Merge remote-tracking branch 'origin/master' into issue-2634-increase-src-path-length

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2632-measure-evaluation-npe.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 2632
+title: "Certain calls to the $evaluate-measure operation could result in a NullPointerException.  This is now corrected."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCompositionDstu3.java

@@ -81,7 +81,7 @@ public class BaseJpaResourceProviderCompositionDstu3 extends JpaResourceProvider
 		startRequest(theServletRequest);
 		try {
 			IBundleProvider bundleProvider = ((IFhirResourceDaoComposition<Composition>) getDao()).getDocumentForComposition(theServletRequest, theId, theCount, theOffset, theLastUpdated, theSortSpec, theRequestDetails);
-			List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
+			List<IBaseResource> resourceList = bundleProvider.getAllResources();
 
 			boolean foundCompositionResource = false;
 			Bundle bundle = new Bundle().setType(Bundle.BundleType.DOCUMENT);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCompositionR4.java

@@ -78,7 +78,7 @@ public class BaseJpaResourceProviderCompositionR4 extends JpaResourceProviderR4<
 		startRequest(theServletRequest);
 		try {
 			IBundleProvider bundleProvider = ((IFhirResourceDaoComposition<Composition>) getDao()).getDocumentForComposition(theServletRequest, theId, theCount, theOffset, theLastUpdated, theSortSpec, theRequestDetails);
-			List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
+			List<IBaseResource> resourceList = bundleProvider.getAllResources();
 
 			boolean foundCompositionResource = false;
 			Bundle bundle = new Bundle().setType(Bundle.BundleType.DOCUMENT);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderCompositionR5.java

@@ -78,7 +78,7 @@ public class BaseJpaResourceProviderCompositionR5 extends JpaResourceProviderR5<
 		startRequest(theServletRequest);
 		try {
 			IBundleProvider bundleProvider = ((IFhirResourceDaoComposition<Composition>) getDao()).getDocumentForComposition(theServletRequest, theId, theCount, theOffset, theLastUpdated, theSortSpec, theRequestDetails);
-			List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
+			List<IBaseResource> resourceList = bundleProvider.getAllResources();
 
 			boolean foundCompositionResource = false;
 			Bundle bundle = new Bundle().setType(Bundle.BundleType.DOCUMENT);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermConceptMappingSvcImpl.java

@@ -202,7 +202,6 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
 			termConceptMap = myConceptMapDao.save(termConceptMap);
 			int codesSaved = 0;
 
-			if (theConceptMap.hasGroup()) {
 			TermConceptMapGroup termConceptMapGroup;
 			for (ConceptMap.ConceptMapGroupComponent group : theConceptMap.getGroup()) {
 
@@ -228,7 +227,7 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
 				termConceptMapGroup.setSourceVersion(group.getSourceVersion());
 				termConceptMapGroup.setTarget(groupTarget);
 				termConceptMapGroup.setTargetVersion(group.getTargetVersion());
-					myConceptMapGroupDao.save(termConceptMapGroup);
+				termConceptMapGroup = myConceptMapGroupDao.save(termConceptMapGroup);
 
 				if (group.hasElement()) {
 					TermConceptMapGroupElement termConceptMapGroupElement;
@@ -240,7 +239,7 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
 						termConceptMapGroupElement.setConceptMapGroup(termConceptMapGroup);
 						termConceptMapGroupElement.setCode(element.getCode());
 						termConceptMapGroupElement.setDisplay(element.getDisplay());
-							myConceptMapGroupElementDao.save(termConceptMapGroupElement);
+						termConceptMapGroupElement = myConceptMapGroupElementDao.save(termConceptMapGroupElement);
 
 						if (element.hasTarget()) {
 							TermConceptMapGroupElementTarget termConceptMapGroupElementTarget;
@@ -264,7 +263,7 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
 					}
 				}
 			}
-			}
+
 		} else {
 			TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapByUrl.get();
 
@@ -558,9 +557,9 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
 
 	private boolean alreadyContainsMapping(List<TranslateConceptResult> elements, TranslateConceptResult translationMatch) {
 		for (TranslateConceptResult nextExistingElement : elements) {
-			if (nextExistingElement.getSystem().equals(translationMatch.getSystem())) {
+			if (StringUtils.equals(nextExistingElement.getSystem(), translationMatch.getSystem())) {
-				if (nextExistingElement.getSystemVersion().equals(translationMatch.getSystemVersion())) {
+				if (StringUtils.equals(nextExistingElement.getSystemVersion(), translationMatch.getSystemVersion())) {
-					if (nextExistingElement.getCode().equals(translationMatch.getCode())) {
+					if (StringUtils.equals(nextExistingElement.getCode(), translationMatch.getCode())) {
 						return true;
 					}
 				}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java

