Merge 08c441ca40 into d4f1766ca5

* Optimize transaction writes

* Cleanup

* Work on tests

* Work on fixes

* Fixes

* Fixes

* Test fixes

* Cleanup

* Cleanup

* Work on tests

* Work on tests

* Test fixes

* Test fixes

* Remove redundant test

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Add changelog

* Checkstyle fixes

* Test fixes

* Spotless

* Test cleanup

* Spotless

* Test fix

* Work on review comments

* Address review comments

* Test fixes

* Ongoing test cleanup work

* Work on tests

* Query count tests passing

* Test fixes

* Test fixes

* Rmove fixme

* Test cleanup

* Test fix

* Remove default method

* Service celanup

* Test fix

* version bump

* Test cleanup

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>7.7.6-SNAPSHOT</version>
+		 <version>7.7.7-SNAPSHOT</version>
 
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TaskChunker.java

@@ -40,13 +40,22 @@ import java.util.stream.Stream;
  */
 public class TaskChunker<T> {
 
-	public void chunk(Collection<T> theInput, int theChunkSize, Consumer<List<T>> theBatchConsumer) {
+	public static <T> void chunk(List<T> theInput, int theChunkSize, Consumer<List<T>> theBatchConsumer) {
+		if (theInput.size() <= theChunkSize) {
+			theBatchConsumer.accept(theInput);
+			return;
+		}
+		chunk((Collection<T>) theInput, theChunkSize, theBatchConsumer);
+	}
+
+	public static <T> void chunk(Collection<T> theInput, int theChunkSize, Consumer<List<T>> theBatchConsumer) {
 		List<T> input;
 		if (theInput instanceof List) {
 			input = (List<T>) theInput;
 		} else {
 			input = new ArrayList<>(theInput);
 		}
+
 		for (int i = 0; i < input.size(); i += theChunkSize) {
 			int to = i + theChunkSize;
 			to = Math.min(to, input.size());
@@ -56,12 +65,11 @@ public class TaskChunker<T> {
 	}
 
 	@Nonnull
-	public <T> Stream<List<T>> chunk(Stream<T> theStream, int theChunkSize) {
+	public static <T> Stream<List<T>> chunk(Stream<T> theStream, int theChunkSize) {
 		return StreamUtil.partition(theStream, theChunkSize);
 	}
 
-	@Nonnull
-	public void chunk(Iterator<T> theIterator, int theChunkSize, Consumer<List<T>> theListConsumer) {
+	public static <T> void chunk(Iterator<T> theIterator, int theChunkSize, Consumer<List<T>> theListConsumer) {
 		chunk(Streams.stream(theIterator), theChunkSize).forEach(theListConsumer);
 	}
 }

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

@@ -87,6 +87,7 @@ ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceVersionConstraintFail
 ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceIndexedCompositeStringUniqueConstraintFailure=The operation has failed with a unique index constraint failure. This probably means that the operation was trying to create/update a resource that would have resulted in a duplicate value for a unique index.
 ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.forcedIdConstraintFailure=The operation has failed with a client-assigned ID constraint failure. This typically means that multiple client threads are trying to create a new resource with the same client-assigned ID at the same time, and this thread was chosen to be rejected. It can also happen when a request disables the Upsert Existence Check.
 ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor.externalizedBinaryStorageExtensionFoundInRequestBody=Illegal extension found in request payload - URL "{0}" and value "{1}"
+ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.cantUndeleteWithDeletesDisabled=Unable to restore previously deleted resource as deletes are disabled on this server.
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
@@ -200,6 +201,7 @@ ca.uhn.fhir.jpa.search.builder.predicate.ResourceLinkPredicateBuilder.invalidTar
 ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl.invalidResourceType=Invalid/unsupported resource type: "{0}"
 
 ca.uhn.fhir.jpa.dao.index.IdHelperService.nonUniqueForcedId=Non-unique ID specified, can not process request
+ca.uhn.fhir.jpa.dao.index.IdHelperService.deletedId=Resource {0} has been deleted
 
 ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl.noIdSupplied=No Partition ID supplied
 ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl.missingPartitionIdOrName=Partition must have an ID and a Name

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/TaskChunkerTest.java

@@ -37,7 +37,7 @@ public class TaskChunkerTest {
 		List<Integer> input = newIntRangeList(0, 35);
 
 		// Execute
-		new TaskChunker<Integer>().chunk(input, 10, myConsumer);
+		TaskChunker.chunk(input, 10, myConsumer);
 
 		// Verify
 		verify(myConsumer, times(4)).accept(myConsumerCaptor.capture());

hapi-fhir-bom/pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-bom</artifactId>
-	<version>7.7.6-SNAPSHOT</version>
+	<version>7.7.7-SNAPSHOT</version>
 
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
@@ -12,7 +12,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-dont-store-reslink-target-partition-date.yaml

@@ -0,0 +1,5 @@
+---
+type: change
+issue: 6460
+title: "The HFJ_RES_LINK table with no longer store the `PARTITION_DATE` value for the indexed link target
+   resource, as this was an unused feature which has been removed as a part of a larger performance optimization."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-improve-transaction-performance-for-external-refs.yaml

@@ -0,0 +1,9 @@
+---
+type: perf
+issue: 6460
+title: "The JPA server FHIR transaction processor will now pre-fetch the target
+   resource state for references to resources that don't also appear in the
+   transaction bundle. This means that if you process a large FHIR transaction containing
+   many references to other resources in the repository that are not also being
+   updated in the same transaction, you should see a very significant improvement
+   in performance."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-improve-transaction-performance-for-ids.yaml

@@ -0,0 +1,7 @@
+---
+type: perf
+issue: 6460
+title: "The JPA server FHIR transaction processor will now more aggressively cache
+   resource IDs for previously seen resources, reducing the number of database reads
+   required when processing transactions. This should provide a noticeable improvement
+   in performance when processing transactions which update pre-existing resources."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-prevent-undeleting-if-deletes-disabled.yaml

@@ -0,0 +1,5 @@
+---
+type: change
+issue: 6460
+title: "If deletes are disabled in the JPA server, it is no longer possible to un-delete
+   a resource (i.e. update a previously deleted resource to make it non-deleted)."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-version-delete-and-update-in-same-transaction-separately.yaml

@@ -0,0 +1,9 @@
+---
+type: change
+issue: 6460
+title: "When performing a FHIR Transaction which deletes and then updates (or otherwise
+   un-deletes) the same resource within a single transaction, the delete was previously
+   not stored as a distinct version (meaning that the resource version was only
+   incremented once, and no delete was actually stored in the resource history. This
+   has been changed so that deletes will always appear as a distinct entry in the
+   resource history."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md

@@ -36,4 +36,4 @@ You then simply have to register the interceptor against your RestfulServer inst
 
 # Demonstration
 
-See the HAPI FHIR Test Server for a demonstration of HAPI FHIR OpenAPI functionality: http://hapi.fhir.org/baseR4/swagger-ui/
+See the HAPI FHIR Test Server for a demonstration of HAPI FHIR OpenAPI functionality: https://hapi.fhir.org/baseR4/swagger-ui/

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/config/HapiFhirLocalContainerEntityManagerFactoryBean.java

@@ -20,7 +20,11 @@
 package ca.uhn.fhir.jpa.config;
 
 import com.google.common.base.Strings;
-import org.hibernate.cfg.AvailableSettings;
+import jakarta.annotation.Nonnull;
+import org.hibernate.cfg.BatchSettings;
+import org.hibernate.cfg.JdbcSettings;
+import org.hibernate.cfg.ManagedBeanSettings;
+import org.hibernate.cfg.QuerySettings;
 import org.hibernate.query.criteria.ValueHandlingMode;
 import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@@ -46,18 +50,19 @@ public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContain
 		myConfigurableListableBeanFactory = theConfigurableListableBeanFactory;
 	}
 
+	@Nonnull
 	@Override
 	public Map<String, Object> getJpaPropertyMap() {
 		Map<String, Object> retVal = super.getJpaPropertyMap();
 
 		// SOMEDAY these defaults can be set in the constructor.  setJpaProperties does a merge.
-		if (!retVal.containsKey(AvailableSettings.CRITERIA_VALUE_HANDLING_MODE)) {
-			retVal.put(AvailableSettings.CRITERIA_VALUE_HANDLING_MODE, ValueHandlingMode.BIND);
+		if (!retVal.containsKey(QuerySettings.CRITERIA_VALUE_HANDLING_MODE)) {
+			retVal.put(QuerySettings.CRITERIA_VALUE_HANDLING_MODE, ValueHandlingMode.BIND);
 		}
 
-		if (!retVal.containsKey(AvailableSettings.CONNECTION_HANDLING)) {
+		if (!retVal.containsKey(JdbcSettings.CONNECTION_HANDLING)) {
 			retVal.put(
-					AvailableSettings.CONNECTION_HANDLING,
+					JdbcSettings.CONNECTION_HANDLING,
 					PhysicalConnectionHandlingMode.DELAYED_ACQUISITION_AND_RELEASE_AFTER_TRANSACTION);
 		}
 
@@ -65,26 +70,25 @@ public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContain
 		 * Set some performance options
 		 */
 
-		if (!retVal.containsKey(AvailableSettings.STATEMENT_BATCH_SIZE)) {
-			retVal.put(AvailableSettings.STATEMENT_BATCH_SIZE, "30");
+		if (!retVal.containsKey(BatchSettings.STATEMENT_BATCH_SIZE)) {
+			retVal.put(BatchSettings.STATEMENT_BATCH_SIZE, "30");
 		}
 
-		if (!retVal.containsKey(AvailableSettings.ORDER_INSERTS)) {
-			retVal.put(AvailableSettings.ORDER_INSERTS, "true");
+		if (!retVal.containsKey(BatchSettings.ORDER_INSERTS)) {
+			retVal.put(BatchSettings.ORDER_INSERTS, "true");
 		}
 
-		if (!retVal.containsKey(AvailableSettings.ORDER_UPDATES)) {
-			retVal.put(AvailableSettings.ORDER_UPDATES, "true");
+		if (!retVal.containsKey(BatchSettings.ORDER_UPDATES)) {
+			retVal.put(BatchSettings.ORDER_UPDATES, "true");
 		}
 
-		if (!retVal.containsKey(AvailableSettings.BATCH_VERSIONED_DATA)) {
-			retVal.put(AvailableSettings.BATCH_VERSIONED_DATA, "true");
+		if (!retVal.containsKey(BatchSettings.BATCH_VERSIONED_DATA)) {
+			retVal.put(BatchSettings.BATCH_VERSIONED_DATA, "true");
 		}
 		// Why is this here, you ask? LocalContainerEntityManagerFactoryBean actually clobbers the setting hibernate
-		// needs
-		// in order to be able to resolve beans, so we add it back in manually here
-		if (!retVal.containsKey(AvailableSettings.BEAN_CONTAINER)) {
-			retVal.put(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(myConfigurableListableBeanFactory));
+		// needs in order to be able to resolve beans, so we add it back in manually here
+		if (!retVal.containsKey(ManagedBeanSettings.BEAN_CONTAINER)) {
+			retVal.put(ManagedBeanSettings.BEAN_CONTAINER, new SpringBeanContainer(myConfigurableListableBeanFactory));
 		}
 
 		return retVal;

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java

@@ -42,7 +42,6 @@ import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.search.SearchBuilderLoadIncludesParameters;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.jpa.util.QueryChunker;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
 import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
 import ca.uhn.fhir.mdm.model.MdmPidTuple;
@@ -59,6 +58,7 @@ import ca.uhn.fhir.util.ExtensionUtil;
 import ca.uhn.fhir.util.HapiExtensions;
 import ca.uhn.fhir.util.Logs;
 import ca.uhn.fhir.util.SearchParameterUtil;
+import ca.uhn.fhir.util.TaskChunker;
 import jakarta.annotation.Nonnull;
 import jakarta.persistence.EntityManager;
 import org.apache.commons.lang3.StringUtils;
@@ -315,8 +315,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
 			// for each patient pid ->
 			//	search for the target resources, with their correct patient references, chunked.
 			// The results will be jammed into myReadPids
-			QueryChunker<JpaPid> queryChunker = new QueryChunker<>();
-			queryChunker.chunk(expandedMemberResourceIds, QUERY_CHUNK_SIZE, (idChunk) -> {
+			TaskChunker.chunk(expandedMemberResourceIds, QUERY_CHUNK_SIZE, (idChunk) -> {
 				try {
 					queryResourceTypeWithReferencesToPatients(pids, idChunk, theParams, theDef);
 				} catch (IOException ex) {

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

@@ -1323,7 +1323,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		 * the previous version entity.
 		 */
 		if (historyEntry == null) {
-			historyEntry = theEntity.toHistory(versionedTags);
+			historyEntry = theEntity.toHistory(versionedTags && theEntity.getDeleted() == null);
 		}
 
 		historyEntry.setEncoding(theChanged.getEncoding());
@@ -1331,7 +1331,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		historyEntry.setResourceTextVc(theChanged.getResourceText());
 
 		ourLog.debug("Saving history entry ID[{}] for RES_ID[{}]", historyEntry.getId(), historyEntry.getResourceId());
-		myResourceHistoryTableDao.save(historyEntry);
+		myEntityManager.persist(historyEntry);
 		theEntity.setCurrentVersionEntity(historyEntry);
 
 		// Save resource source
@@ -1489,6 +1489,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			wasDeleted = theOldResource.isDeleted();
 		}
 
+		if (wasDeleted && !myStorageSettings.isDeleteEnabled()) {
+			String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "cantUndeleteWithDeletesDisabled");
+			throw new InvalidRequestException(Msg.code(2573) + msg);
+		}
+
 		DaoMethodOutcome outcome = toMethodOutcome(
 						theRequestDetails, savedEntity, theResource, theMatchUrl, theOperationType)
 				.setCreated(wasDeleted);

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

@@ -43,6 +43,7 @@ import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
 import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
 import ca.uhn.fhir.jpa.delete.DeleteConflictUtil;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
@@ -567,8 +568,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		// Pre-cache the resource ID
 		jpaPid.setAssociatedResourceId(entity.getIdType(myFhirContext));
-		myIdHelperService.addResolvedPidToForcedId(
-				jpaPid, theRequestPartitionId, getResourceName(), entity.getFhirId(), null);
+		String fhirId = entity.getFhirId();
+		if (fhirId == null) {
+			fhirId = Long.toString(entity.getId());
+		}
+		myIdHelperService.addResolvedPidToFhirId(jpaPid, theRequestPartitionId, getResourceName(), fhirId, null);
 		theTransactionDetails.addResolvedResourceId(jpaPid.getAssociatedResourceId(), jpaPid);
 		theTransactionDetails.addResolvedResource(jpaPid.getAssociatedResourceId(), theResource);
 
@@ -1736,8 +1740,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		validateResourceTypeAndThrowInvalidRequestException(theId);
 
 		BaseHasResource entity;
-		JpaPid pid = myIdHelperService.resolveResourcePersistentIds(
-				requestPartitionId, getResourceName(), theId.getIdPart());
+		JpaPid pid = myIdHelperService
+				.resolveResourceIdentity(
+						requestPartitionId,
+						getResourceName(),
+						theId.getIdPart(),
+						ResolveIdentityMode.includeDeleted().cacheOk())
+				.getPersistentId();
 		Set<Integer> readPartitions = null;
 		if (requestPartitionId.isAllPartitions()) {
 			entity = myEntityManager.find(ResourceTable.class, pid.getId());
@@ -1779,10 +1788,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			}
 		}
 
-		if (entity == null) {
-			throw new ResourceNotFoundException(Msg.code(1996) + "Resource " + theId + " is not known");
-		}
-
 		if (theId.hasVersionIdPart()) {
 			if (!theId.isVersionIdPartValidLong()) {
 				throw new ResourceNotFoundException(Msg.code(978)
@@ -1822,7 +1827,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			}
 		}
 
-		Validate.notNull(entity);
+		if (entity == null) {
+			throw new ResourceNotFoundException(Msg.code(1996) + "Resource " + theId + " is not known");
+		}
+
 		validateResourceType(entity);
 
 		if (theCheckForForcedId) {
@@ -1871,8 +1879,27 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		}
 
 		if (persistentId == null) {
-			persistentId = myIdHelperService.resolveResourcePersistentIds(
-					theRequestPartitionId, getResourceName(), theId.getIdPart());
+			String resourceName = getResourceName();
+			if (myStorageSettings.getResourceClientIdStrategy()
+					== JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC) {
+				if (theId.isIdPartValidLong()) {
+					/*
+					 * If it's a pure numeric ID and we are in ALPHANUMERIC mode, then the number
+					 * corresponds to a DB PID. In this case we want to resolve it regardless of
+					 * which type the client has supplied. This is because DB PIDs are unique across
+					 * all resource types (unlike FHIR_IDs which are namespaced to the resource type).
+					 * We want to load the resource with that PID regardless of type because if
+					 * the user is trying to update it we want to fail if the type is wrong, as
+					 * opposed to trying to create a new instance.
+					 */
+					resourceName = null;
+				}
+			}
+			persistentId = myIdHelperService.resolveResourceIdentityPid(
+					theRequestPartitionId,
+					resourceName,
+					theId.getIdPart(),
+					ResolveIdentityMode.includeDeleted().cacheOk());
 		}
 
