Merge branch 'rel_8_0' into rel_8_0_mb

Author: tadgh

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java

@@ -774,6 +774,7 @@ public String getPropertyName() {
 	// Some of the types in the spec are not yet implemented as well.
 	// @see https://github.com/hapifhir/hapi-fhir/issues/5700
 	String TYPE_STRING = "string";
+	String TYPE_BOOLEAN = "boolean";
 	String TYPE_CODING = "Coding";
 	String TYPE_GROUP = "group";
 
@@ -800,6 +801,29 @@ public String getType() {
 		}
 	}
 
+	class BooleanConceptProperty extends BaseConceptProperty {
+		private final boolean myValue;
+
+		/**
+		 * Constructor
+		 *
+		 * @param theName The name
+		 */
+		public BooleanConceptProperty(String theName, boolean theValue) {
+			super(theName);
+			myValue = theValue;
+		}
+
+		public boolean getValue() {
+			return myValue;
+		}
+
+		@Override
+		public String getType() {
+			return TYPE_BOOLEAN;
+		}
+	}
+
 	class CodingConceptProperty extends BaseConceptProperty {
 		private final String myCode;
 		private final String myCodeSystem;
@@ -1073,7 +1097,7 @@ class ValueSetExpansionOutcome {
 		private final IBaseResource myValueSet;
 		private final String myError;
 
-		private boolean myErrorIsFromServer;
+		private final boolean myErrorIsFromServer;
 
 		public ValueSetExpansionOutcome(String theError, boolean theErrorIsFromServer) {
 			myValueSet = null;
@@ -1199,7 +1223,7 @@ public LookupCodeResult setFound(boolean theFound) {
 		}
 
 		public void throwNotFoundIfAppropriate() {
-			if (isFound() == false) {
+			if (!isFound()) {
 				throw new ResourceNotFoundException(Msg.code(1738) + "Unable to find code[" + getSearchedForCode()
 						+ "] in system[" + getSearchedForSystem() + "]");
 			}
@@ -1270,6 +1294,10 @@ private void populateProperty(
 					StringConceptProperty stringConceptProperty = (StringConceptProperty) theConceptProperty;
 					ParametersUtil.addPartString(theContext, theProperty, "value", stringConceptProperty.getValue());
 					break;
+				case TYPE_BOOLEAN:
+					BooleanConceptProperty booleanConceptProperty = (BooleanConceptProperty) theConceptProperty;
+					ParametersUtil.addPartBoolean(theContext, theProperty, "value", booleanConceptProperty.getValue());
+					break;
 				case TYPE_CODING:
 					CodingConceptProperty codingConceptProperty = (CodingConceptProperty) theConceptProperty;
 					ParametersUtil.addPartCoding(
@@ -1321,7 +1349,7 @@ class TranslateCodeRequest {
 		private final String myTargetValueSetUrl;
 		private final IIdType myResourceId;
 		private final boolean myReverse;
-		private List<IBaseCoding> myCodings;
+		private final List<IBaseCoding> myCodings;
 
 		public TranslateCodeRequest(List<IBaseCoding> theCodings, String theTargetSystemUrl) {
 			myCodings = theCodings;

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -151,6 +151,7 @@ ca.uhn.fhir.jpa.dao.BaseTransactionProcessor.fhirPatchShouldNotUseBinaryResource
 ca.uhn.fhir.jpa.patch.FhirPatch.invalidInsertIndex=Invalid insert index {0} for path {1} - Only have {2} existing entries
 ca.uhn.fhir.jpa.patch.FhirPatch.invalidMoveSourceIndex=Invalid move source index {0} for path {1} - Only have {2} existing entries
 ca.uhn.fhir.jpa.patch.FhirPatch.invalidMoveDestinationIndex=Invalid move destination index {0} for path {1} - Only have {2} existing entries
+ca.uhn.fhir.jpa.patch.FhirPatch.noMatchingElementForPath=No element matches the specified path: {0}
 ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.externalReferenceNotAllowed=Resource contains external reference to URL "{0}" but this server is not configured to allow external references
 ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.failedToExtractPaths=Failed to extract values from resource using FHIRPath "{0}": {1}
 ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl.invalidInclude=Invalid {0} parameter value: "{1}". {2}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_0_0/6599-fix-NPE-in-storage-module.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 6599
+jira: SMILE-9237
+title: "Previously, attempting to restart the Storage module would result in a `NullPointerException` when partition 
+selection mode was set to `PATIENT_ID`, mass ingestion was enabled, and at least one Search Parameter was disabled. This 
+has now been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_0_0/6615-fixing-validation-on-sp.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 6615
+jira: SMILE-9569
+title: "SearchParameter validation was not being skipped on updates, even if requested. This has been fixed"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_0_0/6644-allow-deleting-resources-if-only-references-are-versioned.yaml

@@ -0,0 +1,11 @@
+---
+type: add
+issue: 6644
+jira: SMILE-9604
+title: "By default, referential integrity is enforced on deletes.
+        This change introduces support for an exceptional case such
+        that deletion of a given resource will not be blocked if all
+        references to that resource are versioned. If there is at
+        least one unversioned reference to the resource, deletion will
+        still be blocked.
+"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_0_0/6656-fhir-patch-replace-fix-for-collection-elements.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 6656
+title: "Previously, FHIR patch 'replace' would fail when trying to replace a sub-element of a high cardinality element
+using the the FHIR patch syntax. This has been fixed."
+

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_0_0/6662-remote-terminology-boolean-values-as-string.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 6662
+title: "Fixed remote terminology lookup results showing boolean properties as strings."