@@ -4,6 +4,9 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.TranslateConceptResult;
 import ca.uhn.fhir.context.support.TranslateConceptResults;
 import ca.uhn.fhir.jpa.api.model.TranslationRequest;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupDao;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupElementDao;
+import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupElementTargetDao;
 import ca.uhn.fhir.jpa.entity.TermConceptMap;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CanonicalType;
@@ -16,6 +19,7 @@ import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.transaction.TransactionStatus;
@@ -38,7 +42,12 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4ConceptMapTest.class);
-
+	@Autowired
+	protected ITermConceptMapGroupDao myConceptMapGroupDao;
+	@Autowired
+	protected ITermConceptMapGroupElementDao myConceptMapGroupElementDao;
+	@Autowired
+	protected ITermConceptMapGroupElementTargetDao myConceptMapGroupElementTargetDao;
 	private IIdType myConceptMapId;
 
 	@BeforeEach
@@ -597,6 +606,113 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
 		});
 	}
 
+	/**
+	 * Make sure we can handle mapping where the system has no explicit version
+	 * specified in the ConceptMap
+	 */
+	@Test
+	public void testTranslateWithReverse_NonVersionedSystem() {
+
+		ConceptMap conceptMap1 = new ConceptMap();
+		conceptMap1.setUrl(CM_URL);
+
+		conceptMap1.setSource(new UriType(VS_URL));
+		conceptMap1.setTarget(new UriType(VS_URL_2));
+
+		ConceptMap.ConceptMapGroupComponent group = conceptMap1.addGroup();
+		group.setSource(CS_URL);
+		group.setTarget(CS_URL_2);
+
+		ConceptMap.SourceElementComponent element = group.addElement();
+		element.setCode("12345");
+		element.setDisplay("Source Code 12345");
+
+		ConceptMap.TargetElementComponent target = element.addTarget();
+		target.setCode("34567");
+		target.setDisplay("Target Code 34567");
+		target.setEquivalence(ConceptMapEquivalence.EQUAL);
+
+		element = group.addElement();
+		element.setCode("23456");
+		element.setDisplay("Source Code 23456");
+
+		target = element.addTarget();
+		target.setCode("45678");
+		target.setDisplay("Target Code 45678");
+		target.setEquivalence(ConceptMapEquivalence.WIDER);
+
+		group = conceptMap1.addGroup();
+		group.setSource(CS_URL);
+		group.setTarget(CS_URL_3);
+
+		element = group.addElement();
+		element.setCode("12345");
+		element.setDisplay("Source Code 12345");
+
+		target = element.addTarget();
+		target.setCode("56789");
+		target.setDisplay("Target Code 56789");
+		target.setEquivalence(ConceptMapEquivalence.EQUAL);
+
+		target = element.addTarget();
+		target.setCode("67890");
+		target.setDisplay("Target Code 67890");
+		target.setEquivalence(ConceptMapEquivalence.WIDER);
+
+		group = conceptMap1.addGroup();
+		group.setSource(CS_URL_4);
+		group.setTarget(CS_URL_2);
+
+		element = group.addElement();
+		element.setCode("12345");
+		element.setDisplay("Source Code 12345");
+
+		target = element.addTarget();
+		target.setCode("34567");
+		target.setDisplay("Target Code 34567");
+		target.setEquivalence(ConceptMapEquivalence.NARROWER);
+
+		conceptMap1.setId(myConceptMapId);
+		myConceptMapDao.update(conceptMap1, mySrd).getId().toUnqualifiedVersionless();
+
+
+		runInTransaction(() -> {
+			/*
+			 * Provided:
+			 *   source code
+			 *   reverse = true
+			 */
+			TranslationRequest translationRequest = new TranslationRequest();
+			translationRequest.getCodeableConcept().addCoding()
+				.setCode("34567");
+			translationRequest.setReverse(true);
+
+			TranslateConceptResults translationResult = myConceptMapDao.translate(translationRequest, null);
+
+			assertTrue(translationResult.getResult());
+			assertEquals("Matches found", translationResult.getMessage());
+
+			assertEquals(2, translationResult.getResults().size());
+
+			TranslateConceptResult translationMatch = translationResult.getResults().get(0);
+			assertEquals(ConceptMapEquivalence.EQUAL.toCode(), translationMatch.getEquivalence());
+			assertEquals("12345", translationMatch.getCode());
+			assertEquals("Source Code 12345", translationMatch.getDisplay());
+			assertEquals(CS_URL, translationMatch.getSystem());
+			assertEquals(null, translationMatch.getSystemVersion());
+			assertEquals(CM_URL, translationMatch.getConceptMapUrl());
+
+			translationMatch = translationResult.getResults().get(1);
+			assertEquals(ConceptMapEquivalence.NARROWER.toCode(), translationMatch.getEquivalence());
+			assertEquals("12345", translationMatch.getCode());
+			assertEquals("Source Code 12345", translationMatch.getDisplay());
+			assertEquals(CS_URL_4, translationMatch.getSystem());
+			assertEquals(null, translationMatch.getSystemVersion());
+			assertEquals(CM_URL, translationMatch.getConceptMapUrl());
+		});
+
+	}
+
 	@Test
 	public void testTranslateWithReverseHavingEquivalence() {
 		ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/PartitioningInterceptorR4Test.java