 		ResourceTable entity = myEntityManager.find(ResourceTable.class, persistentId.getId());

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

@@ -192,7 +192,7 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
 		HapiTransactionService.requireTransaction();
 		List<Long> pids = theResolvedIds.stream().map(t -> ((JpaPid) t).getId()).collect(Collectors.toList());
 
-		new QueryChunker<Long>().chunk(pids, idChunk -> {
+		QueryChunker.chunk(pids, idChunk -> {
 
 			/*
 			 * Pre-fetch the resources we're touching in this transaction in mass - this reduced the

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

@@ -81,7 +81,7 @@ public class HistoryBuilder {
 	private FhirContext myCtx;
 
 	@Autowired
-	private IIdHelperService myIdHelperService;
+	private IIdHelperService<JpaPid> myIdHelperService;
 
 	/**
 	 * Constructor
@@ -150,13 +150,13 @@ public class HistoryBuilder {
 		query.setMaxResults(theToIndex - theFromIndex);
 
 		List<ResourceHistoryTable> tables = query.getResultList();
-		if (tables.size() > 0) {
+		if (!tables.isEmpty()) {
 			ImmutableListMultimap<Long, ResourceHistoryTable> resourceIdToHistoryEntries =
 					Multimaps.index(tables, ResourceHistoryTable::getResourceId);
 			Set<JpaPid> pids = resourceIdToHistoryEntries.keySet().stream()
 					.map(JpaPid::fromId)
 					.collect(Collectors.toSet());
-			PersistentIdToForcedIdMap pidToForcedId = myIdHelperService.translatePidsToForcedIds(pids);
+			PersistentIdToForcedIdMap<JpaPid> pidToForcedId = myIdHelperService.translatePidsToForcedIds(pids);
 			ourLog.trace("Translated IDs: {}", pidToForcedId.getResourcePersistentIdOptionalMap());
 
 			for (Long nextResourceId : resourceIdToHistoryEntries.keySet()) {

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

@@ -242,13 +242,15 @@ public class JpaResourceDaoCodeSystem<T extends IBaseResource> extends BaseHapiF
 				theTransactionDetails,
 				theForceUpdate,
 				theCreateNewHistoryEntry);
-		if (!retVal.isUnchangedInCurrentOperation()) {
+		if (thePerformIndexing) {
+			if (!retVal.isUnchangedInCurrentOperation()) {
 
-			org.hl7.fhir.r4.model.CodeSystem cs = myVersionCanonicalizer.codeSystemToCanonical(theResource);
-			addPidToResource(theEntity, cs);
+				org.hl7.fhir.r4.model.CodeSystem cs = myVersionCanonicalizer.codeSystemToCanonical(theResource);
+				addPidToResource(theEntity, cs);
 
-			myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(
-					cs, (ResourceTable) theEntity, theRequest);
+				myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(
+						cs, (ResourceTable) theEntity, theRequest);
+			}
 		}
 
 		return retVal;

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

@@ -22,6 +22,8 @@ package ca.uhn.fhir.jpa.dao;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
+import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -39,12 +41,15 @@ import jakarta.persistence.PersistenceContext;
 import jakarta.persistence.PersistenceContextType;
 import jakarta.servlet.http.HttpServletResponse;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Observation;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.TreeMap;
 
 public class JpaResourceDaoObservation<T extends IBaseResource> extends BaseHapiFhirResourceDao<T>
@@ -138,13 +143,14 @@ public class JpaResourceDaoObservation<T extends IBaseResource> extends BaseHapi
 				patientParams.addAll(theSearchParameterMap.get(getSubjectParamName()));
 			}
 
+			Map<IIdType, ReferenceParam> ids = new HashMap<>();
 			for (List<? extends IQueryParameterType> nextPatientList : patientParams) {
 				for (IQueryParameterType nextOr : nextPatientList) {
 					if (nextOr instanceof ReferenceParam) {
 						ReferenceParam ref = (ReferenceParam) nextOr;
-						JpaPid pid = myIdHelperService.resolveResourcePersistentIds(
-								requestPartitionId, ref.getResourceType(), ref.getIdPart());
-						orderedSubjectReferenceMap.put(pid.getId(), nextOr);
+						IIdType id = myFhirContext.getVersion().newIdType();
+						id.setParts(null, ref.getResourceType(), ref.getIdPart(), null);
+						ids.put(id, ref);
 					} else {
 						throw new IllegalArgumentException(
 								Msg.code(942) + "Invalid token type (expecting ReferenceParam): " + nextOr.getClass());
@@ -152,6 +158,15 @@ public class JpaResourceDaoObservation<T extends IBaseResource> extends BaseHapi
 				}
 			}
 
+			Map<IIdType, IResourceLookup<JpaPid>> resolvedIds = myIdHelperService.resolveResourceIdentities(
+					requestPartitionId,
+					ids.keySet(),
+					ResolveIdentityMode.includeDeleted().cacheOk());
+			for (Map.Entry<IIdType, ReferenceParam> entry : ids.entrySet()) {
+				IResourceLookup<JpaPid> lookup = resolvedIds.get(entry.getKey());
+				orderedSubjectReferenceMap.put(lookup.getPersistentId().getId(), entry.getValue());
+			}
+
 			theSearchParameterMap.remove(getSubjectParamName());
 			theSearchParameterMap.remove(getPatientParamName());
 

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

@@ -303,12 +303,14 @@ public class JpaResourceDaoValueSet<T extends IBaseResource> extends BaseHapiFhi
 				theForceUpdate,
 				theCreateNewHistoryEntry);
 
-		if (getStorageSettings().isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
-			if (retVal.getDeleted() == null) {
-				ValueSet valueSet = myVersionCanonicalizer.valueSetToCanonical(theResource);
-				myTerminologySvc.storeTermValueSet(retVal, valueSet);
-			} else {
-				myTerminologySvc.deleteValueSetAndChildren(retVal);
+		if (thePerformIndexing) {
+			if (getStorageSettings().isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
+				if (retVal.getDeleted() == null) {
+					ValueSet valueSet = myVersionCanonicalizer.valueSetToCanonical(theResource);
+					myTerminologySvc.storeTermValueSet(retVal, valueSet);
+				} else {
+					myTerminologySvc.deleteValueSetAndChildren(retVal);
+				}
 			}
 		}
 

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

@@ -26,25 +26,29 @@ import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect;
+import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
 import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.jpa.util.QueryChunker;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.TaskChunker;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
 import jakarta.annotation.Nullable;
 import jakarta.persistence.EntityManager;
+import jakarta.persistence.FlushModeType;
 import jakarta.persistence.PersistenceContext;
 import jakarta.persistence.PersistenceContextType;
 import jakarta.persistence.PersistenceException;
@@ -67,6 +71,7 @@ import org.springframework.context.ApplicationContext;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.List;
@@ -83,6 +88,7 @@ public class TransactionProcessor extends BaseTransactionProcessor {
 
 	public static final Pattern SINGLE_PARAMETER_MATCH_URL_PATTERN = Pattern.compile("^[^?]+[?][a-z0-9-]+=[^&,]+$");
 	private static final Logger ourLog = LoggerFactory.getLogger(TransactionProcessor.class);
+	public static final int CONDITIONAL_URL_FETCH_CHUNK_SIZE = 100;
 
 	@Autowired
 	private ApplicationContext myApplicationContext;
@@ -146,25 +152,51 @@ public class TransactionProcessor extends BaseTransactionProcessor {
 			List<IBase> theEntries,
 			StopWatch theTransactionStopWatch) {
 
-		ITransactionProcessorVersionAdapter<?, ?> versionAdapter = getVersionAdapter();
-		RequestPartitionId requestPartitionId =
-				super.determineRequestPartitionIdForWriteEntries(theRequest, theEntries);
+		/*
+		 * We temporarily set the flush mode for the duration of the DB transaction
+		 * from the default of AUTO to the temporary value of COMMIT here. We do this
+		 * because in AUTO mode, if any SQL SELECTs are required during the
+		 * processing of an individual transaction entry, the server will flush the
+		 * pending INSERTs/UPDATEs to the database before executing the SELECT.
+		 * This hurts performance since we don't get the benefit of batching those
+		 * write operations as much as possible. The tradeoff here is that we
+		 * could theoretically have transaction operations which try to read
+		 * data previously written in the same transaction, and they won't see it.
+		 * This shouldn't actually be an issue anyhow - we pre-fetch conditional
+		 * URLs and reference targets at the start of the transaction. But this
+		 * tradeoff still feels worth it, since the most common use of transactions
+		 * is for fast writing of data.
+		 *
+		 * Note that it's probably not necessary to reset it back, it should
+		 * automatically go back to the default value after the transaction but
+		 * we reset it just to be safe.
+		 */
+		FlushModeType initialFlushMode = myEntityManager.getFlushMode();
+		try {
+			myEntityManager.setFlushMode(FlushModeType.COMMIT);
 
-		if (requestPartitionId != null) {
-			preFetch(theTransactionDetails, theEntries, versionAdapter, requestPartitionId);
+			ITransactionProcessorVersionAdapter<?, ?> versionAdapter = getVersionAdapter();
+			RequestPartitionId requestPartitionId =
+					super.determineRequestPartitionIdForWriteEntries(theRequest, theEntries);
+
+			if (requestPartitionId != null) {
+				preFetch(theTransactionDetails, theEntries, versionAdapter, requestPartitionId);
+			}
+
+			return super.doTransactionWriteOperations(
+					theRequest,
+					theActionName,
+					theTransactionDetails,
+					theAllIds,
+					theIdSubstitutions,
+					theIdToPersistedOutcome,
+					theResponse,
+					theOriginalRequestOrder,
+					theEntries,
+					theTransactionStopWatch);
+		} finally {
+			myEntityManager.setFlushMode(initialFlushMode);
 		}
-
-		return super.doTransactionWriteOperations(
-				theRequest,
-				theActionName,
-				theTransactionDetails,
-				theAllIds,
-				theIdSubstitutions,
-				theIdToPersistedOutcome,
-				theResponse,
-				theOriginalRequestOrder,
-				theEntries,
-				theTransactionStopWatch);
 	}
 
 	private void preFetch(
@@ -199,40 +231,100 @@ public class TransactionProcessor extends BaseTransactionProcessor {
 			RequestPartitionId theRequestPartitionId,
 			Set<String> foundIds,
 			List<Long> idsToPreFetch) {
-		List<IIdType> idsToPreResolve = new ArrayList<>();
+
+		FhirTerser terser = myFhirContext.newTerser();
+
+		// Key: The ID of the resource
+		// Value: TRUE if we should prefetch the existing resource details and all stored indexes,
+		//        FALSE if we should prefetch only the identity (resource ID and deleted status)
+		Map<IIdType, Boolean> idsToPreResolve = new HashMap<>(theEntries.size() * 3);
+
 		for (IBase nextEntry : theEntries) {
 			IBaseResource resource = theVersionAdapter.getResource(nextEntry);
 			if (resource != null) {
 				String verb = theVersionAdapter.getEntryRequestVerb(myFhirContext, nextEntry);
+
+				/*
+				 * Pre-fetch any resources that are potentially being directly updated by ID
+				 */
 				if ("PUT".equals(verb) || "PATCH".equals(verb)) {
 					String requestUrl = theVersionAdapter.getEntryRequestUrl(nextEntry);
-					if (countMatches(requestUrl, '/') == 1 && countMatches(requestUrl, '?') == 0) {
+					if (countMatches(requestUrl, '?') == 0) {
 						IIdType id = myFhirContext.getVersion().newIdType();
 						id.setValue(requestUrl);
-						idsToPreResolve.add(id);
+						IIdType unqualifiedVersionless = id.toUnqualifiedVersionless();
+						idsToPreResolve.put(unqualifiedVersionless, Boolean.TRUE);
+					}
+				}
+
+				/*
+				 * Pre-fetch any resources that are referred to directly by ID (don't replace
+				 * the TRUE flag with FALSE in case we're updating a resource but also
+				 * pointing to that resource elsewhere in the bundle)
+				 */
+				if ("PUT".equals(verb) || "POST".equals(verb)) {
+					for (ResourceReferenceInfo referenceInfo : terser.getAllResourceReferences(resource)) {
+						IIdType reference = referenceInfo.getResourceReference().getReferenceElement();
+						if (reference != null
+								&& !reference.isLocal()
+								&& !reference.isUuid()
+								&& reference.hasResourceType()
+								&& reference.hasIdPart()
+								&& !reference.getValue().contains("?")) {
+							idsToPreResolve.putIfAbsent(reference.toUnqualifiedVersionless(), Boolean.FALSE);
+						}
 					}
 				}
 			}
 		}
-		List<JpaPid> outcome =
-				myIdHelperService.resolveResourcePersistentIdsWithCache(theRequestPartitionId, idsToPreResolve).stream()
-						.collect(Collectors.toList());
-		for (JpaPid next : outcome) {
-			foundIds.add(
-					next.getAssociatedResourceId().toUnqualifiedVersionless().getValue());
-			theTransactionDetails.addResolvedResourceId(next.getAssociatedResourceId(), next);
-			if (myStorageSettings.getResourceClientIdStrategy() != JpaStorageSettings.ClientIdStrategyEnum.ANY
-					|| !next.getAssociatedResourceId().isIdPartValidLong()) {
-				idsToPreFetch.add(next.getId());
+
+		/*
+		 * If all the entries in the pre-fetch ID map have a value of TRUE, this
+		 * means we only have IDs associated with resources we're going to directly
+		 * update/patch within the transaction. In that case, it's fine to include
+		 * deleted resources, since updating them will bring them back to life.
+		 *
+		 * If we have any FALSE entries, we're also pre-fetching reference targets
+		 * which means we don't want deleted resources, because those are not OK
+		 * to reference.
+		 */
+		boolean preFetchIncludesReferences = idsToPreResolve.values().stream().anyMatch(t -> !t);
+		ResolveIdentityMode resolveMode = preFetchIncludesReferences
+				? ResolveIdentityMode.excludeDeleted().noCacheUnlessDeletesDisabled()
+				: ResolveIdentityMode.includeDeleted().cacheOk();
+
+		Map<IIdType, IResourceLookup<JpaPid>> outcomes = myIdHelperService.resolveResourceIdentities(
+				theRequestPartitionId, idsToPreResolve.keySet(), resolveMode);
+		for (Map.Entry<IIdType, IResourceLookup<JpaPid>> entry : outcomes.entrySet()) {
+			JpaPid next = (JpaPid) entry.getValue().getPersistentId();
+			IIdType unqualifiedVersionlessId = entry.getKey();
+			foundIds.add(unqualifiedVersionlessId.getValue());
+			theTransactionDetails.addResolvedResourceId(unqualifiedVersionlessId, next);
+			if (idsToPreResolve.get(unqualifiedVersionlessId) == Boolean.TRUE) {
+				if (myStorageSettings.getResourceClientIdStrategy() != JpaStorageSettings.ClientIdStrategyEnum.ANY
+						|| (next.getAssociatedResourceId() != null
+								&& !next.getAssociatedResourceId().isIdPartValidLong())) {
+					idsToPreFetch.add(next.getId());
+				}
 			}
 		}
-		for (IIdType next : idsToPreResolve) {
-			if (!foundIds.contains(next.toUnqualifiedVersionless().getValue())) {
+
+		// Any IDs that could not be resolved are presumably not there, so
+		// cache that fact so we don't look again later
+		for (IIdType next : idsToPreResolve.keySet()) {
+			if (!foundIds.contains(next.getValue())) {
 				theTransactionDetails.addResolvedResourceId(next.toUnqualifiedVersionless(), null);
 			}
 		}
 	}
 
+	@Override
+	protected void handleVerbChangeInTransactionWriteOperations() {
+		super.handleVerbChangeInTransactionWriteOperations();
+
+		myEntityManager.flush();
+	}
+
 	private void preFetchConditionalUrls(
 			TransactionDetails theTransactionDetails,
 			List<IBase> theEntries,
@@ -274,12 +366,10 @@ public class TransactionProcessor extends BaseTransactionProcessor {
 			}
 		}
 
-		new QueryChunker<MatchUrlToResolve>()
-				.chunk(
-						searchParameterMapsToResolve,
-						100,
-						map -> preFetchSearchParameterMaps(
-								theTransactionDetails, theRequestPartitionId, map, idsToPreFetch));
+		TaskChunker.chunk(
+				searchParameterMapsToResolve,
+				CONDITIONAL_URL_FETCH_CHUNK_SIZE,
+				map -> preFetchSearchParameterMaps(theTransactionDetails, theRequestPartitionId, map, idsToPreFetch));
 	}
 
 	/**

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.model.PersistentIdToForcedIdMap;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
@@ -35,11 +36,12 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
 import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.jpa.util.QueryChunker;
-import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.server.storage.BaseResourcePersistentId;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.TaskChunker;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.MultimapBuilder;
@@ -60,11 +62,12 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.IdType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.support.TransactionSynchronizationManager;
 
-import java.time.LocalDate;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -79,6 +82,7 @@ import java.util.Set;
 import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.jpa.search.builder.predicate.BaseJoiningPredicateBuilder.replaceDefaultPartitionIdIfNonNull;
+import static ca.uhn.fhir.model.primitive.IdDt.isValidLong;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /**
@@ -102,6 +106,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public class IdHelperService implements IIdHelperService<JpaPid> {
 	public static final Predicate[] EMPTY_PREDICATE_ARRAY = new Predicate[0];
 	public static final String RESOURCE_PID = "RESOURCE_PID";
+	private static final Logger ourLog = LoggerFactory.getLogger(IdHelperService.class);
 
