Merge 71577ff8b1 into 20d3e6bb25

* Fix missing qualifier search for reference search parameter. Reuse tests and run them for both indexing enabled and disabled.

* Fix edge case where the search parameter has multiple paths. Add a test. Fix some of the compile warnings in a test class.

* Fix test setup.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6305-search-missing-qualifier-does-not-work-reference-parameters.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 6305
+title: "Previously, when having StorageSettings#getIndexMissingFields() == IndexEnabledEnum.DISABLED (default value) 
+and attempting to search with the missing qualifier against a resource type with multiple search parameters of type reference, 
+the returned results would be incorrect. This has been fixed."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java

@@ -800,14 +800,19 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
 		subquery.addCustomColumns(1);
 		subquery.addFromTable(getTable());
 
+		String resourceType = theParams.getResourceTablePredicateBuilder().getResourceType();
+		RuntimeSearchParam paramDefinition =
+				mySearchParamRegistry.getRuntimeSearchParam(resourceType, theParams.getParamName());
+		List<String> pathList = paramDefinition.getPathsSplitForResourceType(resourceType);
+
 		Condition subQueryCondition = ComboCondition.and(
 				BinaryCondition.equalTo(
 						getResourceIdColumn(),
 						theParams.getResourceTablePredicateBuilder().getResourceIdColumn()),
-				BinaryCondition.equalTo(
+				BinaryCondition.equalTo(getResourceTypeColumn(), generatePlaceholder(resourceType)),
-						getResourceTypeColumn(),
+				ComboCondition.or(pathList.stream()
-						generatePlaceholder(
+						.map(path -> BinaryCondition.equalTo(getColumnSourcePath(), generatePlaceholder(path)))
-								theParams.getResourceTablePredicateBuilder().getResourceType())));
+						.toArray(BinaryCondition[]::new)));
 
 		subquery.addCondition(subQueryCondition);
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchMissingTest.java

@@ -1,9 +1,10 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import ca.uhn.fhir.i18n.Msg;
-import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamCoords;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
+import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantityNormalized;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -12,7 +13,6 @@ import ca.uhn.fhir.rest.param.QuantityParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.DateType;
 import org.hl7.fhir.r4.model.DecimalType;
@@ -26,57 +26,25 @@ import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Task;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Nested;
 import org.junit.jupiter.api.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import java.util.List;
 import java.util.stream.Collectors;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
-public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
+public class FhirResourceDaoR4SearchMissingTest {
-	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4SearchMissingTest.class);
 
+	@Nested
+	class IndexMissingDisabledTests extends MissingTests {
 		@BeforeEach
-	public void beforeResetMissing() {
+		public void before() {
-		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.ENABLED);
+			myStorageSettings.setIndexMissingFields(StorageSettings.IndexEnabledEnum.DISABLED);
-	}
-
-	@AfterEach
-	public void afterResetSearch() {
-		myStorageSettings.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
-	}
-
-	@Test
-	public void testIndexMissingFieldsDisabledDontAllowInSearch_NonReference() {
-		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
-
-		SearchParameterMap params = new SearchParameterMap();
-		params.add(Patient.SP_ACTIVE, new StringParam().setMissing(true));
-		try {
-			myPatientDao.search(params);
-		} catch (MethodNotAllowedException e) {
-			assertEquals(Msg.code(985) + ":missing modifier is disabled on this server", e.getMessage());
-		}
-	}
-
-	@Test
-	public void testIndexMissingFieldsDisabledDontAllowInSearch_Reference() {
-		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
-
-		SearchParameterMap params = new SearchParameterMap();
-		params.add(Patient.SP_ORGANIZATION, new StringParam().setMissing(true));
-		try {
-			myPatientDao.search(params);
-		} catch (MethodNotAllowedException e) {
-			assertEquals(Msg.code(985) + ":missing modifier is disabled on this server", e.getMessage());
-		}
 		}
 
 		@Test
 		public void testIndexMissingFieldsDisabledDontCreateIndexes() {
-		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
 			Organization org = new Organization();
 			org.setActive(true);
 			myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
@@ -93,8 +61,6 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 
 		@Test
 		public void testIndexMissingFieldsDisabledDontCreateIndexesWithNormalizedQuantitySearchSupported() {
-
-		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
 			myStorageSettings.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED);
 			Organization org = new Organization();
 			org.setActive(true);
@@ -112,8 +78,6 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 
 		@Test
 		public void testIndexMissingFieldsDisabledDontCreateIndexesWithNormalizedQuantityStorageSupported() {
-
-		myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
 			myStorageSettings.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_STORAGE_SUPPORTED);
 			Organization org = new Organization();
 			org.setActive(true);
@@ -128,6 +92,15 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 			});
 
 		}
+	}
+
+	@Nested
+	class IndexMissingEnabledTests extends MissingTests {
+		@BeforeEach
+		public void before() {
+			myStorageSettings.setIndexMissingFields(StorageSettings.IndexEnabledEnum.ENABLED);
+		}
+
 
 		@SuppressWarnings("unused")
 		@Test
@@ -144,11 +117,10 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				task.setRequester(new Reference(oid1));
 				tid1 = myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
 			}
-		IIdType tid2;
 			{
 				Task task = new Task();
 				task.setOwner(new Reference(oid1));
-			tid2 = myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
+				myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
 			}
 