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

@@ -29,6 +29,7 @@
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.interceptor.executor.InterceptorService;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
@@ -47,6 +48,7 @@
 import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
 import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
 import ca.uhn.fhir.jpa.delete.DeleteConflictUtil;
+import ca.uhn.fhir.jpa.interceptor.PatientCompartmentEnforcingInterceptor;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
@@ -72,6 +74,7 @@
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.update.UpdateParameters;
 import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.jpa.util.QueryChunker;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -2492,16 +2495,19 @@ && getStorageSettings().getResourceServerIdStrategy()
 
 		// Start
 		if (outcome == null) {
-			outcome = doUpdateForUpdateOrPatch(
-					theRequest,
-					resourceId,
-					theMatchUrl,
-					thePerformIndexing,
-					theForceUpdateVersion,
-					theResource,
-					entity,
-					update,
-					theTransactionDetails);
+			UpdateParameters updateParameters = new UpdateParameters<>()
+					.setRequestDetails(theRequest)
+					.setResourceIdToUpdate(resourceId)
+					.setMatchUrl(theMatchUrl)
+					.setShouldPerformIndexing(thePerformIndexing)
+					.setShouldForceUpdateVersion(theForceUpdateVersion)
+					.setResource(theResource)
+					.setEntity(entity)
+					.setOperationType(update)
+					.setTransactionDetails(theTransactionDetails)
+					.setShouldForcePopulateOldResourceForProcessing(false);
+
+			outcome = doUpdateForUpdateOrPatch(updateParameters);
 		}
 
 		postUpdateTransaction(theTransactionDetails);
@@ -2523,23 +2529,14 @@ protected void postUpdateTransaction(TransactionDetails theTransactionDetails) {
 	}
 
 	@Override
-	protected DaoMethodOutcome doUpdateForUpdateOrPatch(
-			RequestDetails theRequest,
-			IIdType theResourceId,
-			String theMatchUrl,
-			boolean thePerformIndexing,
-			boolean theForceUpdateVersion,
-			T theResource,
-			IBasePersistedResource theEntity,
-			RestOperationTypeEnum theOperationType,
-			TransactionDetails theTransactionDetails) {
+	protected DaoMethodOutcome doUpdateForUpdateOrPatch(UpdateParameters<T> theUpdateParameters) {
 
 		/*
 		 * We stored a resource searchUrl at creation time to prevent resource duplication.
 		 * We'll clear any currently existing urls from the db, otherwise we could hit
 		 * duplicate index violations if we try to add another (after this create/update)
 		 */
-		ResourceTable entity = (ResourceTable) theEntity;
+		ResourceTable entity = (ResourceTable) theUpdateParameters.getEntity();
 
 		/*
 		 * If we read back the entity from hibernate, and it's already saying
@@ -2555,7 +2552,7 @@ protected DaoMethodOutcome doUpdateForUpdateOrPatch(
 
 		if (entity.isSearchUrlPresent()) {
 			JpaPid persistentId = entity.getResourceId();
-			theTransactionDetails.addUpdatedResourceId(persistentId);
+			theUpdateParameters.getTransactionDetails().addUpdatedResourceId(persistentId);
 
 			entity.setSearchUrlPresent(false); // it will be removed at the end
 		}
@@ -2572,16 +2569,11 @@ protected DaoMethodOutcome doUpdateForUpdateOrPatch(
 					null);
 		}
 
-		return super.doUpdateForUpdateOrPatch(
-				theRequest,
-				theResourceId,
-				theMatchUrl,
-				thePerformIndexing,
-				theForceUpdateVersion,
-				theResource,
-				theEntity,
-				theOperationType,
-				theTransactionDetails);
+		boolean shouldForcePopulateOldResourceForProcessing = myInterceptorBroadcaster instanceof InterceptorService
+				&& ((InterceptorService) myInterceptorBroadcaster)
+						.hasRegisteredInterceptor(PatientCompartmentEnforcingInterceptor.class);
+		theUpdateParameters.setShouldForcePopulateOldResourceForProcessing(shouldForcePopulateOldResourceForProcessing);
+		return super.doUpdateForUpdateOrPatch(theUpdateParameters);
 	}
 
 	/**

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteConflictFinderService.java

@@ -35,10 +35,12 @@ public class DeleteConflictFinderService {
 	protected EntityManager myEntityManager;
 
 	List<ResourceLink> findConflicts(ResourceTable theEntity, int maxResults) {
-		TypedQuery<ResourceLink> query = myEntityManager.createQuery(
-				"SELECT l FROM ResourceLink l WHERE l.myTargetResource.myPid = :target_pid", ResourceLink.class);
+		String queryStr =
+				"SELECT l FROM ResourceLink l WHERE l.myTargetResource.myPid = :target_pid AND (l.myTargetResourceVersion IS NULL)";
+		TypedQuery<ResourceLink> query = myEntityManager.createQuery(queryStr, ResourceLink.class);
 		query.setParameter("target_pid", theEntity.getId());
 		query.setMaxResults(maxResults);
+
 		return query.getResultList();
 	}
 }