 	@Autowired
 	protected IResourceTableDao myResourceTableDao;
@@ -128,20 +133,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		myDontCheckActiveTransactionForUnitTest = theDontCheckActiveTransactionForUnitTest;
 	}
 
-	/**
-	 * Given a forced ID, convert it to its Long value. Since you are allowed to use string IDs for resources, we need to
-	 * convert those to the underlying Long values that are stored, for lookup and comparison purposes.
-	 *
-	 * @throws ResourceNotFoundException If the ID can not be found
-	 */
-	@Override
-	@Nonnull
-	public IResourceLookup<JpaPid> resolveResourceIdentity(
-			@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId)
-			throws ResourceNotFoundException {
-		return resolveResourceIdentity(theRequestPartitionId, theResourceType, theResourceId, false);
-	}
-
 	/**
 	 * Given a forced ID, convert it to its Long value. Since you are allowed to use string IDs for resources, we need to
 	 * convert those to the underlying Long values that are stored, for lookup and comparison purposes.
@@ -153,48 +144,236 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 	@Nonnull
 	public IResourceLookup<JpaPid> resolveResourceIdentity(
 			@Nonnull RequestPartitionId theRequestPartitionId,
-			String theResourceType,
-			final String theResourceId,
-			boolean theExcludeDeleted)
+			@Nullable String theResourceType,
+			@Nonnull final String theResourceId,
+			@Nonnull ResolveIdentityMode theMode)
 			throws ResourceNotFoundException {
-		assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive()
-				: "no transaction active";
 
-		String resourceIdToUse = theResourceId;
-		if (resourceIdToUse.contains("/")) {
-			resourceIdToUse = theResourceId.substring(resourceIdToUse.indexOf("/") + 1);
+		IIdType id;
+		if (theResourceType != null) {
+			id = newIdType(theResourceType + "/" + theResourceId);
+		} else {
+			id = newIdType(theResourceId);
 		}
-		IdDt id = new IdDt(theResourceType, resourceIdToUse);
-		Map<String, List<IResourceLookup<JpaPid>>> matches =
-				translateForcedIdToPids(theRequestPartitionId, Collections.singletonList(id), theExcludeDeleted);
+		List<IIdType> ids = List.of(id);
+		Map<IIdType, IResourceLookup<JpaPid>> outcome = resolveResourceIdentities(theRequestPartitionId, ids, theMode);
 
 		// We only pass 1 input in so only 0..1 will come back
-		if (matches.isEmpty() || !matches.containsKey(resourceIdToUse)) {
+		if (!outcome.containsKey(id)) {
 			throw new ResourceNotFoundException(Msg.code(2001) + "Resource " + id + " is not known");
 		}
 
-		if (matches.size() > 1 || matches.get(resourceIdToUse).size() > 1) {
-			/*
-			 *  This means that:
-			 *  1. There are two resources with the exact same resource type and forced id
-			 *  2. The unique constraint on this column-pair has been dropped
-			 */
-			String msg = myFhirCtx.getLocalizer().getMessage(IdHelperService.class, "nonUniqueForcedId");
-			throw new PreconditionFailedException(Msg.code(1099) + msg);
+		return outcome.get(id);
+	}
+
+	@Nonnull
+	@Override
+	public Map<IIdType, IResourceLookup<JpaPid>> resolveResourceIdentities(
+			@Nonnull RequestPartitionId theRequestPartitionId,
+			Collection<IIdType> theIds,
+			ResolveIdentityMode theMode) {
+		assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive()
+				: "no transaction active";
+
+		if (theIds.isEmpty()) {
+			return new HashMap<>();
 		}
 
-		return matches.get(resourceIdToUse).get(0);
+		Collection<IIdType> ids = new ArrayList<>(theIds);
+		ids.forEach(id -> Validate.isTrue(id.hasIdPart()));
+
+		RequestPartitionId requestPartitionId = replaceDefault(theRequestPartitionId);
+		ListMultimap<IIdType, IResourceLookup<JpaPid>> idToLookup =
+				MultimapBuilder.hashKeys(theIds.size()).arrayListValues(1).build();
+
+		// Do we have any FHIR ID lookups cached for any of the IDs
+		if (theMode.isUseCache(myStorageSettings.isDeleteEnabled()) && !ids.isEmpty()) {
+			resolveResourceIdentitiesForFhirIdsUsingCache(requestPartitionId, theMode, ids, idToLookup);
+		}
+
+		// We still haven't found IDs, let's look them up in the DB
+		if (!ids.isEmpty()) {
+			resolveResourceIdentitiesForFhirIdsUsingDatabase(requestPartitionId, ids, idToLookup);
+		}
+
+		// Convert the multimap into a simple map
+		Map<IIdType, IResourceLookup<JpaPid>> retVal = new HashMap<>();
+		for (Map.Entry<IIdType, IResourceLookup<JpaPid>> next : idToLookup.entries()) {
+			if (next.getValue().getDeleted() != null) {
+				if (theMode.isFailOnDeleted()) {
+					String msg = myFhirCtx
+							.getLocalizer()
+							.getMessageSanitized(
+									IdHelperService.class,
+									"deletedId",
+									next.getKey().getValue());
+					throw new ResourceGoneException(Msg.code(2572) + msg);
+				}
+				if (!theMode.isIncludeDeleted()) {
+					continue;
+				}
+			}
+
+			IResourceLookup previousValue = retVal.put(next.getKey(), next.getValue());
+			if (previousValue != null) {
+				/*
+				 *  This means that either:
+				 *  1. There are two resources with the exact same resource type and forced
+				 *     id. The most likely reason for that is that someone is performing a
+				 *     multi-partition search and there are resources on each partition
+				 *     with the same ID.
+				 *  2. The unique constraint on the FHIR_ID column has been dropped
+				 */
+				ourLog.warn(
+						"Resource ID[{}] corresponds to lookups: {} and {}",
+						next.getKey(),
+						previousValue,
+						next.getValue());
+				String msg = myFhirCtx.getLocalizer().getMessage(IdHelperService.class, "nonUniqueForcedId");
+				throw new PreconditionFailedException(Msg.code(1099) + msg);
+			}
+		}
+
+		return retVal;
 	}
 
 	/**
-	 * Returns a mapping of Id -> IResourcePersistentId.
-	 * If any resource is not found, it will throw ResourceNotFound exception (and no map will be returned)
+	 * Fetch the resource identity ({@link IResourceLookup}) for a collection of
+	 * resource IDs from the internal memory cache if possible. Note that we only
+	 * use cached results if deletes are disabled on the server (since it is
+	 * therefore not possible that we have an entry in the cache that has since
+	 * been deleted but the cache doesn't know about the deletion), or if we
+	 * aren't excluding deleted results anyhow.
+	 *
+	 * @param theRequestPartitionId The partition(s) to search
+	 * @param theIdsToResolve       The IDs we should look up. Any IDs that are resolved
+	 *                              will be removed from this list. Any IDs remaining in
+	 *                              the list after calling this method still haven't
+	 *                              been attempted to be resolved.
+	 * @param theMapToPopulate      The results will be populated into this map
 	 */
-	@Override
-	@Nonnull
-	public Map<String, JpaPid> resolveResourcePersistentIds(
-			@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, List<String> theIds) {
-		return resolveResourcePersistentIds(theRequestPartitionId, theResourceType, theIds, false);
+	private void resolveResourceIdentitiesForFhirIdsUsingCache(
+			@Nonnull RequestPartitionId theRequestPartitionId,
+			ResolveIdentityMode theMode,
+			Collection<IIdType> theIdsToResolve,
+			ListMultimap<IIdType, IResourceLookup<JpaPid>> theMapToPopulate) {
+		for (Iterator<IIdType> idIterator = theIdsToResolve.iterator(); idIterator.hasNext(); ) {
+			IIdType nextForcedId = idIterator.next();
+			MemoryCacheService.ForcedIdCacheKey nextKey = new MemoryCacheService.ForcedIdCacheKey(
+					nextForcedId.getResourceType(), nextForcedId.getIdPart(), theRequestPartitionId);
+			if (theMode.isUseCache(myStorageSettings.isDeleteEnabled())) {
+				List<IResourceLookup<JpaPid>> cachedLookups = myMemoryCacheService.getIfPresent(
+						MemoryCacheService.CacheEnum.RESOURCE_LOOKUP_BY_FORCED_ID, nextKey);
+				if (cachedLookups != null && !cachedLookups.isEmpty()) {
+					idIterator.remove();
+					for (IResourceLookup<JpaPid> cachedLookup : cachedLookups) {
+						if (theMode.isIncludeDeleted() || cachedLookup.getDeleted() == null) {
+							theMapToPopulate.put(nextKey.toIdType(myFhirCtx), cachedLookup);
+						}
+					}
+				}
+			}
+		}
+	}
+
+	/**
+	 * Fetch the resource identity ({@link IResourceLookup}) for a collection of
+	 * resource IDs from the database
+	 *
+	 * @param theRequestPartitionId The partition(s) to search
+	 * @param theIdsToResolve       The IDs we should look up
+	 * @param theMapToPopulate      The results will be populated into this map
+	 */
+	private void resolveResourceIdentitiesForFhirIdsUsingDatabase(
+			RequestPartitionId theRequestPartitionId,
+			Collection<IIdType> theIdsToResolve,
+			ListMultimap<IIdType, IResourceLookup<JpaPid>> theMapToPopulate) {
+
+		/*
+		 * If we have more than a threshold of IDs, we need to chunk the execution to
+		 * avoid having too many parameters in one SQL statement
+		 */
+		int maxPageSize = (SearchBuilder.getMaximumPageSize() / 2) - 10;
+		if (theIdsToResolve.size() > maxPageSize) {
+			TaskChunker.chunk(
+					theIdsToResolve,
+					maxPageSize,
+					chunk -> resolveResourceIdentitiesForFhirIdsUsingDatabase(
+							theRequestPartitionId, chunk, theMapToPopulate));
+			return;
+		}
+
+		CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
+		CriteriaQuery<Tuple> criteriaQuery = cb.createTupleQuery();
+		Root<ResourceTable> from = criteriaQuery.from(ResourceTable.class);
+		criteriaQuery.multiselect(
+				from.get("myId"),
+				from.get("myResourceType"),
+				from.get("myFhirId"),
+				from.get("myDeleted"),
+				from.get("myPartitionIdValue"));
+
+		List<Predicate> outerAndPredicates = new ArrayList<>(2);
+		if (!theRequestPartitionId.isAllPartitions()) {
+			getOptionalPartitionPredicate(theRequestPartitionId, cb, from).ifPresent(outerAndPredicates::add);
+		}
+
+		// one create one clause per id.
+		List<Predicate> innerIdPredicates = new ArrayList<>(theIdsToResolve.size());
+		boolean haveUntypedIds = false;
+		for (IIdType next : theIdsToResolve) {
+			if (!next.hasResourceType()) {
+				haveUntypedIds = true;
+			}
+
+			List<Predicate> idPredicates = new ArrayList<>(2);
+
+			if (myStorageSettings.getResourceClientIdStrategy() == JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC
+					&& next.isIdPartValidLong()) {
+				Predicate typeCriteria = cb.equal(from.get("myId"), next.getIdPartAsLong());
+				idPredicates.add(typeCriteria);
+			} else {
+				if (isNotBlank(next.getResourceType())) {
+					Predicate typeCriteria = cb.equal(from.get("myResourceType"), next.getResourceType());
+					idPredicates.add(typeCriteria);
+				}
+				Predicate idCriteria = cb.equal(from.get("myFhirId"), next.getIdPart());
+				idPredicates.add(idCriteria);
+			}
+
+			innerIdPredicates.add(cb.and(idPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
+		}
+		outerAndPredicates.add(cb.or(innerIdPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
+
+		criteriaQuery.where(cb.and(outerAndPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
+		TypedQuery<Tuple> query = myEntityManager.createQuery(criteriaQuery);
+		List<Tuple> results = query.getResultList();
+		for (Tuple nextId : results) {
+			// Check if the nextId has a resource ID. It may have a null resource ID if a commit is still pending.
+			Long resourcePid = nextId.get(0, Long.class);
+			String resourceType = nextId.get(1, String.class);
+			String fhirId = nextId.get(2, String.class);
+			Date deletedAd = nextId.get(3, Date.class);
+			Integer partitionId = nextId.get(4, Integer.class);
+			if (resourcePid != null) {
+				JpaResourceLookup lookup = new JpaResourceLookup(
+						resourceType, resourcePid, deletedAd, PartitionablePartitionId.with(partitionId, null));
+
+				MemoryCacheService.ForcedIdCacheKey nextKey =
+						new MemoryCacheService.ForcedIdCacheKey(resourceType, fhirId, theRequestPartitionId);
+				IIdType id = nextKey.toIdType(myFhirCtx);
+				theMapToPopulate.put(id, lookup);
+
+				if (haveUntypedIds) {
+					id = nextKey.toIdTypeWithoutResourceType(myFhirCtx);
+					theMapToPopulate.put(id, lookup);
+				}
+
+				List<IResourceLookup<JpaPid>> valueToCache = theMapToPopulate.get(id);
+				myMemoryCacheService.putAfterCommit(
+						MemoryCacheService.CacheEnum.RESOURCE_LOOKUP_BY_FORCED_ID, nextKey, valueToCache);
+			}
+		}
 	}
 
 	/**
@@ -208,7 +387,7 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 			@Nonnull RequestPartitionId theRequestPartitionId,
 			String theResourceType,
 			List<String> theIds,
-			boolean theExcludeDeleted) {
+			ResolveIdentityMode theMode) {
 		assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
 		Validate.notNull(theIds, "theIds cannot be null");
 		Validate.isTrue(!theIds.isEmpty(), "theIds must not be empty");
@@ -224,7 +403,7 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 				// is a forced id
 				// we must resolve!
 				if (myStorageSettings.isDeleteEnabled()) {
-					retVal = resolveResourceIdentity(theRequestPartitionId, theResourceType, id, theExcludeDeleted)
+					retVal = resolveResourceIdentity(theRequestPartitionId, theResourceType, id, theMode)
 							.getPersistentId();
 					retVals.put(id, retVal);
 				} else {
@@ -249,18 +428,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		return retVals;
 	}
 
-	/**
-	 * Given a resource type and ID, determines the internal persistent ID for the resource.
-	 *
-	 * @throws ResourceNotFoundException If the ID can not be found
-	 */
-	@Override
-	@Nonnull
-	public JpaPid resolveResourcePersistentIds(
-			@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId) {
-		return resolveResourcePersistentIds(theRequestPartitionId, theResourceType, theId, false);
-	}
-
 	/**
 	 * Given a resource type and ID, determines the internal persistent ID for the resource.
 	 * Optionally filters out deleted resources.
@@ -273,11 +440,11 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 			@Nonnull RequestPartitionId theRequestPartitionId,
 			String theResourceType,
 			String theId,
-			boolean theExcludeDeleted) {
+			ResolveIdentityMode theMode) {
 		Validate.notNull(theId, "theId must not be null");
 
 		Map<String, JpaPid> retVal = resolveResourcePersistentIds(
-				theRequestPartitionId, theResourceType, Collections.singletonList(theId), theExcludeDeleted);
+				theRequestPartitionId, theResourceType, Collections.singletonList(theId), theMode);
 		return retVal.get(theId); // should be only one
 	}
 
@@ -359,11 +526,11 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 
 				idsToCheck.add(nextId);
 			}
-			new QueryChunker<IIdType>()
-					.chunk(
-							idsToCheck,
-							SearchBuilder.getMaximumPageSize() / 2,
-							ids -> doResolvePersistentIds(theRequestPartitionId, ids, retVal));
+			new QueryChunker<IIdType>();
+			TaskChunker.chunk(
+					idsToCheck,
+					SearchBuilder.getMaximumPageSize() / 2,
+					ids -> doResolvePersistentIds(theRequestPartitionId, ids, retVal));
 		}
 
 		return retVal;
@@ -430,18 +597,30 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 			RequestPartitionId theRequestPartitionId, CriteriaBuilder cb, Root<ResourceTable> from) {
 		if (myPartitionSettings.isAllowUnqualifiedCrossPartitionReference()) {
 			return Optional.empty();
-		} else if (theRequestPartitionId.isDefaultPartition() && myPartitionSettings.getDefaultPartitionId() == null) {
-			Predicate partitionIdCriteria = cb.isNull(from.get("myPartitionIdValue"));
-			return Optional.of(partitionIdCriteria);
-		} else if (!theRequestPartitionId.isAllPartitions()) {
+		} else if (theRequestPartitionId.isAllPartitions()) {
+			return Optional.empty();
+		} else {
 			List<Integer> partitionIds = theRequestPartitionId.getPartitionIds();
 			partitionIds = replaceDefaultPartitionIdIfNonNull(myPartitionSettings, partitionIds);
-			if (partitionIds.size() > 1) {
-				Predicate partitionIdCriteria = from.get("myPartitionIdValue").in(partitionIds);
-				return Optional.of(partitionIdCriteria);
-			} else if (partitionIds.size() == 1) {
-				Predicate partitionIdCriteria = cb.equal(from.get("myPartitionIdValue"), partitionIds.get(0));
-				return Optional.of(partitionIdCriteria);
+			if (partitionIds.contains(null)) {
+				Predicate partitionIdNullCriteria =
+						from.get("myPartitionIdValue").isNull();
+				if (partitionIds.size() == 1) {
+					return Optional.of(partitionIdNullCriteria);
+				} else {
+					Predicate partitionIdCriteria = from.get("myPartitionIdValue")
+							.in(partitionIds.stream().filter(t -> t != null).collect(Collectors.toList()));
+					return Optional.of(cb.or(partitionIdCriteria, partitionIdNullCriteria));
+				}
+			} else {
+				if (partitionIds.size() > 1) {
+					Predicate partitionIdCriteria =
+							from.get("myPartitionIdValue").in(partitionIds);
+					return Optional.of(partitionIdCriteria);
+				} else if (partitionIds.size() == 1) {
+					Predicate partitionIdCriteria = cb.equal(from.get("myPartitionIdValue"), partitionIds.get(0));
+					return Optional.of(partitionIdCriteria);
+				}
 			}
 		}
 		return Optional.empty();
@@ -475,6 +654,7 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		return retVal;
 	}
 