@@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.interceptor.ex.PartitionInterceptorReadPartitionsBasedOnS
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -92,7 +93,7 @@ public class PartitioningInterceptorR4Test extends BaseJpaR4SystemTest {
 
 		StructureDefinition sd = new StructureDefinition();
 		sd.setUrl("http://foo");
-		myStructureDefinitionDao.create(sd);
+		myStructureDefinitionDao.create(sd, new ServletRequestDetails());
 
 		runInTransaction(()->{
 			List<ResourceTable> resources = myResourceTableDao.findAll();
@@ -108,7 +109,7 @@ public class PartitioningInterceptorR4Test extends BaseJpaR4SystemTest {
 
 		StructureDefinition sd = new StructureDefinition();
 		sd.setUrl("http://foo");
-		myStructureDefinitionDao.create(sd);
+		myStructureDefinitionDao.create(sd, new ServletRequestDetails());
 
 		runInTransaction(()->{
 			List<ResourceTable> resources = myResourceTableDao.findAll();
@@ -124,7 +125,7 @@ public class PartitioningInterceptorR4Test extends BaseJpaR4SystemTest {
 		StructureDefinition sd = new StructureDefinition();
 		sd.setUrl("http://foo");
 		try {
-			myStructureDefinitionDao.create(sd);
+			myStructureDefinitionDao.create(sd, new ServletRequestDetails());
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertEquals("Resource type StructureDefinition can not be partitioned", e.getMessage());

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/common/retrieve/JpaFhirRetrieveProvider.java

@@ -95,10 +95,7 @@ public class JpaFhirRetrieveProvider extends SearchParamFhirRetrieveProvider {
         if (bundleProvider.size() == null) {
             return resolveResourceList(bundleProvider.getResources(0, 10000));
         }
-        if (bundleProvider.size() == 0) {
+        List<IBaseResource> resourceList = bundleProvider.getAllResources();
-            return new ArrayList<>();
-        }
-        List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
         return resolveResourceList(resourceList);
     }
 

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/config/CqlDstu3Config.java

@@ -33,10 +33,8 @@ import ca.uhn.fhir.cql.dstu3.provider.MeasureOperationsProvider;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
-import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
-
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
 import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.model.Model;
 import org.cqframework.cql.elm.execution.Library;
@@ -99,7 +97,7 @@ public class CqlDstu3Config extends BaseCqlConfig {
 	@Bean
 	public ElmCacheResourceChangeListener elmCacheResourceChangeListener(IResourceChangeListenerRegistry resourceChangeListenerRegistry, IFhirResourceDao<org.hl7.fhir.dstu3.model.Library> libraryDao,  Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache) {
 		ElmCacheResourceChangeListener listener = new ElmCacheResourceChangeListener(libraryDao, globalLibraryCache);
-		resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", new SearchParameterMap(), listener, 1000);
+		resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", SearchParameterMap.newSynchronous(), listener, 1000);
 		return listener;
 	}
 }

