Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/BaseClient.java

@@ -567,6 +567,10 @@ public abstract class BaseClient implements IRestfulClient {
 
 		@Override
 		public T invokeClient(String theResponseMimeType, InputStream theResponseInputStream, int theResponseStatusCode, Map<String, List<String>> theHeaders) throws BaseServerResponseException {
+			if (theResponseStatusCode == Constants.STATUS_HTTP_204_NO_CONTENT) {
+				return null;
+			}
+
 			EncodingEnum respType = EncodingEnum.forContentType(theResponseMimeType);
 			if (respType == null) {
 				if (myAllowHtmlResponse && theResponseMimeType.toLowerCase().contains(Constants.CT_HTML) && myReturnType != null) {

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2049-add-search-null-guard.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 2049
+title: A potential NPE in the JPA server was fixed. This error could be triggered by searching for resources with
+   unresolvable references. Thanks to Anders Havn for the pull request!

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2050-mutliple-updates-on-one-resource-in-transaction.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 2050
+title: An issue was fixed where multiple JPA server updates to the same resource within the same 
+    database transaction would fail with a database constraint error.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2051-allow-204-transaction-response.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2051
+title: The FHIR Client will now accept an HTTP 204 NO CONTENT as a response to a write operation such
+  as a create/update/transaction/etc.

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

@@ -1057,7 +1057,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 						entity.setLanguage(((IAnyResource) theResource).getLanguageElement().getValue());
 					}
 
-					newParams.setParamsOn(entity);
+					newParams.populateResourceTableSearchParamsPresentFlags(entity);
 					entity.setIndexStatus(INDEX_STATUS_INDEXED);
 					populateFullTextFields(myContext, theResource, entity);
 				}
@@ -1206,6 +1206,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 				// Synchronize search param indexes
 				AddRemoveCount searchParamAddRemoveCount = myDaoSearchParamSynchronizer.synchronizeSearchParamsToDatabase(newParams, entity, existingParams);
 
+				newParams.populateResourceTableParamCollections(entity);
+
 				// Interceptor broadcast: JPA_PERFTRACE_INFO
 				if (!searchParamAddRemoveCount.isEmpty()) {
 					if (JpaInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequest)) {

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

@@ -745,6 +745,9 @@ public class SearchBuilder implements ISearchBuilder {
 						q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
 						List<Long> results = q.getResultList();
 						for (Long resourceLink : results) {
+							if (resourceLink == null) {
+								continue;
+							}
 							if (theReverseMode) {
 								pidsToInclude.add(new ResourcePersistentId(resourceLink));
 							} else {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -887,6 +887,30 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		}
 	}
 
+	@Test
+	public void testCreateThenUpdateInSameTransaction() {
+		Patient initialPatient = new Patient();
+		IIdType id = myPatientDao.create(initialPatient).getId().toUnqualifiedVersionless();
+
+		runInTransaction(() -> {
+			Patient p = new Patient();
+			p.setId(id);
+			p.setActive(true);
+			p.addName().setFamily("FAMILY");
+			myPatientDao.update(p);
+
+			p = new Patient();
+			p.setId(id);
+			p.setActive(false);
+			p.addName().setFamily("FAMILY2");
+			myPatientDao.update(p);
+		});
+
+		assertEquals(1, myPatientDao.search(SearchParameterMap.newSynchronous("name", new StringParam("family2"))).size());
+		assertEquals(1, myPatientDao.search(SearchParameterMap.newSynchronous("active", new TokenParam("false"))).size());
+
+	}
+
 	@Test
 	public void testCreateSummaryFails() {
 		Patient p = new Patient();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -33,7 +33,6 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.BaseValidatingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.util.HapiExtensions;
-import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import ca.uhn.fhir.validation.IValidatorModule;
 import com.google.common.base.Charsets;
@@ -76,6 +75,7 @@ import org.hl7.fhir.dstu3.model.DocumentReference;
 import org.hl7.fhir.dstu3.model.Encounter;
 import org.hl7.fhir.dstu3.model.Encounter.EncounterLocationComponent;
 import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
+import org.hl7.fhir.dstu3.model.Enumerations;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu3.model.Extension;
 import org.hl7.fhir.dstu3.model.IdType;
@@ -96,6 +96,7 @@ import org.hl7.fhir.dstu3.model.Organization;
 import org.hl7.fhir.dstu3.model.Parameters;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Period;
+import org.hl7.fhir.dstu3.model.PlanDefinition;
 import org.hl7.fhir.dstu3.model.Practitioner;
 import org.hl7.fhir.dstu3.model.ProcedureRequest;
 import org.hl7.fhir.dstu3.model.Quantity;
@@ -103,6 +104,7 @@ import org.hl7.fhir.dstu3.model.Questionnaire;
 import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
 import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
 import org.hl7.fhir.dstu3.model.Reference;
+import org.hl7.fhir.dstu3.model.RelatedArtifact;
 import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.dstu3.model.StructureDefinition;
 import org.hl7.fhir.dstu3.model.Subscription;
@@ -112,7 +114,6 @@ import org.hl7.fhir.dstu3.model.UnsignedIntType;
 import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
@@ -138,6 +139,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
+import java.util.UUID;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.hamcrest.MatcherAssert.assertThat;
@@ -362,6 +364,45 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
 	}
 