+	@SuppressWarnings("OptionalAssignedToNull")
 	@Override
 	public Optional<String> translatePidIdToForcedIdWithCache(JpaPid theId) {
 		// do getIfPresent and then put to avoid doing I/O inside the cache.
@@ -492,112 +672,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		return forcedId;
 	}
 
-	private ListMultimap<String, String> organizeIdsByResourceType(Collection<IIdType> theIds) {
-		ListMultimap<String, String> typeToIds =
-				MultimapBuilder.hashKeys().arrayListValues().build();
-		for (IIdType nextId : theIds) {
-			if (myStorageSettings.getResourceClientIdStrategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY
-					|| !isValidPid(nextId)) {
-				if (nextId.hasResourceType()) {
-					typeToIds.put(nextId.getResourceType(), nextId.getIdPart());
-				} else {
-					typeToIds.put("", nextId.getIdPart());
-				}
-			}
-		}
-		return typeToIds;
-	}
-
-	private Map<String, List<IResourceLookup<JpaPid>>> translateForcedIdToPids(
-			@Nonnull RequestPartitionId theRequestPartitionId, Collection<IIdType> theId, boolean theExcludeDeleted) {
-		theId.forEach(id -> Validate.isTrue(id.hasIdPart()));
-
-		if (theId.isEmpty()) {
-			return new HashMap<>();
-		}
-
-		Map<String, List<IResourceLookup<JpaPid>>> retVal = new HashMap<>();
-		RequestPartitionId requestPartitionId = replaceDefault(theRequestPartitionId);
-
-		if (myStorageSettings.getResourceClientIdStrategy() != JpaStorageSettings.ClientIdStrategyEnum.ANY) {
-			List<Long> pids = theId.stream()
-					.filter(t -> isValidPid(t))
-					.map(IIdType::getIdPartAsLong)
-					.collect(Collectors.toList());
-			if (!pids.isEmpty()) {
-				resolvePids(requestPartitionId, pids, retVal);
-			}
-		}
-
-		// returns a map of resourcetype->id
-		ListMultimap<String, String> typeToIds = organizeIdsByResourceType(theId);
-		for (Map.Entry<String, Collection<String>> nextEntry : typeToIds.asMap().entrySet()) {
-			String nextResourceType = nextEntry.getKey();
-			Collection<String> nextIds = nextEntry.getValue();
-
-			if (!myStorageSettings.isDeleteEnabled()) {
-				for (Iterator<String> forcedIdIterator = nextIds.iterator(); forcedIdIterator.hasNext(); ) {
-					String nextForcedId = forcedIdIterator.next();
-					String nextKey = nextResourceType + "/" + nextForcedId;
-					IResourceLookup<JpaPid> cachedLookup =
-							myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey);
-					if (cachedLookup != null) {
-						forcedIdIterator.remove();
-						retVal.computeIfAbsent(nextForcedId, id -> new ArrayList<>())
-								.add(cachedLookup);
-					}
-				}
-			}
-
-			if (!nextIds.isEmpty()) {
-				Collection<Object[]> views;
-				assert isNotBlank(nextResourceType);
-
-				if (requestPartitionId.isAllPartitions()) {
-					views = myResourceTableDao.findAndResolveByForcedIdWithNoType(
-							nextResourceType, nextIds, theExcludeDeleted);
-				} else {
-					if (requestPartitionId.isDefaultPartition()) {
-						views = myResourceTableDao.findAndResolveByForcedIdWithNoTypeInPartitionNull(
-								nextResourceType, nextIds, theExcludeDeleted);
-					} else if (requestPartitionId.hasDefaultPartitionId()) {
-						views = myResourceTableDao.findAndResolveByForcedIdWithNoTypeInPartitionIdOrNullPartitionId(
-								nextResourceType,
-								nextIds,
-								requestPartitionId.getPartitionIdsWithoutDefault(),
-								theExcludeDeleted);
-					} else {
-						views = myResourceTableDao.findAndResolveByForcedIdWithNoTypeInPartition(
-								nextResourceType, nextIds, requestPartitionId.getPartitionIds(), theExcludeDeleted);
-					}
-				}
-
-				for (Object[] next : views) {
-					String resourceType = (String) next[0];
-					Long resourcePid = (Long) next[1];
-					String forcedId = (String) next[2];
-					Date deletedAt = (Date) next[3];
-					Integer partitionId = (Integer) next[4];
-					LocalDate partitionDate = (LocalDate) next[5];
-
-					JpaResourceLookup lookup = new JpaResourceLookup(
-							resourceType,
-							resourcePid,
-							deletedAt,
-							PartitionablePartitionId.with(partitionId, partitionDate));
-					retVal.computeIfAbsent(forcedId, id -> new ArrayList<>()).add(lookup);
-
-					if (!myStorageSettings.isDeleteEnabled()) {
-						String key = resourceType + "/" + forcedId;
-						myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, key, lookup);
-					}
-				}
-			}
-		}
-
-		return retVal;
-	}
-
 	public RequestPartitionId replaceDefault(RequestPartitionId theRequestPartitionId) {
 		if (myPartitionSettings.getDefaultPartitionId() != null) {
 			if (!theRequestPartitionId.isAllPartitions() && theRequestPartitionId.hasDefaultPartitionId()) {
@@ -610,59 +684,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		return theRequestPartitionId;
 	}
 
-	private void resolvePids(
-			@Nonnull RequestPartitionId theRequestPartitionId,
-			List<Long> thePidsToResolve,
-			Map<String, List<IResourceLookup<JpaPid>>> theTargets) {
-		if (!myStorageSettings.isDeleteEnabled()) {
-			for (Iterator<Long> forcedIdIterator = thePidsToResolve.iterator(); forcedIdIterator.hasNext(); ) {
-				Long nextPid = forcedIdIterator.next();
-				String nextKey = Long.toString(nextPid);
-				IResourceLookup<JpaPid> cachedLookup =
-						myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey);
-				if (cachedLookup != null) {
-					forcedIdIterator.remove();
-					theTargets.computeIfAbsent(nextKey, id -> new ArrayList<>()).add(cachedLookup);
-				}
-			}
-		}
-
-		if (!thePidsToResolve.isEmpty()) {
-			Collection<Object[]> lookup;
-			if (theRequestPartitionId.isAllPartitions()) {
-				lookup = myResourceTableDao.findLookupFieldsByResourcePid(thePidsToResolve);
-			} else {
-				if (theRequestPartitionId.isDefaultPartition()) {
-					lookup = myResourceTableDao.findLookupFieldsByResourcePidInPartitionNull(thePidsToResolve);
-				} else if (theRequestPartitionId.hasDefaultPartitionId()) {
-					lookup = myResourceTableDao.findLookupFieldsByResourcePidInPartitionIdsOrNullPartition(
-							thePidsToResolve, theRequestPartitionId.getPartitionIdsWithoutDefault());
-				} else {
-					lookup = myResourceTableDao.findLookupFieldsByResourcePidInPartitionIds(
-							thePidsToResolve, theRequestPartitionId.getPartitionIds());
-				}
-			}
-			lookup.stream()
-					.map(t -> new JpaResourceLookup(
-							(String) t[0],
-							(Long) t[1],
-							(Date) t[2],
-							PartitionablePartitionId.with((Integer) t[3], (LocalDate) t[4])))
-					.forEach(t -> {
-						String id = t.getPersistentId().toString();
-						if (!theTargets.containsKey(id)) {
-							theTargets.put(id, new ArrayList<>());
-						}
-						theTargets.get(id).add(t);
-						if (!myStorageSettings.isDeleteEnabled()) {
-							String nextKey = t.getPersistentId().toString();
-							myMemoryCacheService.putAfterCommit(
-									MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey, t);
-						}
-					});
-		}
-	}
-
 	@Override
 	public PersistentIdToForcedIdMap<JpaPid> translatePidsToForcedIds(Set<JpaPid> theResourceIds) {
 		assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
@@ -673,7 +694,7 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		List<Long> remainingPids =
 				thePids.stream().filter(t -> !retVal.containsKey(t)).collect(Collectors.toList());
 
-		new QueryChunker<Long>().chunk(remainingPids, t -> {
+		QueryChunker.chunk(remainingPids, t -> {
 			List<ResourceTable> resourceEntities = myResourceTableDao.findAllById(t);
 
 			for (ResourceTable nextResourceEntity : resourceEntities) {
@@ -701,33 +722,39 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 	 * Pre-cache a PID-to-Resource-ID mapping for later retrieval by {@link #translatePidsToForcedIds(Set)} and related methods
 	 */
 	@Override
-	public void addResolvedPidToForcedId(
-			JpaPid theJpaPid,
+	public void addResolvedPidToFhirId(
+			@Nonnull JpaPid theJpaPid,
 			@Nonnull RequestPartitionId theRequestPartitionId,
-			String theResourceType,
-			@Nullable String theForcedId,
+			@Nonnull String theResourceType,
+			@Nonnull String theFhirId,
 			@Nullable Date theDeletedAt) {
-		if (theForcedId != null) {
-			if (theJpaPid.getAssociatedResourceId() == null) {
-				populateAssociatedResourceId(theResourceType, theForcedId, theJpaPid);
-			}
-
-			myMemoryCacheService.putAfterCommit(
-					MemoryCacheService.CacheEnum.PID_TO_FORCED_ID,
-					theJpaPid.getId(),
-					Optional.of(theResourceType + "/" + theForcedId));
-			String key = toForcedIdToPidKey(theRequestPartitionId, theResourceType, theForcedId);
-			myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, theJpaPid);
-		} else {
-			myMemoryCacheService.putAfterCommit(
-					MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theJpaPid.getId(), Optional.empty());
+		if (theJpaPid.getAssociatedResourceId() == null) {
+			populateAssociatedResourceId(theResourceType, theFhirId, theJpaPid);
 		}
 
-		if (!myStorageSettings.isDeleteEnabled()) {
-			JpaResourceLookup lookup = new JpaResourceLookup(
-					theResourceType, theJpaPid.getId(), theDeletedAt, theJpaPid.getPartitionablePartitionId());
-			String nextKey = theJpaPid.toString();
-			myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey, lookup);
+		myMemoryCacheService.putAfterCommit(
+				MemoryCacheService.CacheEnum.PID_TO_FORCED_ID,
+				theJpaPid.getId(),
+				Optional.of(theResourceType + "/" + theFhirId));
+		String key = toForcedIdToPidKey(theRequestPartitionId, theResourceType, theFhirId);
+		myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, theJpaPid);
+
+		JpaResourceLookup lookup = new JpaResourceLookup(
+				theResourceType, theJpaPid.getId(), theDeletedAt, theJpaPid.getPartitionablePartitionId());
+
+		MemoryCacheService.ForcedIdCacheKey fhirIdKey =
+				new MemoryCacheService.ForcedIdCacheKey(theResourceType, theFhirId, theRequestPartitionId);
+		myMemoryCacheService.putAfterCommit(
+				MemoryCacheService.CacheEnum.RESOURCE_LOOKUP_BY_FORCED_ID, fhirIdKey, List.of(lookup));
+
+		// If it's a pure-numeric ID, store it in the cache without a type as well
+		// so that we can resolve it this way when loading entities for update
+		if (myStorageSettings.getResourceClientIdStrategy() == JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC
+				&& isValidLong(theFhirId)) {
+			MemoryCacheService.ForcedIdCacheKey fhirIdKeyWithoutType =
+					new MemoryCacheService.ForcedIdCacheKey(null, theFhirId, theRequestPartitionId);
+			myMemoryCacheService.putAfterCommit(
+					MemoryCacheService.CacheEnum.RESOURCE_LOOKUP_BY_FORCED_ID, fhirIdKeyWithoutType, List.of(lookup));
 		}
 	}
 
@@ -736,19 +763,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		myPartitionSettings = thePartitionSettings;
 	}
 
-	public static boolean isValidPid(IIdType theId) {
-		if (theId == null) {
-			return false;
-		}
-
-		String idPart = theId.getIdPart();
-		return isValidPid(idPart);
-	}
-
-	public static boolean isValidPid(String theIdPart) {
-		return StringUtils.isNumeric(theIdPart);
-	}
-
 	@Override
 	@Nonnull
 	public List<JpaPid> getPidsOrThrowException(
@@ -764,7 +778,11 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		if (resourceId == null) {
 			IIdType id = theResource.getIdElement();
 			try {
-				retVal = resolveResourcePersistentIds(theRequestPartitionId, id.getResourceType(), id.getIdPart());
+				retVal = resolveResourceIdentityPid(
+						theRequestPartitionId,
+						id.getResourceType(),
+						id.getIdPart(),
+						ResolveIdentityMode.includeDeleted().cacheOk());
 			} catch (ResourceNotFoundException e) {
 				retVal = null;
 			}
@@ -836,4 +854,23 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 	public JpaPid newPidFromStringIdAndResourceName(String thePid, String theResourceName) {
 		return JpaPid.fromIdAndResourceType(Long.parseLong(thePid), theResourceName);
 	}
+
+	private IIdType newIdType(String theValue) {
+		IIdType retVal = myFhirCtx.getVersion().newIdType();
+		retVal.setValue(theValue);
+		return retVal;
+	}
+
+	public static boolean isValidPid(IIdType theId) {
+		if (theId == null) {
+			return false;
+		}
+
+		String idPart = theId.getIdPart();
+		return isValidPid(idPart);
+	}
+
+	public static boolean isValidPid(String theIdPart) {
+		return StringUtils.isNumeric(theIdPart);
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java

@@ -267,13 +267,14 @@ public class TermValueSet implements Serializable {
 		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
 				.append("id", myId)
 				.append("url", myUrl)
-				.append(myResource != null ? ("resource=" + myResource.toString()) : ("resource=(null)"))
+				.append("version", myVersion)
 				.append("resourcePid", myResourcePid)
 				.append("name", myName)
-				.append(myConcepts != null ? ("concepts - size=" + myConcepts.size()) : ("concepts=(null)"))
+				.append(myConcepts != null ? ("conceptCount=" + myConcepts.size()) : ("concepts=(null)"))
 				.append("totalConcepts", myTotalConcepts)
 				.append("totalConceptDesignations", myTotalConceptDesignations)
 				.append("expansionStatus", myExpansionStatus)
+				.append(myResource != null ? ("resId=" + myResource) : ("resource=(null)"))
 				.toString();
 	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/model/cross/JpaResourceLookup.java

@@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.model.cross;
 
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+import org.apache.commons.lang3.builder.ToStringStyle;
 
 import java.util.Date;
 
@@ -59,4 +61,14 @@ public class JpaResourceLookup implements IResourceLookup<JpaPid> {
 
 		return jpaPid;
 	}
+
+	@Override
+	public String toString() {
+		return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
+				.append("resType", myResourceType)
+				.append("resPid", myResourcePid)
+				.append("deletedAt", myDeletedAt)
+				.append("partId", myPartitionablePartitionId)
+				.toString();
+	}
 }

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

@@ -36,6 +36,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IDao;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
 import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
 import ca.uhn.fhir.jpa.dao.BaseStorageDao;
@@ -49,6 +50,7 @@ import ca.uhn.fhir.jpa.dao.search.ResourceNotFoundInIndexException;
 import ca.uhn.fhir.jpa.entity.ResourceSearchView;
 import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
@@ -84,6 +86,7 @@ import ca.uhn.fhir.rest.api.SortOrderEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
 import ca.uhn.fhir.rest.param.BaseParamWithPrefix;
 import ca.uhn.fhir.rest.param.DateParam;
 import ca.uhn.fhir.rest.param.DateRangeParam;
@@ -117,6 +120,7 @@ import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -533,10 +537,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
 				throw new InvalidRequestException(Msg.code(2027)
 						+ "LastN operation is not enabled on this service, can not process this request");
 			}
-			return myFulltextSearchSvc.lastN(myParams, theMaximumResults).stream()
-					.map(lastNResourceId -> myIdHelperService.resolveResourcePersistentIds(
-							myRequestPartitionId, myResourceName, String.valueOf(lastNResourceId)))
-					.collect(Collectors.toList());
+			List<IResourcePersistentId> persistentIds = myFulltextSearchSvc.lastN(myParams, theMaximumResults);
+			return persistentIds.stream().map(t -> (JpaPid) t).collect(Collectors.toList());
 		} else {
 			throw new InvalidRequestException(
 					Msg.code(2033) + "LastN operation is not enabled on this service, can not process this request");
@@ -557,7 +559,13 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
 				idParamValue = idParm.getValue();
 			}
 