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/config/CqlR4Config.java

@@ -34,10 +34,8 @@ import ca.uhn.fhir.cql.r4.provider.MeasureOperationsProvider;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
-import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
-
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-
+import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
 import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.model.Model;
 import org.cqframework.cql.elm.execution.Library;
@@ -110,7 +108,7 @@ public class CqlR4Config extends BaseCqlConfig {
 	@Bean
 	public ElmCacheResourceChangeListener elmCacheResourceChangeListener(IResourceChangeListenerRegistry resourceChangeListenerRegistry, IFhirResourceDao<org.hl7.fhir.r4.model.Library> libraryDao,  Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache) {
 		ElmCacheResourceChangeListener listener = new ElmCacheResourceChangeListener(libraryDao, globalLibraryCache);
-		resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", new SearchParameterMap(), listener, 1000);
+		resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", SearchParameterMap.newSynchronous(), listener, 1000);
 		return listener;
 	}
 }

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/evaluation/MeasureEvaluation.java

@@ -33,7 +33,6 @@ import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.Extension;
 import org.hl7.fhir.dstu3.model.IdType;
-import org.hl7.fhir.dstu3.model.IntegerType;
 import org.hl7.fhir.dstu3.model.ListResource;
 import org.hl7.fhir.dstu3.model.Measure;
 import org.hl7.fhir.dstu3.model.MeasureReport;
@@ -67,8 +66,8 @@ public class MeasureEvaluation {
 
 	private static final Logger logger = LoggerFactory.getLogger(MeasureEvaluation.class);
 
-    private Interval measurementPeriod;
+	private final Interval measurementPeriod;
-    private DaoRegistry registry;
+	private final DaoRegistry registry;
 
 	public MeasureEvaluation(DaoRegistry registry, Interval measurementPeriod) {
 		this.registry = registry;
@@ -107,21 +106,21 @@ public class MeasureEvaluation {
     }
 
     private List<Patient> getPractitionerPatients(String practitionerRef) {
-        SearchParameterMap map = new SearchParameterMap();
+		 SearchParameterMap map = SearchParameterMap.newSynchronous();
 		 map.add("general-practitioner", new ReferenceParam(
 			 practitionerRef.startsWith("Practitioner/") ? practitionerRef : "Practitioner/" + practitionerRef));
 
 		 List<Patient> patients = new ArrayList<>();
 		 IBundleProvider patientProvider = registry.getResourceDao("Patient").search(map);
-        List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
+		 List<IBaseResource> patientList = patientProvider.getAllResources();
 		 patientList.forEach(x -> patients.add((Patient) x));
 		 return patients;
 	 }
 
     private List<Patient> getAllPatients() {
 		 List<Patient> patients = new ArrayList<>();
-        IBundleProvider patientProvider = registry.getResourceDao("Patient").search(new SearchParameterMap());
+		 IBundleProvider patientProvider = registry.getResourceDao("Patient").search(SearchParameterMap.newSynchronous());
-        List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
+		 List<IBaseResource> patientList = patientProvider.getAllResources();
 		 patientList.forEach(x -> patients.add((Patient) x));
 		 return patients;
 	 }
@@ -567,7 +566,7 @@ public class MeasureEvaluation {
             }
 
             if (!list.isEmpty()) {
-                list.setId("List/" + UUID.randomUUID().toString());
+					list.setId("List/" + UUID.randomUUID());
 					list.setTitle(key);
                 resources.put(list.getId(), list);
                 list.getEntry().forEach(listResource -> evaluatedResourcesList.add(listResource.getItem().getReference()));
@@ -716,9 +715,7 @@ public class MeasureEvaluation {
 					Resource r = (Resource) o;
 					String id = (r.getIdElement().getResourceType() != null ? (r.getIdElement().getResourceType() + "/")
 						: "") + r.getIdElement().getIdPart();
-                if (!codeHashSet.contains(id)) {
 					codeHashSet.add(id);
-                }
 
 					if (!resources.containsKey(id)) {
 						resources.put(id, r);

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/provider/JpaTerminologyProvider.java

@@ -96,8 +96,8 @@ public class JpaTerminologyProvider implements TerminologyProvider {
 			}
 