 			IIdType oid2;
@@ -170,27 +142,36 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 
 			map = new SearchParameterMap();
 			map.add(Organization.SP_NAME, new StringParam().setMissing(true));
-		ids = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
+			ids = toUnqualifiedVersionlessIds(myOrganizationDao.search(map, mySrd));
 			assertThat(ids).containsExactly(oid1);
 
 			ourLog.info("Starting Search 2");
 
 			map = new SearchParameterMap();
 			map.add(Task.SP_REQUESTER, new ReferenceParam("Organization", "name:missing", "true"));
-		ids = toUnqualifiedVersionlessIds(myTaskDao.search(map));
+			ids = toUnqualifiedVersionlessIds(myTaskDao.search(map, mySrd));
 			assertThat(ids).containsExactly(tid1); // NOT tid2
 
 			map = new SearchParameterMap();
 			map.add(Task.SP_REQUESTER, new ReferenceParam("Organization", "name:missing", "false"));
-		ids = toUnqualifiedVersionlessIds(myTaskDao.search(map));
+			ids = toUnqualifiedVersionlessIds(myTaskDao.search(map, mySrd));
 			assertThat(ids).containsExactly(tid3);
 
 			map = new SearchParameterMap();
 			map.add(Patient.SP_ORGANIZATION, new ReferenceParam("Organization", "name:missing", "true"));
-		ids = toUnqualifiedVersionlessIds(myPatientDao.search(map));
+			ids = toUnqualifiedVersionlessIds(myPatientDao.search(map, mySrd));
 			assertThat(ids).isEmpty();
 
 		}
+	}
+
+	static class MissingTests extends BaseJpaR4Test {
+		@AfterEach
+		public void after() {
+			myStorageSettings.setIndexMissingFields(new StorageSettings().getIndexMissingFields());
+			myStorageSettings.setNormalizedQuantitySearchLevel(new StorageSettings().getNormalizedQuantitySearchLevel());
+
+		}
 
 		@Test
 		public void testSearchWithMissingDate() {
@@ -217,7 +198,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				DateParam param = new DateParam();
 				param.setMissing(false);
 				params.add(Patient.SP_BIRTHDATE, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params, mySrd));
 				assertThat(patients).containsSubsequence(notMissing);
 				assertThat(patients).doesNotContainSubsequence(missing);
 			}
@@ -227,7 +208,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				DateParam param = new DateParam();
 				param.setMissing(true);
 				params.add(Patient.SP_BIRTHDATE, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params, mySrd));
 				assertThat(patients).containsSubsequence(missing);
 				assertThat(patients).doesNotContainSubsequence(notMissing);
 			}
@@ -238,9 +219,11 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 			String locId = myLocationDao.create(new Location(), mySrd).getId().toUnqualifiedVersionless().getValue();
 			String locId2 = myLocationDao.create(new Location().setPosition(new Location.LocationPositionComponent(new DecimalType(10), new DecimalType(10))), mySrd).getId().toUnqualifiedVersionless().getValue();
 
-		runInTransaction(() -> {
+			runInTransaction(() -> ourLog.info("Coords:\n * {}",
-			ourLog.info("Coords:\n * {}", myResourceIndexedSearchParamCoordsDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
+					myResourceIndexedSearchParamCoordsDao.findAll().stream()
-		});
+							.map(ResourceIndexedSearchParamCoords::toString).collect(Collectors.joining("\n * "))
+					)
+			);
 
 			{
 				SearchParameterMap params = new SearchParameterMap();
@@ -249,7 +232,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				param.setMissing(true);
 				params.add(Location.SP_NEAR, param);
 				myCaptureQueriesListener.clear();
-			List<String> patients = toUnqualifiedVersionlessIdValues(myLocationDao.search(params));
+				List<String> patients = toUnqualifiedVersionlessIdValues(myLocationDao.search(params, mySrd));
 				myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
 				assertThat(patients).containsSubsequence(locId);
 				assertThat(patients).doesNotContainSubsequence(locId2);
@@ -260,7 +243,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				TokenParam param = new TokenParam();
 				param.setMissing(false);
 				params.add(Location.SP_NEAR, param);
-			List<String> patients = toUnqualifiedVersionlessIdValues(myLocationDao.search(params));
+				List<String> patients = toUnqualifiedVersionlessIdValues(myLocationDao.search(params, mySrd));
 				assertThat(patients).containsSubsequence(locId2);
 				assertThat(patients).doesNotContainSubsequence(locId);
 			}
@@ -271,15 +254,15 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 			MedicationRequest mr1 = new MedicationRequest();
 			mr1.addCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
 			mr1.addDosageInstruction().getTiming().addEventElement().setValueAsString("2017-01-01");
-		IIdType id1 = myMedicationRequestDao.create(mr1).getId().toUnqualifiedVersionless();
+			myMedicationRequestDao.create(mr1, mySrd).getId().toUnqualifiedVersionless();
 
 			MedicationRequest mr2 = new MedicationRequest();
 			mr2.addCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
-		IIdType id2 = myMedicationRequestDao.create(mr2).getId().toUnqualifiedVersionless();
+			IIdType id2 = myMedicationRequestDao.create(mr2, mySrd).getId().toUnqualifiedVersionless();
 