+	@Test
+	public void testSearchWithIncludeAllWithNotResolvableReference() {
+		// Arrange
+		myDaoConfig.setAllowExternalReferences(true);
+
+		Patient patient = new Patient();
+		patient.addName().setFamily(UUID.randomUUID().toString());
+		IIdType createdPatientId = ourClient.create().resource(patient).execute().getId();
+
+		RelatedArtifact relatedArtifactInternalReference = new RelatedArtifact();
+		relatedArtifactInternalReference.setDisplay(UUID.randomUUID().toString());
+		relatedArtifactInternalReference.setType(RelatedArtifact.RelatedArtifactType.PREDECESSOR);
+		relatedArtifactInternalReference.setResource(new Reference(createdPatientId.toUnqualifiedVersionless()));
+
+		RelatedArtifact relatedArtifactExternalReference = new RelatedArtifact();
+		relatedArtifactExternalReference.setDisplay(UUID.randomUUID().toString());
+		relatedArtifactExternalReference.setType(RelatedArtifact.RelatedArtifactType.PREDECESSOR);
+		relatedArtifactExternalReference.setResource(new Reference("http://not-local-host.dk/hapi-fhir-jpaserver/fhir/Patient/2"));
+
+		PlanDefinition planDefinition = new PlanDefinition();
+		planDefinition.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		planDefinition.setName(UUID.randomUUID().toString());
+		planDefinition.setRelatedArtifact(Arrays.asList(relatedArtifactInternalReference, relatedArtifactExternalReference));
+		IIdType createdPlanDefinitionId = ourClient.create().resource(planDefinition).execute().getId();
+
+		// Act
+		Bundle returnedBundle = ourClient.search()
+			.forResource(PlanDefinition.class)
+			.include(PlanDefinition.INCLUDE_ALL)
+			.where(PlanDefinition.NAME.matches().value(planDefinition.getName()))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		// Assert
+		assertEquals(returnedBundle.getEntry().size(), 2);
+		assertEquals(createdPlanDefinitionId, genResourcesOfType(returnedBundle, PlanDefinition.class).get(0).getIdElement());
+		assertEquals(createdPatientId, genResourcesOfType(returnedBundle, Patient.class).get(0).getIdElement());
+	}
+
 	@Test
 	public void testBundleCreateWithTypeTransaction() throws Exception {
 		IGenericClient client = ourClient;

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java

@@ -105,26 +105,30 @@ public final class ResourceIndexedSearchParams {
 		return myLinks;
 	}
 