-			pid = myIdHelperService.resolveResourcePersistentIds(myRequestPartitionId, myResourceName, idParamValue);
+			pid = myIdHelperService
+					.resolveResourceIdentity(
+							myRequestPartitionId,
+							myResourceName,
+							idParamValue,
+							ResolveIdentityMode.includeDeleted().cacheOk())
+					.getPersistentId();
 		}
 		return myFulltextSearchSvc.everything(myResourceName, myParams, pid, theRequestDetails);
 	}
@@ -579,37 +587,46 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
 
 	/**
 	 * Combs through the params for any _id parameters and extracts the PIDs for them
-	 *
-	 * @param theTargetPids
 	 */
 	private void extractTargetPidsFromIdParams(Set<Long> theTargetPids) {
 		// get all the IQueryParameterType objects
 		// for _id -> these should all be StringParam values
-		HashSet<String> ids = new HashSet<>();
+		HashSet<IIdType> ids = new HashSet<>();
 		List<List<IQueryParameterType>> params = myParams.get(IAnyResource.SP_RES_ID);
 		for (List<IQueryParameterType> paramList : params) {
 			for (IQueryParameterType param : paramList) {
+				String id;
 				if (param instanceof StringParam) {
 					// we expect all _id values to be StringParams
-					ids.add(((StringParam) param).getValue());
+					id = ((StringParam) param).getValue();
 				} else if (param instanceof TokenParam) {
-					ids.add(((TokenParam) param).getValue());
+					id = ((TokenParam) param).getValue();
 				} else {
 					// we do not expect the _id parameter to be a non-string value
 					throw new IllegalArgumentException(
 							Msg.code(1193) + "_id parameter must be a StringParam or TokenParam");
 				}
+
+				IIdType idType = myContext.getVersion().newIdType();
+				if (id.contains("/")) {
+					idType.setValue(id);
+				} else {
+					idType.setValue(myResourceName + "/" + id);
+				}
+				ids.add(idType);
 			}
 		}
 
 		// fetch our target Pids
 		// this will throw if an id is not found
-		Map<String, JpaPid> idToPid = myIdHelperService.resolveResourcePersistentIds(
-				myRequestPartitionId, myResourceName, new ArrayList<>(ids));
+		Map<IIdType, IResourceLookup<JpaPid>> idToIdentity = myIdHelperService.resolveResourceIdentities(
+				myRequestPartitionId,
+				new ArrayList<>(ids),
+				ResolveIdentityMode.failOnDeleted().noCacheUnlessDeletesDisabled());
 
 		// add the pids to targetPids
-		for (JpaPid pid : idToPid.values()) {
-			theTargetPids.add(pid.getId());
+		for (IResourceLookup pid : idToIdentity.values()) {
+			theTargetPids.add((Long) pid.getPersistentId().getId());
 		}
 	}
 

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

@@ -21,24 +21,27 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
 
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
+import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
 import ca.uhn.fhir.jpa.util.QueryParameterUtils;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.TokenParamModifier;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import com.healthmarketscience.sqlbuilder.Condition;
 import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
 import jakarta.annotation.Nullable;
-import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.HashSet;
+import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
@@ -68,9 +71,8 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
 		Set<JpaPid> allOrPids = null;
 		SearchFilterParser.CompareOperation defaultOperation = SearchFilterParser.CompareOperation.eq;
 
-		boolean allIdsAreForcedIds = true;
 		for (List<? extends IQueryParameterType> nextValue : theValues) {
-			Set<JpaPid> orPids = new HashSet<>();
+			Set<IIdType> ids = new LinkedHashSet<>();
 			boolean haveValue = false;
 			for (IQueryParameterType next : nextValue) {
 				String value = next.getValueAsQueryToken(getFhirContext());
@@ -78,21 +80,14 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
 					value = value.substring(1);
 				}
 
-				IdType valueAsId = new IdType(value);
 				if (isNotBlank(value)) {
-					if (!myIdHelperService.idRequiresForcedId(valueAsId.getIdPart()) && allIdsAreForcedIds) {
-						allIdsAreForcedIds = false;
-					}
 					haveValue = true;
-					try {
-						boolean excludeDeleted = true;
-						JpaPid pid = myIdHelperService.resolveResourcePersistentIds(
-								theRequestPartitionId, theResourceName, valueAsId.getIdPart(), excludeDeleted);
-						orPids.add(pid);
-					} catch (ResourceNotFoundException e) {
-						// This is not an error in a search, it just results in no matches
-						ourLog.debug("Resource ID {} was requested but does not exist", valueAsId.getIdPart());
+					if (!value.contains("/")) {
+						value = theResourceName + "/" + value;
 					}
+					IIdType id = getFhirContext().getVersion().newIdType();
+					id.setValue(value);
+					ids.add(id);
 				}
 
 				if (next instanceof TokenParam) {
@@ -101,6 +96,20 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
 					}
 				}
 			}
+
+			Set<JpaPid> orPids = new HashSet<>();
+
+			// We're joining this to a query that will explicitly ask for non-deleted,
+			// so we really only want the PID and can safely cache (even if a previously
+			// deleted status was cached, since it might now be undeleted)
+			Map<IIdType, IResourceLookup<JpaPid>> resolvedPids = myIdHelperService.resolveResourceIdentities(
+					theRequestPartitionId,
+					ids,
+					ResolveIdentityMode.includeDeleted().cacheOk());
+			for (IResourceLookup<JpaPid> lookup : resolvedPids.values()) {
+				orPids.add(lookup.getPersistentId());
+			}
+
 			if (haveValue) {
 				if (allOrPids == null) {
 					allOrPids = orPids;
@@ -122,17 +131,19 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
 
 			List<Long> resourceIds = JpaPid.toLongList(allOrPids);
 			if (theSourceJoinColumn == null) {
-				BaseJoiningPredicateBuilder queryRootTable = super.getOrCreateQueryRootTable(!allIdsAreForcedIds);
+				BaseJoiningPredicateBuilder queryRootTable = super.getOrCreateQueryRootTable(true);
 				Condition predicate;
 				switch (operation) {
 					default:
 					case eq:
 						predicate = queryRootTable.createPredicateResourceIds(false, resourceIds);
-						return queryRootTable.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
+						break;
 					case ne:
 						predicate = queryRootTable.createPredicateResourceIds(true, resourceIds);
-						return queryRootTable.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
+						break;
 				}
+				predicate = queryRootTable.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
+				return predicate;
 			} else {
 				DbColumn resIdColumn = getResourceIdColumn(theSourceJoinColumn);
 				return QueryParameterUtils.toEqualToOrInPredicate(

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
@@ -382,8 +383,11 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		// Note that this creates the TermCodeSystem and TermCodeSystemVersion entities if needed
 		IIdType csId = myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(theCodeSystemResource, theRequest);
 
-		JpaPid codeSystemResourcePid = myIdHelperService.resolveResourcePersistentIds(
-				RequestPartitionId.allPartitions(), csId.getResourceType(), csId.getIdPart());
+		JpaPid codeSystemResourcePid = myIdHelperService.resolveResourceIdentityPid(
+				RequestPartitionId.allPartitions(),
+				csId.getResourceType(),
+				csId.getIdPart(),
+				ResolveIdentityMode.includeDeleted().cacheOk());
 		ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid.getId());
 
 		ourLog.info("CodeSystem resource has ID: {}", csId.getValue());

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

@@ -34,6 +34,7 @@ import ca.uhn.fhir.jpa.api.dao.IDao;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
 import ca.uhn.fhir.jpa.config.util.ConnectionPoolInfoProvider;
 import ca.uhn.fhir.jpa.config.util.IConnectionPoolInfoProvider;
@@ -470,7 +471,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 		myCodeSystemCurrentVersionCache.invalidateAll();
 	}
 
-	public void deleteValueSetForResource(ResourceTable theResourceTable) {
+	public Optional<TermValueSet> deleteValueSetForResource(ResourceTable theResourceTable) {
 		// Get existing entity so it can be deleted.
 		Optional<TermValueSet> optionalExistingTermValueSetById =
 				myTermValueSetDao.findByResourcePid(theResourceTable.getId());
@@ -481,8 +482,19 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			ourLog.info("Deleting existing TermValueSet[{}] and its children...", existingTermValueSet.getId());
 			deletePreCalculatedValueSetContents(existingTermValueSet);
 			myTermValueSetDao.deleteById(existingTermValueSet.getId());
+
+			/*
+			 * If we're updating an existing ValueSet within a transaction, we need to make
+			 * sure to manually flush now since otherwise we'll try to create a new
+			 * TermValueSet entity and fail with a constraint error on the URL, since
+			 * this one won't be deleted yet
+			 */
+			myTermValueSetDao.flush();
+
 			ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
 		}
+
+		return optionalExistingTermValueSetById;
 	}
 
 	private void deletePreCalculatedValueSetContents(TermValueSet theValueSet) {
@@ -2081,10 +2093,11 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 	}
 
 	private JpaPid getValueSetResourcePersistentId(ValueSet theValueSet) {
-		return myIdHelperService.resolveResourcePersistentIds(
+		return myIdHelperService.resolveResourceIdentityPid(
 				RequestPartitionId.allPartitions(),
 				theValueSet.getIdElement().getResourceType(),
-				theValueSet.getIdElement().getIdPart());
+				theValueSet.getIdElement().getIdPart(),
+				ResolveIdentityMode.includeDeleted().cacheOk());
 	}
 
 	protected IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(
@@ -2527,6 +2540,13 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 	@Override
 	@Transactional
 	public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {
+		// If we're in a transaction, we need to flush now so that we can correctly detect
+		// duplicates if there are multiple ValueSets in the same TX with the same URL
+		// (which is an error, but we need to catch it). It'd be better to catch this by
+		// inspecting the URLs in the bundle or something, since flushing hurts performance
+		// but it's not expected that loading valuesets is going to be a huge high frequency
+		// thing so it probably doesn't matter
+		myEntityManager.flush();
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
 		if (isPlaceholder(theValueSet)) {
@@ -2552,7 +2572,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 		termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);
 
 		// Delete version being replaced
-		deleteValueSetForResource(theResourceTable);
+		Optional<TermValueSet> deletedTrmValueSet = deleteValueSetForResource(theResourceTable);
 
 		/*
 		 * Do the upload.
@@ -2560,11 +2580,17 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 		String url = termValueSet.getUrl();
 		String version = termValueSet.getVersion();
 		Optional<TermValueSet> optionalExistingTermValueSetByUrl;
-		if (version != null) {
-			optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndVersion(url, version);
+
+		if (deletedTrmValueSet.isPresent()
+				&& Objects.equals(deletedTrmValueSet.get().getUrl(), url)
+				&& Objects.equals(deletedTrmValueSet.get().getVersion(), version)) {
+			// If we just deleted the valueset marker, we don't need to check if it exists
+			// in the database
+			optionalExistingTermValueSetByUrl = Optional.empty();
 		} else {
-			optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(url);
+			optionalExistingTermValueSetByUrl = getTermValueSet(version, url);
 		}
+
 		if (optionalExistingTermValueSetByUrl.isEmpty()) {
 
 			myTermValueSetDao.save(termValueSet);
@@ -2602,6 +2628,16 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 		}
 	}
 
+	private Optional<TermValueSet> getTermValueSet(String version, String url) {
+		Optional<TermValueSet> optionalExistingTermValueSetByUrl;
+		if (version != null) {
+			optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndVersion(url, version);
+		} else {
+			optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(url);
+		}
+		return optionalExistingTermValueSetByUrl;
+	}
+
 	@Override
 	@Transactional
 	public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/QueryChunker.java

@@ -35,11 +35,11 @@ import java.util.stream.Stream;
  */
 public class QueryChunker<T> extends TaskChunker<T> {
 
-	public void chunk(Collection<T> theInput, Consumer<List<T>> theBatchConsumer) {
+	public static <T> void chunk(Collection<T> theInput, Consumer<List<T>> theBatchConsumer) {
 		chunk(theInput, SearchBuilder.getMaximumPageSize(), theBatchConsumer);
 	}
 
-	public Stream<List<T>> chunk(Stream<T> theStream) {
+	public static <T> Stream<List<T>> chunk(Stream<T> theStream) {
 		return chunk(theStream, SearchBuilder.getMaximumPageSize());
 	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/index/IdHelperServiceTest.java

@@ -3,36 +3,39 @@ package ca.uhn.fhir.jpa.dao.index;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import jakarta.persistence.EntityManager;
-import jakarta.persistence.Tuple;
-import jakarta.persistence.criteria.Path;
-import jakarta.persistence.criteria.Root;
+import jakarta.persistence.TypedQuery;
+import jakarta.persistence.criteria.CriteriaQuery;
+import org.hibernate.sql.results.internal.TupleImpl;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
-import org.mockito.ArgumentMatchers;
+import org.mockito.Answers;
 import org.mockito.InjectMocks;
 import org.mockito.Mock;
 import org.mockito.Spy;
 import org.mockito.junit.jupiter.MockitoExtension;
 
+import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
+import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.lenient;
-import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -40,7 +43,6 @@ import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.mockito.Mockito.eq;
 import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
 
 @ExtendWith(MockitoExtension.class)
 public class IdHelperServiceTest {
@@ -60,29 +62,33 @@ public class IdHelperServiceTest {
     @Mock
     private MemoryCacheService myMemoryCacheService;
 
-    @Mock
+    @Mock(answer = Answers.RETURNS_DEEP_STUBS)
     private EntityManager myEntityManager;
 
     @Mock
     private PartitionSettings myPartitionSettings;
 
-    @BeforeEach
+	@Mock
+	private TypedQuery myTypedQuery;
+
+	@BeforeEach
     void setUp() {
         myHelperSvc.setDontCheckActiveTransactionForUnitTest(true);
 
 		// lenient because some tests require this setup, and others do not
 		lenient().doReturn(true).when(myStorageSettings).isDeleteEnabled();
-		lenient().doReturn(JpaStorageSettings.ClientIdStrategyEnum.ANY).when(myStorageSettings).getResourceClientIdStrategy();
     }
 
     @Test
     public void testResolveResourcePersistentIds() {
+		lenient().doReturn(JpaStorageSettings.ClientIdStrategyEnum.ANY).when(myStorageSettings).getResourceClientIdStrategy();
+
         //prepare params
         RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionIdAndName(1, "Partition-A");
         String resourceType = "Patient";
         Long id = 123L;
         List<String> ids = List.of(String.valueOf(id));
-        boolean theExcludeDeleted = false;
+        ResolveIdentityMode mode = ResolveIdentityMode.includeDeleted().noCacheUnlessDeletesDisabled();
 
         //prepare results
         Patient expectedPatient = new Patient();
@@ -91,19 +97,21 @@ public class IdHelperServiceTest {
         // configure mock behaviour
 		when(myStorageSettings.isDeleteEnabled()).thenReturn(true);
 
-		final ResourceNotFoundException resourceNotFoundException = assertThrows(ResourceNotFoundException.class, () -> myHelperSvc.resolveResourcePersistentIds(requestPartitionId, resourceType, ids, theExcludeDeleted));
+		final ResourceNotFoundException resourceNotFoundException = assertThrows(ResourceNotFoundException.class, () -> myHelperSvc.resolveResourcePersistentIds(requestPartitionId, resourceType, ids, mode));
 		assertEquals("HAPI-2001: Resource Patient/123 is not known", resourceNotFoundException.getMessage());
     }
 
     @Test
     public void testResolveResourcePersistentIdsDeleteFalse() {
+		lenient().doReturn(JpaStorageSettings.ClientIdStrategyEnum.ANY).when(myStorageSettings).getResourceClientIdStrategy();
+
         //prepare Params
         RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionIdAndName(1, "Partition-A");
         Long id = 123L;
         String resourceType = "Patient";
         List<String> ids = List.of(String.valueOf(id));
         String forcedId = "(all)/" + resourceType + "/" + id;
-        boolean theExcludeDeleted = false;
+        ResolveIdentityMode mode = ResolveIdentityMode.includeDeleted().noCacheUnlessDeletesDisabled();
 
         //prepare results
         Patient expectedPatient = new Patient();
@@ -112,7 +120,7 @@ public class IdHelperServiceTest {
         // configure mock behaviour
         when(myStorageSettings.isDeleteEnabled()).thenReturn(false);
 
-		Map<String, JpaPid> actualIds = myHelperSvc.resolveResourcePersistentIds(requestPartitionId, resourceType, ids, theExcludeDeleted);
+		Map<String, JpaPid> actualIds = myHelperSvc.resolveResourcePersistentIds(requestPartitionId, resourceType, ids, mode);
 
 		//verifyResult
 		assertFalse(actualIds.isEmpty());
@@ -120,20 +128,35 @@ public class IdHelperServiceTest {
     }
 
 
-    private Root<ResourceTable> getMockedFrom() {
-        @SuppressWarnings("unchecked")
-        Path<Object> path = mock(Path.class);
-        @SuppressWarnings("unchecked")
-        Root<ResourceTable> from = mock(Root.class);
-        when(from.get(ArgumentMatchers.<String>any())).thenReturn(path);
-        return from;
-    }
 