 			IBundleProvider bundleProvider = myValueSetDao
-				.search(new SearchParameterMap().add(ValueSet.SP_URL, new UriParam(valueSet.getId())));
+				.search(SearchParameterMap.newSynchronous().add(ValueSet.SP_URL, new UriParam(valueSet.getId())));
-			List<IBaseResource> valueSets = bundleProvider.getResources(0, bundleProvider.size());
+			List<IBaseResource> valueSets = bundleProvider.getAllResources();
 			if (valueSets.isEmpty()) {
 				throw new IllegalArgumentException(String.format("Could not resolve value set %s.", valueSet.getId()));
 			} else if (valueSets.size() == 1) {

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/provider/LibraryResolutionProviderImpl.java

@@ -67,7 +67,7 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
 			version = parts[1];
 		}
 
-		SearchParameterMap map = new SearchParameterMap();
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
 		map.add("url", new UriParam(resourceUrl));
 		if (version != null) {
 			map.add("version", new TokenParam(version));
@@ -75,10 +75,10 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
 
 		ca.uhn.fhir.rest.api.server.IBundleProvider bundleProvider = myLibraryDao.search(map);
 
-		if (bundleProvider.size() == 0) {
+		if (bundleProvider.size() == null || bundleProvider.size() == 0) {
 			return null;
 		}
-		List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
+		List<IBaseResource> resourceList = bundleProvider.getAllResources();
 		return LibraryResolutionProvider.selectFromList(resolveLibraries(resourceList), version, x -> x.getVersion());
 	}
 
@@ -97,14 +97,14 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
 
 	private Iterable<org.hl7.fhir.dstu3.model.Library> getLibrariesByName(String name) {
 		// Search for libraries by name
-		SearchParameterMap map = new SearchParameterMap();
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
 		map.add("name", new StringParam(name, true));
 		ca.uhn.fhir.rest.api.server.IBundleProvider bundleProvider = myLibraryDao.search(map);
 
-		if (bundleProvider.size() == 0) {
+		if (bundleProvider.size() == null || bundleProvider.size() == 0) {
 			return new ArrayList<>();
 		}
-		List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
+		List<IBaseResource> resourceList = bundleProvider.getAllResources();
 		return resolveLibraries(resourceList);
 	}
 

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/evaluation/MeasureEvaluation.java

@@ -35,7 +35,6 @@ import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.ListResource;
 import org.hl7.fhir.r4.model.Measure;
 import org.hl7.fhir.r4.model.MeasureReport;
@@ -68,9 +67,9 @@ public class MeasureEvaluation {
 
 	private static final Logger logger = LoggerFactory.getLogger(MeasureEvaluation.class);
 
-	private DataProvider provider;
+	private final DataProvider provider;
-	private Interval measurementPeriod;
+	private final Interval measurementPeriod;
-	private DaoRegistry registry;
+	private final DaoRegistry registry;
 
 	public MeasureEvaluation(DataProvider provider, DaoRegistry registry, Interval measurementPeriod) {
 		this.provider = provider;
@@ -106,21 +105,21 @@ public class MeasureEvaluation {
 	}
 
 	private List<Patient> getPractitionerPatients(String practitionerRef) {
-		SearchParameterMap map = new SearchParameterMap();
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
 		map.add("general-practitioner", new ReferenceParam(
 			practitionerRef.startsWith("Practitioner/") ? practitionerRef : "Practitioner/" + practitionerRef));
 
 		List<Patient> patients = new ArrayList<>();
 		IBundleProvider patientProvider = registry.getResourceDao("Patient").search(map);
-		List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
+		List<IBaseResource> patientList = patientProvider.getAllResources();
 		patientList.forEach(x -> patients.add((Patient) x));
 		return patients;
 	}
 
 	private List<Patient> getAllPatients() {
 		List<Patient> patients = new ArrayList<>();
-		IBundleProvider patientProvider = registry.getResourceDao("Patient").search(new SearchParameterMap());
+		IBundleProvider patientProvider = registry.getResourceDao("Patient").search(SearchParameterMap.newSynchronous());
-		List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
+		List<IBaseResource> patientList = patientProvider.getAllResources();
 		patientList.forEach(x -> patients.add((Patient) x));
 		return patients;
 	}
@@ -552,7 +551,7 @@ public class MeasureEvaluation {
 			}
 
 			if (!list.isEmpty()) {
-				list.setId("List/" + UUID.randomUUID().toString());
+				list.setId("List/" + UUID.randomUUID());
 				list.setTitle(key);
 				resources.put(list.getId(), list);
 				list.getEntry().forEach(listResource -> evaluatedResourcesList.add(listResource.getItem().getReference()));
@@ -701,9 +700,7 @@ public class MeasureEvaluation {
 				Resource r = (Resource) o;
 				String id = (r.getIdElement().getResourceType() != null ? (r.getIdElement().getResourceType() + "/") : "")
 					+ r.getIdElement().getIdPart();
-				if (!codeHashSet.contains(id)) {
 				codeHashSet.add(id);
-				}
 
 				if (!resources.containsKey(id)) {
 					resources.put(id, r);