 			SearchParameterMap map = new SearchParameterMap();
 			map.add(MedicationRequest.SP_DATE, new DateParam().setMissing(true));
-		IBundleProvider results = myMedicationRequestDao.search(map);
+			IBundleProvider results = myMedicationRequestDao.search(map, mySrd);
 			List<String> ids = toUnqualifiedVersionlessIdValues(results);
 
 			assertThat(ids).containsExactly(id2.getValue());
@@ -308,7 +291,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				QuantityParam param = new QuantityParam();
 				param.setMissing(false);
 				params.add(Observation.SP_VALUE_QUANTITY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params, mySrd));
 				assertThat(patients).doesNotContainSubsequence(missing);
 				assertThat(patients).containsSubsequence(notMissing);
 			}
@@ -318,7 +301,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				QuantityParam param = new QuantityParam();
 				param.setMissing(true);
 				params.add(Observation.SP_VALUE_QUANTITY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params, mySrd));
 				assertThat(patients).containsSubsequence(missing);
 				assertThat(patients).doesNotContainSubsequence(notMissing);
 			}
@@ -343,8 +326,16 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 			}
 
 			runInTransaction(() -> {
-			ourLog.info("Quantity Indexes:\n * {}", myResourceIndexedSearchParamQuantityDao.findAll().stream().filter(t -> t.getParamName().equals("value-quantity")).map(t -> t.toString()).collect(Collectors.joining("\n * ")));
+				ourLog.info("Quantity Indexes:\n * {}",
-			ourLog.info("Normalized Quantity Indexes:\n * {}", myResourceIndexedSearchParamQuantityNormalizedDao.findAll().stream().filter(t -> t.getParamName().equals("value-quantity")).map(t -> t.toString()).collect(Collectors.joining("\n * ")));
+						myResourceIndexedSearchParamQuantityDao.findAll().stream()
+								.filter(t -> t.getParamName().equals("value-quantity")).map(ResourceIndexedSearchParamQuantity::toString).collect(Collectors.joining("\n * ")
+								)
+				);
+				ourLog.info("Normalized Quantity Indexes:\n * {}",
+						myResourceIndexedSearchParamQuantityNormalizedDao.findAll().stream().
+								filter(t -> t.getParamName().equals("value-quantity")).map(ResourceIndexedSearchParamQuantityNormalized::toString).collect(Collectors.joining("\n * ")
+								)
+				);
 			});
 
 			// Quantity Param
@@ -354,7 +345,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				QuantityParam param = new QuantityParam();
 				param.setMissing(false);
 				params.add(Observation.SP_VALUE_QUANTITY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params, mySrd));
 				assertThat(patients).doesNotContainSubsequence(missing);
 				assertThat(patients).containsSubsequence(notMissing);
 			}
@@ -365,7 +356,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				param.setMissing(true);
 				params.add(Observation.SP_VALUE_QUANTITY, param);
 				myCaptureQueriesListener.clear();
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params, mySrd));
 				myCaptureQueriesListener.logSelectQueries();
 				assertThat(patients).containsSubsequence(missing);
 				assertThat(patients).doesNotContainSubsequence(notMissing);
@@ -397,7 +388,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				QuantityParam param = new QuantityParam();
 				param.setMissing(false);
 				params.add(Observation.SP_VALUE_QUANTITY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params, mySrd));
 				assertThat(patients).doesNotContainSubsequence(missing);
 				assertThat(patients).containsSubsequence(notMissing);
 			}
@@ -407,7 +398,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				QuantityParam param = new QuantityParam();
 				param.setMissing(true);
 				params.add(Observation.SP_VALUE_QUANTITY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params, mySrd));
 				assertThat(patients).containsSubsequence(missing);
 				assertThat(patients).doesNotContainSubsequence(notMissing);
 			}
@@ -440,7 +431,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				ReferenceParam param = new ReferenceParam();
 				param.setMissing(false);
 				params.add(Patient.SP_ORGANIZATION, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params, mySrd));
 				assertThat(patients).doesNotContainSubsequence(missing);
 				assertThat(patients).containsSubsequence(notMissing);
 			}
@@ -450,13 +441,36 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				ReferenceParam param = new ReferenceParam();
 				param.setMissing(true);
 				params.add(Patient.SP_ORGANIZATION, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params, mySrd));
 				assertThat(patients).containsSubsequence(missing);
 				assertThat(patients).doesNotContainSubsequence(notMissing);
 				assertThat(patients).doesNotContainSubsequence(orgId);
 			}
 		}
 