-    private List<Tuple> getMockedTupleList(Long idNumber, String resourceType, String id) {
-        Tuple tuple = mock(Tuple.class);
-        when(tuple.get(eq(0), eq(Long.class))).thenReturn(idNumber);
-        when(tuple.get(eq(1), eq(String.class))).thenReturn(resourceType);
-        when(tuple.get(eq(2), eq(String.class))).thenReturn(id);
-        return List.of(tuple);
-    }
+
+
+	@Test
+	public void testResolveResourceIdentity_defaultFunctionality(){
+		lenient().doReturn(JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC).when(myStorageSettings).getResourceClientIdStrategy();
+
+		RequestPartitionId partitionId = RequestPartitionId.fromPartitionIdAndName(1, "partition");
+		String resourceType = "Patient";
+		String resourceForcedId = "AAA";
+
+		Object[] tuple = new Object[] {
+			1L,
+			"Patient",
+			"AAA",
+			new Date(),
+			null
+		};
+
+		when(myEntityManager.createQuery(any(CriteriaQuery.class))).thenReturn(myTypedQuery);
+		when(myTypedQuery.getResultList()).thenReturn(List.of(
+			new TupleImpl(null, tuple)
+		));
+
+		IResourceLookup<JpaPid> result = myHelperSvc.resolveResourceIdentity(partitionId, resourceType, resourceForcedId, ResolveIdentityMode.includeDeleted().noCacheUnlessDeletesDisabled());
+		assertEquals(tuple[0], result.getPersistentId().getId());
+		assertEquals(tuple[1], result.getResourceType());
+		assertEquals(tuple[3], result.getDeleted());
+	}
+
+
 }

hapi-fhir-jpaserver-elastic-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseR4SearchLastN.java

@@ -72,7 +72,7 @@ abstract public class BaseR4SearchLastN extends BaseJpaTest {
 	protected static IIdType patient2Id = null;
 	// Using static variables including the flag below so that we can initalize the database and indexes once
 	// (all of the tests only read from the DB and indexes and so no need to re-initialze them for each test).
-	private static Calendar observationDate = new GregorianCalendar();
+	private static final Calendar observationDate = new GregorianCalendar();
 	protected final String observationCd0 = "code0";
 	protected final String observationCd1 = "code1";
 	protected final String observationCd2 = "code2";
@@ -120,9 +120,10 @@ abstract public class BaseR4SearchLastN extends BaseJpaTest {
 		// enabled to also create extended lucene index during creation of test data
 		boolean hsearchSaved = myStorageSettings.isAdvancedHSearchIndexing();
 		myStorageSettings.setAdvancedHSearchIndexing(true);
+		myStorageSettings.setDeleteEnabled(false);
 
 		// Using a static flag to ensure that test data and elasticsearch index is only created once.
-		// Creating this data and the index is time consuming and as such want to avoid having to repeat for each test.
+		// Creating this data and the index is time-consuming and as such want to avoid having to repeat for each test.
 		// Normally would use a static @BeforeClass method for this purpose, but Autowired objects cannot be accessed in static methods.
 
 		Patient pt = new Patient();

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java

@@ -120,9 +120,10 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
 
 		ourLog.info("Queries:\n * " + String.join("\n * ", queries));
 
+		// 1 query to resolve the subject PIDs
 		// 3 queries to actually perform the search
 		// 1 query to lookup up Search from cache, and 2 chunked queries to retrieve resources by PID.
-		assertThat(queries).hasSize(6);
+		assertThat(queries).hasSize(7);
 
 		// The first chunked query should have a full complement of PIDs
 		StringBuilder firstQueryPattern = new StringBuilder(".*RES_ID in \\('[0-9]+'");
@@ -130,7 +131,7 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
 			firstQueryPattern.append(",'[0-9]+'");
 		}
 		firstQueryPattern.append("\\).*");
-		assertThat(queries.get(4)).matches(firstQueryPattern.toString());
+		assertThat(queries.get(5)).matches(firstQueryPattern.toString());
 
 		// the second chunked query should be padded with "-1".
 		StringBuilder secondQueryPattern = new StringBuilder(".*RES_ID in \\('[0-9]+'");
@@ -141,7 +142,7 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
 			secondQueryPattern.append(",'-1'");
 		}
 		secondQueryPattern.append("\\).*");
-		assertThat(queries.get(5)).matches(secondQueryPattern.toString());
+		assertThat(queries.get(6)).matches(secondQueryPattern.toString());
 
 	}
 

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java

@@ -79,6 +79,10 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
 		// Set chunk size to 50
 		SearchBuilder.setMaxPageSizeForTest(50);
 
+		// Run once to fill caches
+		toUnqualifiedVersionlessIdValues(myObservationDao.observationsLastN(params, mockSrd(), null));
+
+		// Actually test
 		myCaptureQueriesListener.clear();
 		List<String> results = toUnqualifiedVersionlessIdValues(myObservationDao.observationsLastN(params, mockSrd(), null));
 		assertThat(results).hasSize(75);

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4ElasticsearchIT.java

@@ -277,8 +277,7 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest implements I
 		myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(codeSystem, codeSystemVersion,
 			new SystemRequestDetails(), Collections.singletonList(valueSet), Collections.emptyList());
 
-//		myTerminologyDeferredStorageSvc.saveAllDeferred();
-		await().atMost(10, SECONDS).until(() -> {
+		await().atMost(20, SECONDS).until(() -> {
 			myTerminologyDeferredStorageSvc.saveDeferred();
 			return myTerminologyDeferredStorageSvc.isStorageQueueEmpty(true);
 		});

hapi-fhir-jpaserver-hfql/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-ips/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java

@@ -53,7 +53,7 @@ import java.util.Date;
 import java.util.List;
 import java.util.Optional;
 
-public class MdmLinkDaoSvc<P extends IResourcePersistentId, M extends IMdmLink<P>> {
+public class MdmLinkDaoSvc<P extends IResourcePersistentId<?>, M extends IMdmLink<P>> {
 
 	private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
 

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
 import ca.uhn.fhir.mdm.api.IGoldenResourceMergerSvc;
 import ca.uhn.fhir.mdm.api.IMdmLink;
@@ -235,10 +236,11 @@ public class GoldenResourceMergerSvcImpl implements IGoldenResourceMergerSvc {
 		List<? extends IMdmLink> toLinks = myMdmLinkDaoSvc.findMdmLinksByGoldenResource(theToResource);
 		List<IMdmLink> toDelete = new ArrayList<>();
 
-		IResourcePersistentId goldenResourcePid = myIdHelperService.resolveResourcePersistentIds(
+		IResourcePersistentId goldenResourcePid = myIdHelperService.resolveResourceIdentityPid(
 				getPartitionIdForResource(theToResource),
 				theToResource.getIdElement().getResourceType(),
-				theToResource.getIdElement().getIdPart());
+				theToResource.getIdElement().getIdPart(),
+				ResolveIdentityMode.includeDeleted().cacheOk());
 
 		// reassign links:
 		// to <- from

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

@@ -44,7 +44,7 @@ import java.util.Set;
 import java.util.stream.Collectors;
 
 @Service
-public class FindCandidateByExampleSvc<P extends IResourcePersistentId> extends BaseCandidateFinder {
+public class FindCandidateByExampleSvc<P extends IResourcePersistentId<?>> extends BaseCandidateFinder {
 	private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
 
 	@Autowired

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

@@ -7,7 +7,10 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
 import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
+import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
+import ca.uhn.fhir.jpa.model.cross.JpaResourceLookup;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
+import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
 import ca.uhn.fhir.mdm.api.IMdmLinkQuerySvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
@@ -24,6 +27,7 @@ import ca.uhn.fhir.mdm.util.MdmResourceUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -127,7 +131,7 @@ public class MdmSurvivorshipSvcImplTest {
 
 		List<IBaseResource> resources = new ArrayList<>();
 		List<MdmLinkJson> links = new ArrayList<>();
-		Map<String, IResourcePersistentId> sourceIdToPid = new HashMap<>();
+		Map<IIdType, IResourceLookup<JpaPid>> sourceIdToPid = new HashMap<>();
 		for (int i = 0; i < 10; i++) {
 			// we want our resources to be slightly different
 			Patient patient = new Patient();
@@ -152,7 +156,7 @@ public class MdmSurvivorshipSvcImplTest {
 			link.setSourceId(patient.getId());
 			link.setGoldenResourceId(goldenPatient.getId());
 			links.add(link);
-			sourceIdToPid.put(patient.getId(), link.getSourcePid());
+			sourceIdToPid.put(patient.getIdElement(), new JpaResourceLookup("Patient", (Long) link.getSourcePid().getId(), null, new PartitionablePartitionId()));
 		}
 
 		IFhirResourceDao resourceDao = mock(IFhirResourceDao.class);
@@ -176,7 +180,7 @@ public class MdmSurvivorshipSvcImplTest {
 		when(myMdmSettings.getMdmRules())
 			.thenReturn(new MdmRulesJson());
 		doReturn(sourceIdToPid).when(myIIdHelperService)
-			.resolveResourcePersistentIds(any(RequestPartitionId.class), anyString(), any(List.class));
+			.resolveResourceIdentities(any(RequestPartitionId.class), any(List.class), any());
 		// we will return a non-empty list to reduce mocking
 		when(myEIDHelper.getExternalEid(any()))
 			.thenReturn(Collections.singletonList(new CanonicalEID("example", "value", "use")));
@@ -199,14 +203,14 @@ public class MdmSurvivorshipSvcImplTest {
 		verify(resourceDao)
 			.update(eq(goldenPatientRebuilt), any(RequestDetails.class));
 
-		ArgumentCaptor<List<String>> idsCaptor = ArgumentCaptor.forClass(List.class);
-		verify(myIIdHelperService).resolveResourcePersistentIds(any(RequestPartitionId.class), anyString(), idsCaptor.capture());
+		ArgumentCaptor<List<IIdType>> idsCaptor = ArgumentCaptor.forClass(List.class);
+		verify(myIIdHelperService).resolveResourceIdentities(any(RequestPartitionId.class), idsCaptor.capture(), any());
 		assertNotNull(idsCaptor.getValue());
 		assertFalse(idsCaptor.getValue().isEmpty());
-		for (String id : idsCaptor.getValue()) {
-			assertFalse(id.contains("/"));
-			assertFalse(id.contains("Patient"));
-		}
+		List<String> ids = idsCaptor.getValue().stream().map(IIdType::getValue).toList();
+
+		List<String> expectedIds = resources.stream().map(t -> t.getIdElement().toUnqualifiedVersionless().getValue()).toList();
+		assertThat(ids).asList().containsExactlyInAnyOrder(expectedIds.toArray());
 	}
 
 	private MdmTransactionContext createTransactionContext() {

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/mdm/batch2/clear/MdmClearStepTest.java

@@ -103,7 +103,7 @@ class MdmClearStepTest extends BaseMdmR4Test {
 			assertPatientExists(myGoldenId);
 			fail("Resource cannot be found");
 		} catch (ResourceNotFoundException e) {
-			assertEquals("HAPI-2001: Resource " + myGoldenId + " is not known", e.getMessage());
+			assertEquals("HAPI-1996: Resource " + myGoldenId + " is not known", e.getMessage());
 		}
 	}
 

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTable.java

@@ -334,6 +334,8 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	}
 
 	public void setTransientForcedId(String theTransientForcedId) {
+		assert theTransientForcedId == null || !theTransientForcedId.contains("/")
+				: "Invalid FHIR ID: " + theTransientForcedId;
 		myTransientForcedId = theTransientForcedId;
 	}
 }

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java

@@ -383,9 +383,6 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 	@Transient
 	private transient ResourceHistoryTable myCurrentVersionEntity;
 
-	@Transient
-	private transient ResourceHistoryTable myNewVersionEntity;
-
 	@Transient
 	private transient boolean myVersionUpdatedInCurrentTransaction;
 
@@ -836,16 +833,8 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 	 * multiple {@link ResourceHistoryTable} entities will result in a constraint error.
 	 */
 	public ResourceHistoryTable toHistory(boolean theCreateVersionTags) {
-		boolean createVersionTags = theCreateVersionTags;
 
-		ResourceHistoryTable retVal = myNewVersionEntity;
-		if (retVal == null) {
-			retVal = new ResourceHistoryTable();
-			myNewVersionEntity = retVal;
-		} else {
-			// Tags should already be set
-			createVersionTags = false;
-		}
+		ResourceHistoryTable retVal = new ResourceHistoryTable();
 
 		retVal.setResourceId(myId);
 		retVal.setResourceType(myResourceType);
@@ -855,12 +844,20 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
 		retVal.setPartitionId(getPartitionId());
 
 		retVal.setHasTags(isHasTags());
-		if (isHasTags() && createVersionTags) {
+		if (isHasTags() && theCreateVersionTags) {
 			for (ResourceTag next : getTags()) {
 				retVal.addTag(next);
 			}
 		}
 
+		// If we've deleted and updated the same resource in the same transaction,
+		// we need to actually create 2 distinct versions
+		if (getCurrentVersionEntity() != null
+				&& getCurrentVersionEntity().getId() != null
+				&& getVersion() == getCurrentVersionEntity().getVersion()) {
+			myVersion++;
+		}
+
 		populateHistoryEntityVersionAndDates(retVal);
 
 		return retVal;

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-dstu2/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -1,10 +1,5 @@
 package ca.uhn.fhir.jpa.dao.dstu2;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-import static org.junit.jupiter.api.Assertions.assertFalse;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
@@ -84,6 +79,8 @@ import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -95,7 +92,11 @@ import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.assertj.core.api.Assertions.assertThat;
-import static org.junit.jupiter.api.Assertions.fail;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 
 
@@ -439,37 +440,20 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		}
 	}
 
-	@Test
-	public void testCreateWithIllegalReference() {
+	@ParameterizedTest
+	@ValueSource(booleans = {true, false})
+	public void testCreateWithIllegalReference_WrongTypeForId(boolean theClientAssignedId) {
+		IIdType id1;
+
 		Observation o1 = new Observation();
 		o1.getCode().addCoding().setSystem("foo").setCode("testChoiceParam01");
-		IIdType id1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
-
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReference(id1);
-			myPatientDao.create(p, mySrd);
-			fail("");
-		} catch (UnprocessableEntityException e) {
-			assertEquals(Msg.code(931) + "Invalid reference found at path 'Patient.managingOrganization'. Resource type 'Observation' is not valid for this path", e.getMessage());
+		if (theClientAssignedId) {
+			o1.setId("A");
+			id1 = myObservationDao.update(o1, mySrd).getId().toUnqualifiedVersionless();
+		} else {
+			id1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
 		}
 
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReference(new IdDt("Organization", id1.getIdPart()));
-			myPatientDao.create(p, mySrd);
-			fail("");
-		} catch (UnprocessableEntityException e) {
-			assertEquals(Msg.code(1095) + "Resource contains reference to unknown resource ID Organization/" + id1.getIdPart(), e.getMessage());
-		}
-
-		// Now with a forced ID
-
-		o1 = new Observation();
-		o1.setId("testCreateWithIllegalReference");
-		o1.getCode().addCoding().setSystem("foo").setCode("testChoiceParam01");
-		id1 = myObservationDao.update(o1, mySrd).getId().toUnqualifiedVersionless();
-
 		try {
 			Patient p = new Patient();
 			p.getManagingOrganization().setReference(id1);
@@ -485,9 +469,8 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 			myPatientDao.create(p, mySrd);
 			fail("");
 		} catch (InvalidRequestException e) {
-			assertEquals(Msg.code(1094) + "Resource Organization/testCreateWithIllegalReference not found, specified in path: Patient.managingOrganization", e.getMessage());
+			assertEquals(Msg.code(1094) + "Resource Organization/" + id1.getIdPart() + " not found, specified in path: Patient.managingOrganization", e.getMessage());
 		}
-
 	}
 
 	@Test
@@ -677,8 +660,8 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 	}
 
 	/**
-	 * See #773
-	 */
+     * See #773
+     */
 	@Test
 	public void testDeleteResourceWithOutboundDeletedResources() {
 		myStorageSettings.setEnforceReferentialIntegrityOnDelete(false);
@@ -1387,8 +1370,8 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 	}
 
 	/**
-	 * See #196
-	 */
+     * See #196
+     */
 	@Test
 	public void testInvalidChainNames() {
 		ReferenceParam param = null;
@@ -1678,46 +1661,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
-	@Test
-	public void testReadInvalidVersion() throws Exception {
-		String methodName = "testReadInvalidVersion";
-
-		Patient pat = new Patient();
-		pat.addIdentifier().setSystem("urn:system").setValue(methodName);
-		IIdType id = myPatientDao.create(pat, mySrd).getId();
-
-		assertEquals(methodName, myPatientDao.read(id, mySrd).getIdentifier().get(0).getValue());
-
-		try {
-			myPatientDao.read(id.withVersion("0"), mySrd);
-			fail("");
-		} catch (ResourceNotFoundException e) {
-			assertEquals(Msg.code(979) + "Version \"0\" is not valid for resource Patient/" + id.getIdPart(), e.getMessage());
-		}
-
-		try {
-			myPatientDao.read(id.withVersion("2"), mySrd);
-			fail("");
-		} catch (ResourceNotFoundException e) {
-			assertEquals(Msg.code(979) + "Version \"2\" is not valid for resource Patient/" + id.getIdPart(), e.getMessage());
-		}
-
-		try {
-			myPatientDao.read(id.withVersion("H"), mySrd);
-			fail("");
-		} catch (ResourceNotFoundException e) {
-			assertEquals(Msg.code(978) + "Version \"H\" is not valid for resource Patient/" + id.getIdPart(), e.getMessage());
-		}
-
-		try {
-			myPatientDao.read(new IdDt("Patient/9999999999999/_history/1"), mySrd);
-			fail("");
-		} catch (ResourceNotFoundException e) {
-			assertEquals(Msg.code(1996) + "Resource Patient/9999999999999/_history/1 is not known", e.getMessage());
-		}
-
-	}
-
 	@Test
 	public void testReadWithDeletedResource() {
 		String methodName = "testReadWithDeletedResource";

hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -2574,25 +2574,25 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 	@Test
 	public void testUpdateRejectsInvalidTypes() {
 