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/provider/JpaTerminologyProvider.java

@@ -94,8 +94,8 @@ public class JpaTerminologyProvider implements TerminologyProvider {
 			}
 
 			IBundleProvider bundleProvider = myValueSetDao
-				.search(new SearchParameterMap().add(ValueSet.SP_URL, new UriParam(valueSet.getId())));
+				.search(SearchParameterMap.newSynchronous().add(ValueSet.SP_URL, new UriParam(valueSet.getId())));
-			List<IBaseResource> valueSets = bundleProvider.getResources(0, bundleProvider.size());
+			List<IBaseResource> valueSets = bundleProvider.getAllResources();
 			if (valueSets.isEmpty()) {
 				throw new IllegalArgumentException(String.format("Could not resolve value set %s.", valueSet.getId()));
 			} else if (valueSets.size() == 1) {

hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/provider/LibraryResolutionProviderImpl.java

@@ -86,7 +86,7 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
 			version = parts[1];
 		}
 
-		SearchParameterMap map = new SearchParameterMap();
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
 		map.add("url", new UriParam(resourceUrl));
 		if (version != null) {
 			map.add("version", new TokenParam(version));
@@ -94,23 +94,23 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
 
 		ca.uhn.fhir.rest.api.server.IBundleProvider bundleProvider = myLibraryDao.search(map);
 
-		if (bundleProvider.size() == 0) {
+		if (bundleProvider.size() == null || bundleProvider.size() == 0) {
 			return null;
 		}
-		List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
+		List<IBaseResource> resourceList = bundleProvider.getAllResources();
 		return LibraryResolutionProvider.selectFromList(resolveLibraries(resourceList), version, x -> x.getVersion());
 	}
 
 	private Iterable<org.hl7.fhir.r4.model.Library> getLibrariesByName(String name) {
 		// Search for libraries by name
-		SearchParameterMap map = new SearchParameterMap();
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
 		map.add("name", new StringParam(name, true));
 		ca.uhn.fhir.rest.api.server.IBundleProvider bundleProvider = myLibraryDao.search(map);
 
-		if (bundleProvider.size() == 0) {
+		if (bundleProvider.size() == null || bundleProvider.size() == 0) {
 			return new ArrayList<>();
 		}
-		List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
+		List<IBaseResource> resourceList = bundleProvider.getAllResources();
 		return resolveLibraries(resourceList);
 	}
 

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmCandidateSearchSvc.java

@@ -20,15 +20,15 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
  * #L%
  */
 
-import ca.uhn.fhir.mdm.api.IMdmSettings;
-import ca.uhn.fhir.mdm.log.Logs;
-import ca.uhn.fhir.mdm.rules.json.MdmFilterSearchParamJson;
-import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.mdm.svc.MdmSearchParamSvc;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.mdm.api.IMdmSettings;
+import ca.uhn.fhir.mdm.log.Logs;
+import ca.uhn.fhir.mdm.rules.json.MdmFilterSearchParamJson;
+import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -136,7 +136,7 @@ public class MdmCandidateSearchSvc {
 		//3.
 		IFhirResourceDao<?> resourceDao = myDaoRegistry.getResourceDao(theResourceType);
 		IBundleProvider search = resourceDao.search(searchParameterMap);
-		List<IBaseResource> resources = search.getResources(0, search.size());
+		List<IBaseResource> resources = search.getAllResources();
 
 		int initialSize = theMatchedPidsToResources.size();
 

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmBatchSvcImplIT.java

@@ -1,9 +1,9 @@
 package ca.uhn.fhir.jpa.mdm.svc;
 
-import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
+import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
 import ca.uhn.test.concurrency.PointcutLatch;
 import org.apache.commons.lang3.time.DateUtils;
 import org.junit.jupiter.api.AfterEach;
@@ -14,7 +14,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import java.io.IOException;
 import java.util.Date;
 