+
+		@Test
+		public void testSearchWithMissingReference_resourceTypeWithMultipleReferences() {
+			IIdType patientId = createPatient();
+			IIdType observationId = createObservation(withSubject(patientId));
+
+			SearchParameterMap params = new SearchParameterMap();
+			params.add(Observation.SP_PERFORMER, new ReferenceParam().setMissing(true));
+			IBundleProvider bundleProvider = myObservationDao.search(params, mySrd);
+			assertThat(bundleProvider.getAllResourceIds()).containsExactly(observationId.getIdPart());
+		}
+
+		@Test
+		public void testSearchWithMissingReference_searchParamMultiplePaths() {
+			IIdType encounterId = createEncounter();
+			createObservation(withEncounter(encounterId.getValue()));
+
+			SearchParameterMap params = new SearchParameterMap();
+			params.add(Observation.SP_ENCOUNTER, new ReferenceParam().setMissing(true));
+			IBundleProvider bundleProvider = myObservationDao.search(params, mySrd);
+			assertThat(bundleProvider.getAllResourceIds()).isEmpty();
+		}
+
 		@Test
 		public void testSearchWithMissingString() {
 			IIdType orgId = myOrganizationDao.create(new Organization(), mySrd).getId();
@@ -482,7 +496,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				StringParam param = new StringParam();
 				param.setMissing(false);
 				params.add(Patient.SP_FAMILY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params, mySrd));
 				assertThat(patients).doesNotContainSubsequence(missing);
 				assertThat(patients).containsSubsequence(notMissing);
 			}
@@ -492,7 +506,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				StringParam param = new StringParam();
 				param.setMissing(true);
 				params.add(Patient.SP_FAMILY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params, mySrd));
 				assertThat(patients).containsSubsequence(missing);
 				assertThat(patients).doesNotContainSubsequence(notMissing);
 			}
@@ -520,7 +534,7 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				TokenParam param = new TokenParam();
 				param.setMissing(false);
 				params.add(Observation.SP_CODE, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params, mySrd));
 				assertThat(patients).doesNotContainSubsequence(missing);
 				assertThat(patients).containsSubsequence(notMissing);
 			}
@@ -530,10 +544,11 @@ public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
 				TokenParam param = new TokenParam();
 				param.setMissing(true);
 				params.add(Observation.SP_CODE, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+				List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params, mySrd));
 				assertThat(patients).containsSubsequence(missing);
 				assertThat(patients).doesNotContainSubsequence(notMissing);
 			}
 		}
+	}
 
 }

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -217,7 +217,7 @@ import static org.mockito.Mockito.when;
 public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4Test.class);
 	private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
-	private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
+	private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
 	@Autowired
 	private ISearchDao mySearchEntityDao;
 
@@ -413,15 +413,15 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient pt1 = new Patient();
 		pt1.addName().setFamily("Elizabeth");
-		String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
+		String pt1id = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 		Patient pt2 = new Patient();
 		pt2.addName().setFamily("fghijk");
-		String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
+		String pt2id = myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 		Patient pt3 = new Patient();
 		pt3.addName().setFamily("zzzzz");
-		myPatientDao.create(pt3).getId().toUnqualifiedVersionless().getValue();
+		myPatientDao.create(pt3, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 
 		Bundle output = myClient
@@ -450,7 +450,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient pt1 = new Patient();
 		pt1.addName().setFamily("Smith%");
-		String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
+		String pt1id = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 		Bundle output = myClient
 			.search()
@@ -463,7 +463,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient pt2 = new Patient();
 		pt2.addName().setFamily("Sm%ith");
-		String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
+		String pt2id = myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless().getValue();
 
 		output = myClient
 			.search()
@@ -740,7 +740,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient p = new Patient();
 		p.addName().setFamily("FAM").addGiven("GIV");
-		IIdType id = myPatientDao.create(p).getId();
+		IIdType id = myPatientDao.create(p, mySrd).getId();
 
 		myClient.read().resource("Patient").withId(id.toUnqualifiedVersionless()).execute();
 
@@ -763,7 +763,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient p = new Patient();
 		p.addName().setFamily("FAM").addGiven("GIV");
-		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+		IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
 
 		myClient
 			.delete()
@@ -1025,57 +1025,58 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	public void testCreateAndReadBackResourceWithContainedReferenceToContainer() {
 		myFhirContext.setParserErrorHandler(new StrictErrorHandler());
 