-		Patient p1 = new Patient();
-		p1.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsInvalidTypes");
-		p1.addName().addFamily("Tester").addGiven("testUpdateRejectsInvalidTypes");
-		IdDt p1id = (IdDt) myClient.create().resource(p1).execute().getId();
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("urn:system").setValue("testUpdateRejectsInvalidTypes");
+		patient.addName().addFamily("Tester").addGiven("testUpdateRejectsInvalidTypes");
+		IdDt p1id = (IdDt) myClient.create().resource(patient).execute().getId();
 
-		Organization p2 = new Organization();
-		p2.getNameElement().setValue("testUpdateRejectsInvalidTypes");
+		Organization org = new Organization();
+		org.getNameElement().setValue("testUpdateRejectsInvalidTypes");
 		try {
-			myClient.update().resource(p2).withId("Organization/" + p1id.getIdPart()).execute();
+			myClient.update().resource(org).withId("Organization/" + p1id.getIdPart()).execute();
 			fail("");
 		} catch (UnprocessableEntityException e) {
-			// good
+			assertThat(e.getMessage()).contains("HAPI-0930: Existing resource ID[Patient/" + p1id.getIdPart() + "] is of type[Patient] - Cannot update with [Organization]");
 		}
 
 		try {
-			myClient.update().resource(p2).withId("Patient/" + p1id.getIdPart()).execute();
+			myClient.update().resource(org).withId("Patient/" + p1id.getIdPart()).execute();
 			fail("");
 		} catch (UnprocessableEntityException e) {
-			// good
+			assertThat(e.getMessage()).contains("HAPI-0930: Existing resource ID[Patient/" + p1id.getIdPart() + "] is of type[Patient] - Cannot update with [Organization]");
 		}
 
 	}

hapi-fhir-jpaserver-test-dstu3/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -798,57 +798,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	}
 
-	@Test
-	public void testCreateWithIllegalReference() {
-		Observation o1 = new Observation();
-		o1.getCode().addCoding().setSystem("foo").setCode("testChoiceParam01");
-		IIdType id1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
-
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReferenceElement(id1);
-			myPatientDao.create(p, mySrd);
-			fail("");
-		} catch (UnprocessableEntityException e) {
-			assertEquals(Msg.code(931) + "Invalid reference found at path 'Patient.managingOrganization'. Resource type 'Observation' is not valid for this path", e.getMessage());
-		}
-
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReferenceElement(new IdType("Organization", id1.getIdPart()));
-			myPatientDao.create(p, mySrd);
-			fail("");
-		} catch (UnprocessableEntityException e) {
-			assertEquals(Msg.code(1095) + "Resource contains reference to unknown resource ID Organization/" + id1.getIdPart(), e.getMessage());
-		}
-
-		// Now with a forced ID
-
-		o1 = new Observation();
-		o1.setId("testCreateWithIllegalReference");
-		o1.getCode().addCoding().setSystem("foo").setCode("testChoiceParam01");
-		id1 = myObservationDao.update(o1, mySrd).getId().toUnqualifiedVersionless();
-
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReferenceElement(id1);
-			myPatientDao.create(p, mySrd);
-			fail("");
-		} catch (UnprocessableEntityException e) {
-			assertEquals(Msg.code(931) + "Invalid reference found at path 'Patient.managingOrganization'. Resource type 'Observation' is not valid for this path", e.getMessage());
-		}
-
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReferenceElement(new IdType("Organization", id1.getIdPart()));
-			myPatientDao.create(p, mySrd);
-			fail("");
-		} catch (InvalidRequestException e) {
-			assertEquals(Msg.code(1094) + "Resource Organization/testCreateWithIllegalReference not found, specified in path: Patient.managingOrganization", e.getMessage());
-		}
-
-	}
-
 	@Test
 	public void testCreateWithInvalid() {
 		Observation o1 = new Observation();
@@ -2345,7 +2294,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 			myPatientDao.read(new IdType("Patient/9999999999999/_history/1"), mySrd);
 			fail("");
 		} catch (ResourceNotFoundException e) {
-			assertEquals(Msg.code(1996) + "Resource Patient/9999999999999/_history/1 is not known", e.getMessage());
+			assertEquals(Msg.code(2001) + "Resource Patient/9999999999999 is not known", e.getMessage());
 		}
 
 	}

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetVersionedTest.java

@@ -1024,6 +1024,8 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
 		ValueSet updatedValueSet_v1 = valueSet_v1;
 		updatedValueSet_v1.setName(valueSet_v1.getName().concat(" - MODIFIED"));
 
+		logAllValueSets();
+
 		String url = myClient.getServerBase().concat("/").concat(myExtensionalVsId_v1.getValueAsString());
 		Bundle bundle = new Bundle();
 		bundle.setType(Bundle.BundleType.TRANSACTION);
@@ -1056,7 +1058,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
 			.getRequest()
 			.setMethod(Bundle.HTTPVerb.PUT)
 			.setUrl("ValueSet/" + updatedValueSet_v2.getIdElement().getIdPart());
-		ourLog.debug("Transaction Bundle:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
+		ourLog.info("Transaction Bundle:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
 		myClient.transaction().withBundle(bundle).execute();
 
 		updatedValueSet_v2 = myValueSetDao.read(myExtensionalVsId_v2);

hapi-fhir-jpaserver-test-r4/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -71,6 +71,7 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.anyLong;
+import static org.mockito.ArgumentMatchers.anyString;
 import static org.mockito.ArgumentMatchers.isNotNull;
 import static org.mockito.Mockito.doReturn;
 import static org.mockito.Mockito.lenient;
@@ -136,7 +137,7 @@ class BaseHapiFhirResourceDaoTest {
 	private ArgumentCaptor<SearchParameterMap> mySearchParameterMapCaptor;
 
 	// we won't inject this
-	private FhirContext myFhirContext = FhirContext.forR4Cached();
+	private final FhirContext myFhirContext = FhirContext.forR4Cached();
 
 	@InjectMocks
 	private TestResourceDao mySvc;
@@ -236,16 +237,17 @@ class BaseHapiFhirResourceDaoTest {
 		// mock
 		when(myRequestPartitionHelperSvc.determineReadPartitionForRequestForRead(
 			any(RequestDetails.class),
-			Mockito.anyString(),
+			anyString(),
 			any(IIdType.class)
 		)).thenReturn(partitionId);
-		when(myIdHelperService.resolveResourcePersistentIds(
+		when(myIdHelperService.resolveResourceIdentityPid(
 			any(RequestPartitionId.class),
-			Mockito.anyString(),
-			Mockito.anyString()
+			anyString(),
+			anyString(),
+			any()
 		)).thenReturn(jpaPid);
 		when(myEntityManager.find(
-			any(Class.class),
+			any(),
 			anyLong()
 		)).thenReturn(entity);
 		// we don't stub myConfig.getResourceClientIdStrategy()

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

@@ -1,213 +0,0 @@
-package ca.uhn.fhir.jpa.dao.index;
-
-import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
-import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
-import ca.uhn.fhir.jpa.model.config.PartitionSettings;
-import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
-import ca.uhn.fhir.jpa.model.dao.JpaPid;
-import ca.uhn.fhir.jpa.util.MemoryCacheService;
-import org.hl7.fhir.r4.model.Patient;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.mockito.InjectMocks;
-import org.mockito.Mock;
-import org.mockito.Mockito;
-import org.mockito.junit.jupiter.MockitoExtension;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Date;
-import java.util.List;
-import java.util.Map;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-
-import static org.assertj.core.api.Assertions.assertThat;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.ArgumentMatchers.anyBoolean;
-import static org.mockito.Mockito.when;
-
-@ExtendWith(MockitoExtension.class)
-public class IdHelperServiceTest {
-
-	@Mock
-	private JpaStorageSettings myStorageSettings;
-
-	@Mock
-	private IResourceTableDao myResourceTableDao;
-
-	@Mock
-	private MemoryCacheService myMemoryCacheService;
-
-	@Mock
-	private PartitionSettings myPartitionSettings;
-
-	@InjectMocks
-	private IdHelperService myHelperService;
-
-	@BeforeEach
-	public void beforeEach() {
-		myHelperService.setDontCheckActiveTransactionForUnitTest(true);
-	}
-
-	@Test
-	public void resolveResourcePersistentIds_withValidPids_returnsMap() {
-		RequestPartitionId partitionId = RequestPartitionId.allPartitions();
-		String resourceType = Patient.class.getSimpleName();
-		List<String> patientIdsToResolve = new ArrayList<>();
-		patientIdsToResolve.add("123");
-		patientIdsToResolve.add("456");
-
-		// test
-		Map<String, JpaPid> idToPid = myHelperService.resolveResourcePersistentIds(partitionId,
-			resourceType,
-			patientIdsToResolve);
-
-		assertFalse(idToPid.isEmpty());
-		for (String pid : patientIdsToResolve) {
-			assertThat(idToPid).containsKey(pid);
-		}
-	}
-
-	@Test
-	public void resolveResourcePersistentIds_withForcedIdsAndDeleteEnabled_returnsMap() {
-		RequestPartitionId partitionId = RequestPartitionId.allPartitions();
-		String resourceType = Patient.class.getSimpleName();
-		List<String> patientIdsToResolve = new ArrayList<>();
-		patientIdsToResolve.add("RED");
-		patientIdsToResolve.add("BLUE");
-
-		Object[] redView = new Object[] {
-			"Patient",
-			123l,
-			"RED",
-			new Date(),
-			null,
-			null
-		};
-		Object[] blueView = new Object[] {
-			"Patient",
-			456l,
-			"BLUE",
-			new Date(),
-			null,
-			null
-		};
-
-		// when
-		when(myStorageSettings.isDeleteEnabled())
-			.thenReturn(true);
-		when(myResourceTableDao.findAndResolveByForcedIdWithNoType(Mockito.anyString(),
-			Mockito.anyList(), Mockito.anyBoolean()))
-			.thenReturn(Collections.singletonList(redView))
-			.thenReturn(Collections.singletonList(blueView));
-
-		// test
-		Map<String, JpaPid> map = myHelperService.resolveResourcePersistentIds(
-			partitionId,
-			resourceType,
-			patientIdsToResolve);
-
-		assertFalse(map.isEmpty());
-		for (String id : patientIdsToResolve) {
-			assertThat(map).containsKey(id);
-		}
-	}
-
-	@Test
-	public void resolveResourcePersistenIds_withForcedIdAndDeleteDisabled_returnsMap() {
-		RequestPartitionId partitionId = RequestPartitionId.allPartitions();
-		String resourceType = Patient.class.getSimpleName();
-		List<String> patientIdsToResolve = new ArrayList<>();
-		patientIdsToResolve.add("RED");
-		patientIdsToResolve.add("BLUE");
-
-		JpaPid red = JpaPid.fromIdAndVersion(123L, 123L);
-		JpaPid blue = JpaPid.fromIdAndVersion(456L, 456L);
-
-		// we will pretend the lookup value is in the cache
-		when(myMemoryCacheService.getThenPutAfterCommit(any(MemoryCacheService.CacheEnum.class),
-			Mockito.anyString(),
-			any(Function.class)))
-			.thenReturn(red)
-			.thenReturn(blue);
-
-		// test
-		Map<String, JpaPid> map = myHelperService.resolveResourcePersistentIds(
-			partitionId,
-			resourceType,
-			patientIdsToResolve
-		);
-
-		assertFalse(map.isEmpty());
-		for (String id : patientIdsToResolve) {
-			assertThat(map).containsKey(id);
-		}
-		assertThat(map).containsEntry("RED", red);
-		assertThat(map).containsEntry("BLUE", blue);
-	}
-
-	@Test
-	public void testResolveResourceIdentity_defaultFunctionality(){
-		RequestPartitionId partitionId = RequestPartitionId.fromPartitionIdAndName(1, "partition");
-		String resourceType = "Patient";
-		String resourceForcedId = "AAA";
-
-		Object[] forcedIdView = new Object[6];
-		forcedIdView[0] = resourceType;
-		forcedIdView[1] = 1L;
-		forcedIdView[2] = resourceForcedId;
-		forcedIdView[3] = null;
-		forcedIdView[4] = null;
-		forcedIdView[5] = null;
-
-		Collection<Object[]> testForcedIdViews = new ArrayList<>();
-		testForcedIdViews.add(forcedIdView);
-		when(myResourceTableDao.findAndResolveByForcedIdWithNoTypeInPartition(any(), any(), any(), anyBoolean())).thenReturn(testForcedIdViews);
-
-		IResourceLookup<JpaPid> result = myHelperService.resolveResourceIdentity(partitionId, resourceType, resourceForcedId);
-		assertEquals(forcedIdView[0], result.getResourceType());
-		assertEquals(forcedIdView[1], result.getPersistentId().getId());
-		assertEquals(forcedIdView[3], result.getDeleted());
-	}
-
-	@Test
-	public void testResolveResourcePersistentIds_mapDefaultFunctionality(){
-		RequestPartitionId partitionId = RequestPartitionId.fromPartitionIdAndName(1, "partition");
-		String resourceType = "Patient";
-		List<String> ids = Arrays.asList("A", "B", "C");
-
-		JpaPid resourcePersistentId1 = JpaPid.fromId(1L);
-		JpaPid resourcePersistentId2 = JpaPid.fromId(2L);
-		JpaPid resourcePersistentId3 = JpaPid.fromId(3L);
-		when(myMemoryCacheService.getThenPutAfterCommit(any(), any(), any()))
-			.thenReturn(resourcePersistentId1)
-			.thenReturn(resourcePersistentId2)
-			.thenReturn(resourcePersistentId3);
-		Map<String, JpaPid> result = myHelperService.resolveResourcePersistentIds(partitionId, resourceType, ids)
-			.entrySet().stream().collect(Collectors.toMap(Map.Entry::getKey, entry -> entry.getValue()));
-		assertThat(result.keySet()).hasSize(3);
-		assertEquals(1L, result.get("A").getId());
-		assertEquals(2L, result.get("B").getId());
-		assertEquals(3L, result.get("C").getId());
-	}
-
-	@Test
-	public void testResolveResourcePersistentIds_resourcePidDefaultFunctionality(){
-		RequestPartitionId partitionId = RequestPartitionId.fromPartitionIdAndName(1, "partition");
-		String resourceType = "Patient";
-		Long id = 1L;
-
-		JpaPid jpaPid1 = JpaPid.fromId(id);
-		when(myStorageSettings.getResourceClientIdStrategy()).thenReturn(JpaStorageSettings.ClientIdStrategyEnum.ANY);
-		when(myMemoryCacheService.getThenPutAfterCommit(any(), any(), any())).thenReturn(jpaPid1);
-		JpaPid result = myHelperService.resolveResourcePersistentIds(partitionId, resourceType, id.toString());
-		assertEquals(id, result.getId());
-	}
-}

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/BasePartitioningR4Test.java

@@ -14,6 +14,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.searchparam.submit.interceptor.SearchParamValidatingInterceptor;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.HapiExtensions;
 import com.helger.commons.lang.StackTraceHelper;
@@ -52,6 +53,9 @@ public abstract class BasePartitioningR4Test extends BaseJpaR4SystemTest {
 	private boolean myHaveDroppedForcedIdUniqueConstraint;
 	@Autowired
 	private IPartitionLookupSvc myPartitionConfigSvc;
+	@Autowired
+	private SearchParamValidatingInterceptor mySearchParamValidatingInterceptor;
+	private boolean myRegisteredSearchParamValidatingInterceptor;
 
 	@AfterEach
 	public void after() {
@@ -68,6 +72,10 @@ public abstract class BasePartitioningR4Test extends BaseJpaR4SystemTest {
 		myStorageSettings.setAutoCreatePlaceholderReferenceTargets(new JpaStorageSettings().isAutoCreatePlaceholderReferenceTargets());
 		myStorageSettings.setMassIngestionMode(new JpaStorageSettings().isMassIngestionMode());
 		myStorageSettings.setMatchUrlCacheEnabled(new JpaStorageSettings().getMatchUrlCache());
+
+		if (myRegisteredSearchParamValidatingInterceptor) {
+			myInterceptorRegistry.unregisterInterceptor(mySearchParamValidatingInterceptor);
+		}
 	}
 
 	protected void assertNoRemainingPartitionIds() {
@@ -112,6 +120,10 @@ public abstract class BasePartitioningR4Test extends BaseJpaR4SystemTest {
 			myPartitionConfigSvc.getPartitionById(i);
 		}
 