-class MdmBatchSvcImplTest extends BaseMdmR4Test {
+class MdmBatchSvcImplIT extends BaseMdmR4Test {
 
 	@Autowired
 	IMdmSubmitSvc myMdmSubmitSvc;

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/resthook/SubscriptionDeliveringRestHookSubscriber.java

@@ -66,7 +66,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 @Scope("prototype")
 public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDeliverySubscriber {
-	private static Logger ourLog = LoggerFactory.getLogger(SubscriptionDeliveringRestHookSubscriber.class);
+	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionDeliveringRestHookSubscriber.class);
 
 	@Autowired
 	private DaoRegistry myDaoRegistry;
@@ -155,7 +155,7 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
 		IBundleProvider searchResults = dao.search(payloadSearchMap);
 
 		BundleBuilder builder = new BundleBuilder(myFhirContext);
-		for (IBaseResource next : searchResults.getResources(0, searchResults.size())) {
+		for (IBaseResource next : searchResults.getAllResources()) {
 			builder.addTransactionUpdateEntry(next);
 		}
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/IBundleProvider.java

@@ -1,11 +1,13 @@
 package ca.uhn.fhir.rest.api.server;
 
+import ca.uhn.fhir.context.ConfigurationException;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
+import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 
@@ -113,6 +115,26 @@ public interface IBundleProvider {
 	@Nonnull
 	List<IBaseResource> getResources(int theFromIndex, int theToIndex);
 
+	/**
+	 * Get all resources
+	 *
+	 * @return getResources(0, this.size ()).  Return an empty list if size() is zero.
+	 * @throws ConfigurationException if size() is null
+	 */
+	@Nonnull
+	default List<IBaseResource> getAllResources() {
+		List<IBaseResource> retval = new ArrayList<>();
+
+		Integer size = size();
+		if (size == null) {
+			throw new ConfigurationException("Attempt to request all resources from an asynchronous search result.  The SearchParameterMap for this search probably should have been synchronous.");
+		}
+		if (size > 0) {
+			retval.addAll(getResources(0, size));
+		}
+		return retval;
+	}
+
 	/**
 	 * Returns the UUID associated with this search. Note that this
 	 * does not need to return a non-null value unless it a

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/TransactionMethodBinding.java

@@ -19,12 +19,6 @@ package ca.uhn.fhir.rest.server.method;
  * limitations under the License.
  * #L%
  */
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.lang.reflect.Method;
-import java.util.List;
-
-import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
@@ -34,13 +28,20 @@ import ca.uhn.fhir.rest.annotation.Transaction;
 import ca.uhn.fhir.rest.annotation.TransactionParam;
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
-import ca.uhn.fhir.rest.api.server.*;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.IRestfulServer;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.rest.server.method.TransactionParameter.ParamStyle;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import javax.annotation.Nonnull;
+import java.lang.reflect.Method;
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class TransactionMethodBinding extends BaseResourceReturningMethodBinding {
 
@@ -127,7 +128,7 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
 		 * " entries, but server method response contained " + retVal.size() + " entries (must be the same)"); } }
 		 */
 
-		List<IBaseResource> retResources = retVal.getResources(0, retVal.size());
+		List<IBaseResource> retResources = retVal.getAllResources();
 		for (int i = 0; i < retResources.size(); i++) {
 			IBaseResource newRes = retResources.get(i);
 			if (newRes.getIdElement() == null || newRes.getIdElement().isEmpty()) {

hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/api/server/IBundleProviderTest.java

@@ -1,12 +1,15 @@
 package ca.uhn.fhir.rest.api.server;
 
+import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.rest.server.SimpleBundleProvider;
 import com.google.common.collect.Lists;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.junit.jupiter.api.Test;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.Mockito.mock;
 
 public class IBundleProviderTest {
@@ -39,4 +42,19 @@ public class IBundleProviderTest {
 		assertFalse(provider.isEmpty());
 	}
 
+	@Test
+	void getResources() {
+		SimpleBundleProvider provider = new SimpleBundleProvider() {
+			@Override
+			public Integer size() {
+				return null;
+			}
+		};
+		try {
+			provider.getAllResources();
+			fail();
+		} catch (ConfigurationException e) {
+			assertEquals("Attempt to request all resources from an asynchronous search result.  The SearchParameterMap for this search probably should have been synchronous.", e.getMessage());
+		}
+	}
 }