao.read(new IdDt(resp.getEntry().get(1).getResponse().getLocation()), mySrd);
-		o2 = myObservationDao.read(new IdDt(resp.getEntry().get(2).getResponse().getLocation()), mySrd);
-		assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
-		assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
-
-	}
-
 	/**
 	 * This is not the correct way to do it, but we'll allow it to be lenient
 	 */
@@ -1562,4 +1697,9 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
 }

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

@@ -12,6 +12,7 @@ import org.apache.commons.io.IOUtils;
 import org.hibernate.search.jpa.FullTextEntityManager;
 import org.hibernate.search.jpa.Search;
 import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport;
+import org.hl7.fhir.dstu3.model.Appointment;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -90,12 +91,15 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 
 
 	@Autowired
-	@Qualifier("myCodeSystemDaoDstu3")
+	@Qualifier("myAppointmentDaoDstu3")
-	protected IFhirResourceDao<CodeSystem> myCodeSystemDao;
+	protected IFhirResourceDao<Appointment> myAppointmentDao;
 	@Autowired
 	@Qualifier("myBundleDaoDstu3")
 	protected IFhirResourceDao<Bundle> myBundleDao;
 	@Autowired
+	@Qualifier("myCodeSystemDaoDstu3")
+	protected IFhirResourceDao<CodeSystem> myCodeSystemDao;
+	@Autowired
 	@Qualifier("myConceptMapDaoDstu3")
 	protected IFhirResourceDao<ConceptMap> myConceptMapDao;
 	@Autowired
@@ -139,14 +143,14 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myNamingSystemDaoDstu3")
 	protected IFhirResourceDao<NamingSystem> myNamingSystemDao;
-	@Autowired
-	@Qualifier("myObservationDaoDstu3")
-	protected IFhirResourceDao<Observation> myObservationDao;
 	
 @Autowired
-@Qualifier("myOrganizationDaoDstu3")
+@Qualifier("myObservationDaoDstu3")
-protected IFhirResourceDao<Organization> myOrganizationDao;
+protected IFhirResourceDao<Observation> myObservationDao;
 	
+	@Autowired
+	@Qualifier("myOrganizationDaoDstu3")
+	protected IFhirResourceDao<Organization> myOrganizationDao;
 	@Autowired
 	@Qualifier("myPatientDaoDstu3")
 	protected IFhirResourceDaoPatient<Patient> myPatientDao;

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

@@ -22,6 +22,7 @@ import java.io.UnsupportedEncodingException;
 import java.util.List;
 
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.dstu3.model.Appointment;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryRequestComponent;
@@ -58,6 +59,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.IBundleProvider;
@@ -77,6 +79,64 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
+	@Test
+	public void testTransactionWithNullReference() {
+		Patient p = new Patient();
+		p.addName().addFamily("family");
+		final IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+		
+		Bundle inputBundle = new Bundle();
+
+		//@formatter:off
+		Patient app0 = new Patient();
+		app0.addName().addFamily("NEW PATIENT");
+		String placeholderId0 = IdDt.newRandomUuid().getValue();
+		inputBundle
+			.addEntry()
+				.setResource(app0)
+				.setFullUrl(placeholderId0)
+				.getRequest()
+					.setMethod(HTTPVerb.POST)
+					.setUrl("Patient");
+		//@formatter:on
+		
+		//@formatter:off
+		Appointment app1 = new Appointment();
+		app1.addParticipant().getActor().setReference(id.getValue());
+		inputBundle
+			.addEntry()
+				.setResource(app1)
+				.getRequest()
+					.setMethod(HTTPVerb.POST)
+					.setUrl("Appointment");
+		//@formatter:on
+
+		//@formatter:off
+		Appointment app2 = new Appointment();
+		app2.addParticipant().getActor().setDisplay("NO REF");
+		app2.addParticipant().getActor().setDisplay("YES REF").setReference(placeholderId0);
+		inputBundle
+			.addEntry()
+				.setResource(app2)
+				.getRequest()
+					.setMethod(HTTPVerb.POST)
+					.setUrl("Appointment");
+		//@formatter:on
+
+		Bundle outputBundle = mySystemDao.transaction(mySrd, inputBundle);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
+		
+		assertEquals(3, outputBundle.getEntry().size());
+		IdDt id0 = new IdDt(outputBundle.getEntry().get(0).getResponse().getLocation());
+		IdDt id2 = new IdDt(outputBundle.getEntry().get(2).getResponse().getLocation());
+		
+		app2 = myAppointmentDao.read(id2, mySrd);
+		assertEquals("NO REF", app2.getParticipant().get(0).getActor().getDisplay());
+		assertEquals(null, app2.getParticipant().get(0).getActor().getReference());
+		assertEquals("YES REF", app2.getParticipant().get(1).getActor().getDisplay());
+		assertEquals(id0.toUnqualifiedVersionless().getValue(), app2.getParticipant().get(1).getActor().getReference());
+	}
+
 
 	@Test
 	public void testReindexing() {

src/changes/changes.xml

@@ -51,6 +51,11 @@
 				Note that existing databases will need to modify index "IDX_FORCEDID" as
 				it is no longer unique, and perform a reindexing pass.
 			</action>
+			<action type="fix">
+				JPA server transactions sometimes created an incorrect resource reference
+				if a resource being saved contained references that had a display value but
+				not an actual reference. Thanks to David Hay for reporting!
+			</action>
 		</release>
 		<release version="1.5" date="2016-04-20">
 			<action type="fix" issue="339">