-		String input = "{\n" +
+		String input = """
-			"  \"resourceType\": \"Organization\",\n" +
+{
-			"  \"id\": \"1\",\n" +
+  "resourceType": "Organization",
-			"  \"meta\": {\n" +
+  "id": "1",
-			"    \"tag\": [\n" +
+  "meta": {
-			"      {\n" +
+    "tag": [
-			"        \"system\": \"https://blah.org/deployment\",\n" +
+      {
-			"        \"code\": \"e69414dd-b5c2-462d-bcfd-9d04d6b16596\",\n" +
+        "system": "https://blah.org/deployment",
-			"        \"display\": \"DEPLOYMENT\"\n" +
+        "code": "e69414dd-b5c2-462d-bcfd-9d04d6b16596",
-			"      },\n" +
+        "display": "DEPLOYMENT"
-			"      {\n" +
+      },
-			"        \"system\": \"https://blah.org/region\",\n" +
+      {
-			"        \"code\": \"b47d7a5b-b159-4bed-a8f8-3258e6603adb\",\n" +
+        "system": "https://blah.org/region",
-			"        \"display\": \"REGION\"\n" +
+        "code": "b47d7a5b-b159-4bed-a8f8-3258e6603adb",
-			"      },\n" +
+        "display": "REGION"
-			"      {\n" +
+      },
-			"        \"system\": \"https://blah.org/provider\",\n" +
+      {
-			"        \"code\": \"28c30004-0333-40cf-9e7f-3f9e080930bd\",\n" +
+        "system": "https://blah.org/provider",
-			"        \"display\": \"PROVIDER\"\n" +
+        "code": "28c30004-0333-40cf-9e7f-3f9e080930bd",
-			"      }\n" +
+        "display": "PROVIDER"
-			"    ]\n" +
+      }
-			"  },\n" +
+    ]
-			"  \"contained\": [\n" +
+  },
-			"    {\n" +
+  "contained": [
-			"      \"resourceType\": \"Location\",\n" +
+    {
-			"      \"id\": \"2\",\n" +
+      "resourceType": "Location",
-			"      \"position\": {\n" +
+      "id": "2",
-			"        \"longitude\": 51.443238301454289,\n" +
+      "position": {
-			"        \"latitude\": 7.34196905697293\n" +
+        "longitude": 51.443238301454289,
-			"      },\n" +
+        "latitude": 7.34196905697293
-			"      \"managingOrganization\": {\n" +
+      },
-			"        \"reference\": \"#\"\n" +
+      "managingOrganization": {
-			"      }\n" +
+        "reference": "#"
-			"    }\n" +
+      }
-			"  ],\n" +
+    }
-			"  \"type\": [\n" +
+  ],
-			"    {\n" +
+  "type": [
-			"      \"coding\": [\n" +
+    {
-			"        {\n" +
+      "coding": [
-			"          \"system\": \"https://blah.org/fmc/OrganizationType\",\n" +
+        {
-			"          \"code\": \"CLINIC\",\n" +
+          "system": "https://blah.org/fmc/OrganizationType",
-			"          \"display\": \"Clinic\"\n" +
+          "code": "CLINIC",
-			"        }\n" +
+          "display": "Clinic"
-			"      ]\n" +
+        }
-			"    }\n" +
+      ]
-			"  ],\n" +
+    }
-			"  \"name\": \"testOrg\"\n" +
+  ],
-			"}";
+  "name": "testOrg"
+}""";
 
 		Organization org = myFhirContext.newJsonParser().parseResource(Organization.class, input);
-		IIdType id = myOrganizationDao.create(org).getId();
+		IIdType id = myOrganizationDao.create(org, mySrd).getId();
 		org = myOrganizationDao.read(id);
 
 		String output = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(org);
@@ -1095,9 +1096,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		}
 		List<IBaseResource> outcome = myClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
 
-		runInTransaction(() -> {
+		runInTransaction(() -> assertEquals(100, myResourceTableDao.count()));
-			assertEquals(100, myResourceTableDao.count());
-		});
 
 		Bundle found = myClient
 			.search()
@@ -1306,7 +1305,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	}
 
 	@Test
-	public void testCreateQuestionnaireResponseWithValidation() throws IOException {
+	public void testCreateQuestionnaireResponseWithValidation() {
 		CodeSystem cs = new CodeSystem();
 		cs.setUrl("http://cs");
 		cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
@@ -1906,8 +1905,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		 * Try it with a raw socket call. The Apache client won't let us use the unescaped "|" in the URL but we want to make sure that works too..
 		 */
 		Socket sock = new Socket();
+		try (sock) {
 			sock.setSoTimeout(3000);
-		try {
 			sock.connect(new InetSocketAddress("localhost", myPort));
 			sock.getOutputStream().write(("DELETE /fhir/context/Patient?identifier=http://ghh.org/patient|" + methodName + " HTTP/1.1\n").getBytes(StandardCharsets.UTF_8));
 			sock.getOutputStream().write("Host: localhost\n".getBytes(StandardCharsets.UTF_8));
@@ -1915,7 +1914,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			BufferedReader socketInput = new BufferedReader(new InputStreamReader(sock.getInputStream()));
 
-			// String response = "";
 			StringBuilder b = new StringBuilder();
 			char[] buf = new char[1000];
 			while (socketInput.read(buf) != -1) {
@@ -1925,9 +1923,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			ourLog.debug("Resp: {}", resp);
 		} catch (SocketTimeoutException e) {
-			e.printStackTrace();
+			ourLog.debug(e.getMessage(), e);
-		} finally {
-			sock.close();
 		}
 
 		Thread.sleep(1000);
@@ -2398,7 +2394,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertThat(idValues).as(idValues.toString()).hasSize(10);
 
 		idValues = searchAndReturnUnqualifiedIdValues(myServerBase + "/_history?_at=gt" + InstantDt.withCurrentTime().getYear());
-		assertThat(idValues).hasSize(0);
+		assertThat(idValues).isEmpty();
 	}
 
 
@@ -2427,7 +2423,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			myMemoryCacheService.invalidateCaches(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID);
 		}
 
-		Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).execute();
+		Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).execute();
 		assertEquals(1, history.getEntry().size());
 		BundleEntryComponent historyEntry0 = history.getEntry().get(0);
 		// validate entry.fullUrl
@@ -2476,7 +2472,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			myMemoryCacheService.invalidateCaches(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID);
 		}
 
-		Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).execute();
+		Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).execute();
 		assertEquals(1, history.getEntry().size());
 		BundleEntryComponent historyEntry0 = history.getEntry().get(0);
 		// validate entry.fullUrl
@@ -2508,7 +2504,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		ourLog.info("Res ID: {}", id);
 