-	public void setParamsOn(ResourceTable theEntity) {
+	public void populateResourceTableSearchParamsPresentFlags(ResourceTable theEntity) {
-		theEntity.setParamsString(myStringParams);
 		theEntity.setParamsStringPopulated(myStringParams.isEmpty() == false);
-		theEntity.setParamsToken(myTokenParams);
 		theEntity.setParamsTokenPopulated(myTokenParams.isEmpty() == false);
-		theEntity.setParamsNumber(myNumberParams);
 		theEntity.setParamsNumberPopulated(myNumberParams.isEmpty() == false);
-		theEntity.setParamsQuantity(myQuantityParams);
 		theEntity.setParamsQuantityPopulated(myQuantityParams.isEmpty() == false);
-		theEntity.setParamsDate(myDateParams);
 		theEntity.setParamsDatePopulated(myDateParams.isEmpty() == false);
-		theEntity.setParamsUri(myUriParams);
 		theEntity.setParamsUriPopulated(myUriParams.isEmpty() == false);
-		theEntity.setParamsCoords(myCoordsParams);
 		theEntity.setParamsCoordsPopulated(myCoordsParams.isEmpty() == false);
 		theEntity.setParamsCompositeStringUniquePresent(myCompositeStringUniques.isEmpty() == false);
-		theEntity.setResourceLinks(myLinks);
 		theEntity.setHasLinks(myLinks.isEmpty() == false);
 	}
 
+
+	public void populateResourceTableParamCollections(ResourceTable theEntity) {
+		theEntity.setParamsString(myStringParams);
+		theEntity.setParamsToken(myTokenParams);
+		theEntity.setParamsNumber(myNumberParams);
+		theEntity.setParamsQuantity(myQuantityParams);
+		theEntity.setParamsDate(myDateParams);
+		theEntity.setParamsUri(myUriParams);
+		theEntity.setParamsCoords(myCoordsParams);
+		theEntity.setResourceLinks(myLinks);
+	}
+
 	void setUpdatedTime(Date theUpdateTime) {
 		setUpdatedTime(myStringParams, theUpdateTime);
 		setUpdatedTime(myNumberParams, theUpdateTime);

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

@@ -2397,33 +2397,6 @@ public class GenericClientDstu2Test {
 		assertEquals("Patient/2/_history/2", response.getEntry().get(1).getResponse().getLocation());
 	}
 
-	@Test
-	public void testTransactionHandle204NoBody() throws Exception {
-
-		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
-
-		ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new Bundle();
-		bundle.setType(BundleTypeEnum.TRANSACTION);
-
-		ca.uhn.fhir.model.dstu2.resource.Bundle.Entry entry = bundle.addEntry();
-		entry.setResource(new Patient());
-		entry.getRequest().setMethod(HTTPVerbEnum.PUT);
-
-
-
-		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
-		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
-		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), Constants.STATUS_HTTP_204_NO_CONTENT, ""));
-		when(myHttpResponse.getEntity() ).thenReturn(null);
-
-		try {
-			client.transaction().withBundle(bundle).execute();
-			fail("Should throw an exception");
-		} catch (NonFhirResponseException e) {
-			assertEquals(Constants.STATUS_HTTP_204_NO_CONTENT, e.getStatusCode());
-		}
-	}
-
 	@Test
 	public void testUpdateConditional() throws Exception {
 		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/GenericClientR4Test.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.ParamPrefixEnum;
 import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
 import ca.uhn.fhir.rest.server.exceptions.UnclassifiedServerFailureException;
+import ca.uhn.fhir.util.TransactionBuilder;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import com.helger.commons.io.stream.StringInputStream;
@@ -36,6 +37,7 @@ import org.apache.http.client.methods.HttpPut;
 import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.message.BasicHeader;
 import org.apache.http.message.BasicStatusLine;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.Binary;
 import org.hl7.fhir.r4.model.BooleanType;
@@ -2106,6 +2108,31 @@ public class GenericClientR4Test extends BaseGenericClientR4Test {
 
 	}
 
+	@Test
+	public void testTransactionWithResponseHttp204NoContent() throws IOException {
+		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
+
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 204, "No Content"));
+		when(myHttpResponse.getEntity()).thenReturn(null);
+		when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
+			@Override
+			public Header[] answer(InvocationOnMock theInvocation) {
+				return new Header[0];
+			}
+		});
+
+		TransactionBuilder builder = new TransactionBuilder(ourCtx);
+		builder.addCreateEntry(new Patient().setActive(true));
+
+		IBaseBundle outcome = client.transaction().withBundle(builder.getBundle()).execute();
+		assertNull(outcome);
+
+		assertEquals("http://example.com/fhir", capt.getAllValues().get(0).getURI().toASCIIString());
+
+	}
+
 	@Test
 	public void testUpdateById() throws Exception {
 		IParser p = ourCtx.newXmlParser();