-		Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).prettyPrint().summaryMode(SummaryEnum.DATA).execute();
+		Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).prettyPrint().summaryMode(SummaryEnum.DATA).execute();
 		assertThat(history.getEntry()).hasSize(3);
 		assertEquals(id.withVersion("3").getValue(), history.getEntry().get(0).getResource().getId());
 		assertThat(((Patient) history.getEntry().get(0).getResource()).getName()).hasSize(1);
@@ -2746,7 +2742,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		int total = 20;
 		Organization org = new Organization();
 		org.setName("ORG");
-		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+		IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
 
 		Coding tagCode = new Coding();
 		tagCode.setCode("test");
@@ -2757,7 +2753,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 				.addTag(tagCode);
 			t.setStatus(Task.TaskStatus.REQUESTED);
 			t.getOwner().setReference(orgId.getValue());
-			myTaskDao.create(t);
+			myTaskDao.create(t, mySrd);
 		}
 		HashSet<String> ids = new HashSet<>();
 
@@ -2835,12 +2831,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 				if (orgCount > 0) {
 					Organization org = new Organization();
 					org.setName("ORG");
-					IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+					IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
 
 					orgCount--;
 					t.getOwner().setReference(orgId.getValue());
 				}
-				myTaskDao.create(t);
+				myTaskDao.create(t, mySrd);
 			}
 		}
 
@@ -2909,12 +2905,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 				if (orgCount > 0) {
 					Organization org = new Organization();
 					org.setName("ORG");
-					IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+					IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
 
 					orgCount--;
 					t.getOwner().setReference(orgId.getValue());
 				}
-				myTaskDao.create(t);
+				myTaskDao.create(t, mySrd);
 			}
 		}
 
@@ -2961,13 +2957,13 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	public void testIncludeCountDoesntIncludeIncludes() {
 		Organization org = new Organization();
 		org.setName("ORG");
-		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+		IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
 
 		for (int i = 0; i < 10; i++) {
 			Patient pt = new Patient();
 			pt.getManagingOrganization().setReference(orgId.getValue());
 			pt.addName().setFamily("FAM" + i);
-			myPatientDao.create(pt);
+			myPatientDao.create(pt, mySrd);
 		}
 
 		Bundle bundle = myClient
@@ -3168,7 +3164,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
 		assertEquals("2", newPt.getIdElement().getVersionIdPart());
-		assertEquals(false, newPt.getActive());
+		assertFalse(newPt.getActive());
 	}
 
 	@Test
@@ -3196,7 +3192,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
 		assertEquals("1", newPt.getIdElement().getVersionIdPart());
-		assertEquals(true, newPt.getActive());
+		assertTrue(newPt.getActive());
 	}
 
 	@Test
@@ -3226,7 +3222,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
 		assertEquals("2", newPt.getIdElement().getVersionIdPart());
-		assertEquals(false, newPt.getActive());
+		assertFalse(newPt.getActive());
 	}
 
 	@Test
@@ -3255,7 +3251,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
 		assertEquals("2", newPt.getIdElement().getVersionIdPart());
-		assertEquals(false, newPt.getActive());
+		assertFalse(newPt.getActive());
 	}
 
 	@Test
@@ -3323,12 +3319,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		{
 			Bundle returned = myClient.search().forResource(Patient.class).encodedXml().returnBundle(Bundle.class).execute();
-			assertThat(returned.getEntry().size()).isGreaterThan(1);
+			assertThat(returned.getEntry()).hasSizeGreaterThan(1);
 			assertEquals(BundleType.SEARCHSET, returned.getType());
 		}
 		{
 			Bundle returned = myClient.search().forResource(Patient.class).encodedJson().returnBundle(Bundle.class).execute();
-			assertThat(returned.getEntry().size()).isGreaterThan(1);
+			assertThat(returned.getEntry()).hasSizeGreaterThan(1);
 		}
 	}
 
@@ -3350,7 +3346,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			}
 		});
 
-		Bundle bundle = myClient.history().onServer().andReturnBundle(Bundle.class).execute();
+		Bundle bundle = myClient.history().onServer().returnBundle(Bundle.class).execute();
 		assertEquals(1, bundle.getTotal());
 		assertThat(bundle.getEntry()).hasSize(1);
 		assertEquals(id2.getIdPart(), bundle.getEntry().get(0).getResource().getIdElement().getIdPart());
@@ -3507,15 +3503,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertThat(text).doesNotContain("\"B\"");
 			assertThat(text).doesNotContain("\"B1\"");
 		}
-
-
-//		HttpGet read = new HttpGet(ourServerBase + "/Observation?patient=P5000000302&_sort:desc=code&code:in=http://fkcfhir.org/fhir/vs/ccdacapddialysisorder");
-//		try (CloseableHttpResponse response = ourHttpClient.execute(read)) {
-//			String text = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-//			ourLog.info(text);
-//			assertEquals(Constants.STATUS_HTTP_200_OK, response.getStatusLine().getStatusCode());
-//			assertThat(text).doesNotContain("\"text\",\"type\"");
-//		}
 	}
 
 	@Test
@@ -3873,9 +3860,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		p.addName().setFamily(methodName + "1");
 		IIdType pid1 = myClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
 
-		Thread.sleep(10);
 		long time1 = System.currentTimeMillis();
-		Thread.sleep(10);
 
 		Patient p2 = new Patient();
 		p2.addName().setFamily(methodName + "2");
@@ -4064,9 +4049,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	public void testSearchLastUpdatedParamRp() throws InterruptedException {
 		String methodName = "testSearchLastUpdatedParamRp";
 
-		int sleep = 100;
-		Thread.sleep(sleep);
-
 		DateTimeType beforeAny = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
 		IIdType id1a;
 		{
@@ -4083,9 +4065,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			id1b = myClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
 		}
 
-		Thread.sleep(1100);
 		DateTimeType beforeR2 = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
-		Thread.sleep(1100);
 
 		IIdType id2;
 		{
@@ -4249,13 +4229,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
 		matches = bundle.getEntry().size();
 
-		assertThat(matches).isGreaterThan(0);
+		assertThat(matches).isPositive();
 	}
 
 	@Test
 	public void testSearchReturnsSearchDate() throws Exception {
 		Date before = new Date();
-		Thread.sleep(1);
 
 		//@formatter:off
 		Bundle found = myClient
@@ -4266,7 +4245,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			.execute();
 		//@formatter:on
 
-		Thread.sleep(1);
 		Date after = new Date();
 
 		InstantType updated = found.getMeta().getLastUpdatedElement();
@@ -4300,7 +4278,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -4313,7 +4291,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -4326,7 +4304,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -4339,24 +4317,24 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		// > 1m
 		String uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt1|http://unitsofmeasure.org|m");
-		ourLog.info("uri = " + uri);
+		ourLog.info("uri = {}", uri);
 		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
 		assertThat(ids).hasSize(3);
 
 		//>= 100cm
 		uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt100|http://unitsofmeasure.org|cm");
-		ourLog.info("uri = " + uri);
+		ourLog.info("uri = {}", uri);
 		ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
 		assertThat(ids).hasSize(3);
 
 		//>= 10dm
 		uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt10|http://unitsofmeasure.org|dm");
-		ourLog.info("uri = " + uri);
+		ourLog.info("uri = {}", uri);
 		ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
 		assertThat(ids).hasSize(3);
 	}
@@ -4381,7 +4359,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -4392,7 +4370,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -4403,7 +4381,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -4414,7 +4392,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		String uri;
@@ -4451,7 +4429,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -4462,7 +4440,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -4474,7 +4452,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		myCaptureQueriesListener.clear();
@@ -4490,8 +4468,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		//-- check use normalized quantity table to search
 		String searchSql = myCaptureQueriesListener.getSelectQueries().get(0).getSql(true, true);
-		assertThat(searchSql).doesNotContain("HFJ_SPIDX_QUANTITY t0");
+		assertThat(searchSql).doesNotContain("HFJ_SPIDX_QUANTITY t0").contains("HFJ_SPIDX_QUANTITY_NRML");
-		assertThat(searchSql).contains("HFJ_SPIDX_QUANTITY_NRML");
 	}
 
 	@Test
@@ -5044,7 +5021,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -5056,7 +5033,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			oid2 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -5068,7 +5045,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -5080,7 +5057,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			oid4 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		String uri = myServerBase + "/Observation?_sort=code-value-quantity";
@@ -5092,7 +5069,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			found = myFhirContext.newXmlParser().parseResource(Bundle.class, output);
 		}
 
-		ourLog.debug("Bundle: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
+		ourLog.debug("Bundle: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
 
 		List<IIdType> list = toUnqualifiedVersionlessIds(found);
 		assertThat(found.getEntry()).hasSize(4);
@@ -5129,7 +5106,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -5145,7 +5122,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			oid2 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -5161,7 +5138,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -5176,7 +5153,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			comp.setValue(new Quantity().setValue(250));
 			oid4 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		String uri = myServerBase + "/Observation?_sort=combo-code-value-quantity";
@@ -5188,7 +5165,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			found = myFhirContext.newXmlParser().parseResource(Bundle.class, output);
 		}
 
-		ourLog.debug("Bundle: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
+		ourLog.debug("Bundle: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
 
 		List<IIdType> list = toUnqualifiedVersionlessIds(found);
 		assertThat(found.getEntry()).hasSize(4);
@@ -5264,9 +5241,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		List<IIdType> list = toUnqualifiedVersionlessIds(found);
 		ourLog.info(methodName + " found: " + list.toString() + " - Wanted " + orgMissing + " but not " + orgNotMissing);
-		assertThat(list).doesNotContain(orgNotMissing);
+		assertThat(list).doesNotContain(orgNotMissing).doesNotContain(deletedIdMissingTrue).contains(orgMissing);
-		assertThat(list).doesNotContain(deletedIdMissingTrue);
-		assertThat(list).contains(orgMissing);
 	}
 
 	@Test
@@ -5927,7 +5902,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		}
 
 		Date before = new Date();
-		Thread.sleep(100);
 
 		pt = new Patient();
 		pt.setId(id.getIdPart());
@@ -6450,7 +6424,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
 			obs.setValue(new Quantity().setValueElement(new DecimalType(125.12)).setUnit("CM").setSystem(UcumServiceUtil.UCUM_CODESYSTEM_URL).setCode("cm"));
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 
 			IIdType opid1 = myObservationDao.create(obs, mySrd).getId();
 
@@ -6463,7 +6437,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
 			obs.setValue(new Quantity().setValueElement(new DecimalType(24.12)).setUnit("CM").setSystem(UcumServiceUtil.UCUM_CODESYSTEM_URL).setCode("cm"));
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 
 			myObservationDao.update(obs, mySrd);
 		}
@@ -6479,7 +6453,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -6492,7 +6466,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		{
@@ -6505,25 +6479,25 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 			myObservationDao.create(obs, mySrd);
 
-			ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
+			ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
 		}
 
 		// > 1m
 		String uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt1|http://unitsofmeasure.org|m");
-		ourLog.info("uri = " + uri);
+		ourLog.info("uri = {}", uri);
 		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
 		assertThat(ids).hasSize(2);
 
 
 		//>= 100cm
 		uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt100|http://unitsofmeasure.org|cm");
-		ourLog.info("uri = " + uri);
+		ourLog.info("uri = {}", uri);
 		ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
 		assertThat(ids).hasSize(2);
 
 		//>= 10dm
 		uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt10|http://unitsofmeasure.org|dm");
-		ourLog.info("uri = " + uri);
+		ourLog.info("uri = {}", uri);
 		ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
 		assertThat(ids).hasSize(2);
 	}
@@ -6540,7 +6514,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			patient.setBirthDateElement(new DateType("2073"));
 			pid0 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
 
-			ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
+			ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
 
 			ourLog.info("pid0 " + pid0);
 		}
@@ -6553,7 +6527,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
 			Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
-			ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
+			ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
 		}
 
 		uri = myServerBase + "/Patient?_total=accurate&birthdate=gt2072-01-01";
@@ -6564,7 +6538,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
 			Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
-			ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
+			ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
 		}
 
 	}
@@ -6995,9 +6969,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 				&& theInput.IsEnforceRefOnType
 				&& theInput.IsEnforceRefOnWrite).isFalse();
 		} catch (InvalidRequestException ex) {
-			assertThat(ex.getMessage().contains(
+			assertThat(ex.getMessage()).as(ex.getMessage()).contains("Invalid resource reference");
-				"Invalid resource reference"
-			)).as(ex.getMessage()).isTrue();
 		} finally {
 			myStorageSettings.setEnforceReferentialIntegrityOnWrite(isEnforceRefOnWrite);
 			myStorageSettings.setEnforceReferenceTargetTypes(isEnforceRefTargetTypes);
@@ -7331,9 +7303,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 						patient.setBirthDate(cal.getTime());
 					}
 					return patient;
-				}, (isMissing) -> {
+				}, (isMissing) -> doSearch(Patient.class, Patient.BIRTHDATE.isMissing(isMissing)));
-					return doSearch(Patient.class, Patient.BIRTHDATE.isMissing(isMissing));
-				});
 		}
 
 		@ParameterizedTest
@@ -7346,9 +7316,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 						patient.setGender(AdministrativeGender.FEMALE);
 					}
 					return patient;
-				}, isMissing -> {
+				}, isMissing -> doSearch(Patient.class, Patient.GENDER.isMissing(isMissing)));
-					return doSearch(Patient.class, Patient.GENDER.isMissing(isMissing));
-				});
 		}
 
 		@ParameterizedTest
@@ -7364,9 +7332,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 						patient.setGeneralPractitioner(Collections.singletonList(new Reference(practitionerId)));
 					}
 					return patient;
-				}, isMissing -> {
+				}, isMissing -> doSearch(Patient.class, Patient.GENERAL_PRACTITIONER.isMissing(isMissing)));
-					return doSearch(Patient.class, Patient.GENERAL_PRACTITIONER.isMissing(isMissing));
-				});
 		}
 
 		@ParameterizedTest
@@ -7409,9 +7375,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 						sp.setUrl("http://example.com");
 					}
 					return sp;
-				}, isMissing -> {
+				}, isMissing -> doSearch(SearchParameter.class, SearchParameter.URL.isMissing(isMissing)));
-					return doSearch(SearchParameter.class, SearchParameter.URL.isMissing(isMissing));
-				});
 		}
 
 		@ParameterizedTest
@@ -7424,9 +7388,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 						obs.setValue(new Quantity(3));
 					}
 					return obs;
-				}, isMissing -> {
+				}, isMissing -> doSearch(Observation.class, Observation.VALUE_QUANTITY.isMissing(isMissing)));
-					return doSearch(Observation.class, Observation.VALUE_QUANTITY.isMissing(isMissing));
-				});
 		}
 
 		@ParameterizedTest
@@ -7457,7 +7419,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			Y doTask(X theInput);
 		}
 
-		private static class MissingSearchTestParameters {
+		public static class MissingSearchTestParameters {
 			/**
 			 * The setting for IndexMissingFields
 			 */

pom.xml

@@ -2143,7 +2143,7 @@
 			<dependency>
 				<groupId>org.webjars.npm</groupId>
 				<artifactId>bootstrap</artifactId>
-				<version>4.5.2</version>
+				<version>5.3.3</version>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars</groupId>