+		if (myInterceptorRegistry.getAllRegisteredInterceptors().stream().noneMatch(t->t instanceof SearchParamValidatingInterceptor)) {
+			myRegisteredSearchParamValidatingInterceptor = true;
+			myInterceptorRegistry.registerInterceptor(mySearchParamValidatingInterceptor);
+		}
 	}
 
 	protected void registerPartitionInterceptor() {

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4DeleteTest.java

@@ -8,9 +8,11 @@ import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
+import jakarta.persistence.Id;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.IdType;
@@ -36,6 +38,24 @@ public class FhirResourceDaoR4DeleteTest extends BaseJpaR4Test {
 		myStorageSettings.setDeleteEnabled(new JpaStorageSettings().isDeleteEnabled());
 	}
 
+	@Test
+	public void testPreventUnDeleteIfDeletesDisabled() {
+		// Setup
+		createPatient(withId("A"), withActiveTrue());
+		myPatientDao.delete(new IdType("Patient/A"), mySrd);
+
+		// Test
+		myStorageSettings.setDeleteEnabled(false);
+		try {
+			createPatient(withId("A"), withActiveFalse());
+			fail();
+		} catch (InvalidRequestException e) {
+			// Verify
+			assertThat(e.getMessage()).contains("HAPI-2573: Unable to restore previously deleted resource as deletes are disabled");
+		}
+	}
+
+
 	@Test
 	public void testDeleteMarksResourceAndVersionAsDeleted() {
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java

@@ -7,8 +7,8 @@ import ca.uhn.fhir.batch2.api.VoidModel;
 import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
 import ca.uhn.fhir.batch2.jobs.chunk.TypedPidJson;
 import ca.uhn.fhir.batch2.jobs.expunge.DeleteExpungeStep;
-import ca.uhn.fhir.batch2.jobs.reindex.v1.ReindexStepV1;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.jobs.reindex.v2.ReindexStepV2;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.batch2.model.WorkChunk;
 import ca.uhn.fhir.context.FhirContext;
@@ -40,6 +40,7 @@ import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.param.ReferenceParam;
+import ca.uhn.fhir.rest.param.TokenOrListParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.SimpleBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@@ -51,6 +52,7 @@ import ca.uhn.fhir.test.utilities.server.HashMapResourceProviderExtension;
 import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
 import ca.uhn.fhir.util.BundleBuilder;
 import jakarta.annotation.Nonnull;
+import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.BooleanType;
@@ -100,6 +102,7 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Date;
 import java.util.List;
+import java.util.UUID;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
@@ -149,7 +152,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 	@Autowired
 	private ISubscriptionTriggeringSvc mySubscriptionTriggeringSvc;
 	@Autowired
-	private ReindexStepV1 myReindexStepV1;
+	private ReindexStepV2 myReindexStep;
 	@Autowired
 	private DeleteExpungeStep myDeleteExpungeStep;
 	@Autowired
@@ -248,6 +251,70 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 	}
 
+	@Test
+	public void testTransactionWithManyResourceLinks() {
+		// Setup
+		List<IIdType> patientIds = new ArrayList<>();
+		List<IIdType> orgIds = new ArrayList<>();
+		List<IIdType> coverageIds = new ArrayList<>();
+		AtomicInteger counter = new AtomicInteger(0);
+		for (int i = 0; i < 10; i++) {
+			// Server-assigned numeric ID
+			coverageIds.add(createResource("Coverage", withStatus("active")));
+			// Client-assigned string ID
+			patientIds.add(createPatient(withId(UUID.randomUUID().toString()), withActiveTrue()));
+			orgIds.add(createOrganization(withId(UUID.randomUUID().toString()), withName("FOO")));
+		}
+
+		Supplier<ExplanationOfBenefit> creator = () -> {
+			int nextCount = counter.getAndIncrement();
+			assert nextCount < coverageIds.size();
+
+			ExplanationOfBenefit retVal = new ExplanationOfBenefit();
+			retVal.getMeta().addTag().setSystem("http://foo").setCode(Integer.toString(nextCount % 3));
+			retVal.setId(UUID.randomUUID().toString());
+			retVal.setPatient(new Reference(patientIds.get(nextCount)));
+			retVal.setInsurer(new Reference(orgIds.get(nextCount)));
+			retVal.addInsurance().setCoverage(new Reference(coverageIds.get(nextCount)));
+			return retVal;
+		};
+
+		Supplier<Bundle> transactionCreator = () -> {
+			BundleBuilder bb = new BundleBuilder(myFhirContext);
+			bb.addTransactionUpdateEntry(creator.get());
+			bb.addTransactionUpdateEntry(creator.get());
+			bb.addTransactionUpdateEntry(creator.get());
+			bb.addTransactionUpdateEntry(creator.get());
+			bb.addTransactionUpdateEntry(creator.get());
+			return bb.getBundleTyped();
+		};
+
+		// Test
+		myCaptureQueriesListener.clear();
+		mySystemDao.transaction(mySrd, transactionCreator.get());
+		myCaptureQueriesListener.logInsertQueries();
+		myCaptureQueriesListener.logSelectQueries();
+
+		// Verify
+		assertEquals(0, myCaptureQueriesListener.countInsertQueriesRepeated());
+		assertEquals(33, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(4, myCaptureQueriesListener.countSelectQueries());
+		assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+
+		// Test again
+		myCaptureQueriesListener.clear();
+		mySystemDao.transaction(mySrd, transactionCreator.get());
+
+		// Verify again
+		assertEquals(0, myCaptureQueriesListener.countInsertQueriesRepeated());
+		assertEquals(30, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueries());
+		assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+	}
+
+
 	/*
 	 * See the class javadoc before changing the counts in this test!
 	 */
@@ -331,7 +398,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		myCaptureQueriesListener.clear();
 		group = updateGroup(group, patientList.subList(initialPatientsCount, allPatientsCount));
 
-		assertQueryCount(10, 1, 2, 0);
+		assertQueryCount(9, 1, 2, 0);
 
 		assertThat(group.getMember()).hasSize(allPatientsCount);
 
@@ -356,7 +423,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		group = updateGroup(group, Collections.emptyList());
 
 		myCaptureQueriesListener.logSelectQueries();
-		assertQueryCount(5, 1, 2, 0);
+		assertQueryCount(4, 1, 2, 0);
 
 		assertThat(group.getMember()).hasSize(30);
 
@@ -938,7 +1005,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		patient.setActive(true);
 
 		myCaptureQueriesListener.clear();
-		myPatientDao.update(patient);
+		myPatientDao.update(patient, mySrd);
 
 		/*
 		 * Add a resource with a forced ID target link
@@ -947,7 +1014,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		myCaptureQueriesListener.clear();
 		Observation observation = new Observation();
 		observation.getSubject().setReference("Patient/P");
-		myObservationDao.create(observation);
+		myObservationDao.create(observation, mySrd);
 		myCaptureQueriesListener.logAllQueriesForCurrentThread();
 		// select: lookup forced ID
 		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
@@ -998,14 +1065,13 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		Observation observation = new Observation();
 		observation.getSubject().setReference("Patient/P");
 		myObservationDao.create(observation);
-		myCaptureQueriesListener.logAllQueriesForCurrentThread();
-		// select: lookup forced ID
-		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
-		assertNoPartitionSelectors();
+		myCaptureQueriesListener.logSelectQueries();
+		assertEquals(0, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
 		// insert to: HFJ_RESOURCE, HFJ_RES_VER, HFJ_RES_LINK
 		assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
+		assertNoPartitionSelectors();
 
 		/*
 		 * Add another
@@ -1064,7 +1130,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 			instance,
 			mock(WorkChunk.class)
 		);
-		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, mock(IJobDataSink.class));
+		RunOutcome outcome = myReindexStep.run(stepExecutionDetails, mock(IJobDataSink.class));
 
 		// validate
 		assertThat(myCaptureQueriesListener.getSelectQueriesForCurrentThread()).hasSize(theExpectedSelectCount);
@@ -1109,7 +1175,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 			instance,
 			mock(WorkChunk.class)
 		);
-		RunOutcome outcome = myReindexStepV1.run(stepExecutionDetails, mock(IJobDataSink.class));
+		RunOutcome outcome = myReindexStep.run(stepExecutionDetails, mock(IJobDataSink.class));
 		assertEquals(20, outcome.getRecordsProcessed());
 
         // validate
@@ -1343,6 +1409,57 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		return ids;
 	}
 
+	@Test
+	public void testSearchByMultipleIds() {
+		// Setup
+		List<String> idValues = new ArrayList<>();
+		for (int i = 0; i < 5; i++) {
+			// Client assigned and server assigned IDs
+			idValues.add(createPatient(withId(UUID.randomUUID().toString()), withActiveTrue()).toUnqualifiedVersionless().getValue());
+			idValues.add(createPatient(withActiveTrue()).toUnqualifiedVersionless().getValue());
+		}
+		String[] idValueArray = idValues.toArray(new String[0]);
+
+		// Test
+		SearchParameterMap map = SearchParameterMap.newSynchronous();
+		map.add(IAnyResource.SP_RES_ID, new TokenOrListParam(null, idValueArray));
+		myCaptureQueriesListener.clear();
+		IBundleProvider outcome = myPatientDao.search(map, mySrd);
+		List<String> values = toUnqualifiedVersionlessIdValues(outcome);
+
+		// Verify
+		myCaptureQueriesListener.logSelectQueries();
+		assertEquals(2, myCaptureQueriesListener.countSelectQueries());
+		assertThat(values).asList().containsExactlyInAnyOrder(idValueArray);
+
+		// Now invalidate the caches, should add one more query
+		myMemoryCacheService.invalidateAllCaches();
+		map = SearchParameterMap.newSynchronous();
+		map.add(IAnyResource.SP_RES_ID, new TokenOrListParam(null, idValueArray));
+		myCaptureQueriesListener.clear();
+		outcome = myPatientDao.search(map, mySrd);
+		values = toUnqualifiedVersionlessIdValues(outcome);
+
+		// Verify
+		myCaptureQueriesListener.logSelectQueries();
+		assertEquals(3, myCaptureQueriesListener.countSelectQueries());
+		assertThat(values).asList().containsExactlyInAnyOrder(idValueArray);
+
+		// And again, should be cached once more
+		map = SearchParameterMap.newSynchronous();
+		map.add(IAnyResource.SP_RES_ID, new TokenOrListParam(null, idValueArray));
+		myCaptureQueriesListener.clear();
+		outcome = myPatientDao.search(map, mySrd);
+		values = toUnqualifiedVersionlessIdValues(outcome);
+
+		// Verify
+		myCaptureQueriesListener.logSelectQueries();
+		assertEquals(2, myCaptureQueriesListener.countSelectQueries());
+		assertThat(values).asList().containsExactlyInAnyOrder(idValueArray);
+
+	}
+
+
 
 	/**
 	 * See the class javadoc before changing the counts in this test!
@@ -1582,12 +1699,13 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		myCaptureQueriesListener.clear();
 		IBundleProvider outcome = dao.search(map, mySrd);
 		toUnqualifiedVersionlessIdValues(outcome);
-		assertEquals(4, myCaptureQueriesListener.countSelectQueries());
+		myCaptureQueriesListener.logSelectQueries();
+		assertEquals(3, myCaptureQueriesListener.countSelectQueries());
 
 		myCaptureQueriesListener.clear();
 		outcome = dao.search(map, mySrd);
 		toUnqualifiedVersionlessIdValues(outcome);
-		assertEquals(4, myCaptureQueriesListener.countSelectQueries());
+		assertEquals(3, myCaptureQueriesListener.countSelectQueries());
 	}
 
 
@@ -1869,6 +1987,62 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		runInTransaction(() -> assertEquals(2, myResourceTableDao.count()));
 	}
 
+	/**
+	 * Make sure that even if we're using versioned references, we still take
+	 * advantage of query pre-fetching.
+	 */
+	@Test
+	public void testTransactionPreFetchFullyQualifiedVersionedIds() {
+		// Setup
+		myStorageSettings.getTreatBaseUrlsAsLocal().add("http://localhost");
+		myFhirContext.getParserOptions().setStripVersionsFromReferences(false);
+
+		createPatient(withId("P0"), withActiveTrue());
+		createPatient(withId("P1"), withActiveTrue());
+		createEncounter(withId("E0"), withSubject("Patient/P0"), withStatus("planned"));
+		createObservation(withId("O0"), withSubject("Patient/P0"));
+
+		Bundle input = new Bundle();
+		input.setType(Bundle.BundleType.TRANSACTION);
+
+		Patient patient = new Patient();
+		patient.setId("Patient/P1");
+		patient.setActive(false);
+		input.addEntry()
+			.setResource(patient)
+			.setFullUrl("http://localhost/Patient/P1/_history/1")
+			.getRequest()
+			.setUrl("Patient/P1/_history/1")
+			.setMethod(Bundle.HTTPVerb.PUT);
+
+		Observation observation = new Observation();
+		observation.setId("Observation/O0");
+		observation.setSubject(new Reference("http://localhost/Patient/P0/_history/1"));
+		observation.setEncounter(new Reference("http://localhost/Encounter/E0/_history/1"));
+		input.addEntry()
+			.setResource(observation)
+			.setFullUrl("http://localhost/Observation/O0/_history/1")
+			.getRequest()
+			.setUrl("Observation/O0/_history/1")
+			.setMethod(Bundle.HTTPVerb.PUT);
+
+		myCaptureQueriesListener.clear();
+		mySystemDao.transaction(mySrd, input);
+
+		// Verify
+		myCaptureQueriesListener.logSelectQueries();
+		assertEquals(4, myCaptureQueriesListener.countSelectQueries());
+		assertEquals(5, myCaptureQueriesListener.countUpdateQueries());
+		assertEquals(3, myCaptureQueriesListener.countInsertQueries());
+		assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
+		assertEquals(1, myCaptureQueriesListener.countCommits());
+
+		observation = myObservationDao.read(new IdType("Observation/O0"), mySrd);
+		ourLog.info("Observation:{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(observation));
+		assertEquals("Patient/P0/_history/1", observation.getSubject().getReference());
+		assertEquals("Encounter/E0/_history/1", observation.getEncounter().getReference());
+	}
+
 	/**
 	 * See the class javadoc before changing the counts in this test!
 	 */
@@ -2061,9 +2235,8 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		myCaptureQueriesListener.clear();
 		mySystemDao.transaction(mySrd, input);
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(1, countMatches(myCaptureQueriesListener.getSelectQueries().get(0).getSql(true, false), "'6445233466262474106'"));
-		assertEquals(1, countMatches(myCaptureQueriesListener.getSelectQueries().get(1).getSql(true, false), "'LOC'"));
 		assertEquals(6, runInTransaction(() -> myResourceTableDao.count()));
 
 		// Second identical pass
@@ -2114,7 +2287,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 			myCaptureQueriesListener.clear();
 			mySystemDao.transaction(mySrd, input);
 			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-			assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+			assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 			assertEquals(6, runInTransaction(() -> myResourceTableDao.count()));
 
 			// Second identical pass
@@ -2172,7 +2345,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		myCaptureQueriesListener.clear();
 		mySystemDao.transaction(mySrd, input);
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(7, runInTransaction(() -> myResourceTableDao.count()));
 
 		// Second identical pass
@@ -2227,7 +2400,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		myCaptureQueriesListener.clear();
 		mySystemDao.transaction(mySrd, input);
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(7, runInTransaction(() -> myResourceTableDao.count()));
 
 		// Second identical pass
@@ -2649,7 +2822,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 		// Lookup the two existing IDs to make sure they are legit
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(10, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
@@ -2677,7 +2850,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 		// Lookup the two existing IDs to make sure they are legit
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(10, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
@@ -2721,7 +2894,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		// Lookup the two existing IDs to make sure they are legit
 		myCaptureQueriesListener.logInsertQueriesForCurrentThread();
 		myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(10, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
@@ -2749,7 +2922,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 		// Lookup the two existing IDs to make sure they are legit
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(10, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
@@ -2795,7 +2968,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 		// Lookup the two existing IDs to make sure they are legit
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(0, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(10, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
@@ -3068,8 +3241,13 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		Bundle input = loadResource(myFhirContext, Bundle.class, "/r4/test-patient-bundle.json");
 
 		myCaptureQueriesListener.clear();
-		Bundle output = mySystemDao.transaction(mySrd, input);
-		myCaptureQueriesListener.logSelectQueries();
+		Bundle output;
+		try {
+			output = mySystemDao.transaction(mySrd, input);
+		} finally {
+			myCaptureQueriesListener.logSelectQueries();
+			myCaptureQueriesListener.logInsertQueries();
+		}
 
 		assertEquals(17, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(6189, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
@@ -3113,6 +3291,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		Bundle output = mySystemDao.transaction(mySrd, input);
 
 		// Verify
+		myCaptureQueriesListener.logUpdateQueries();
 		assertEquals(3, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(6, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
@@ -3127,6 +3306,15 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 			assertEquals(1, myResourceHistoryTableDao.count());
 		});
 
+		IdType id = new IdType(output.getEntry().get(0).getResponse().getLocation());
+		assertEquals("1", id.getVersionIdPart());
+		id = new IdType(output.getEntry().get(1).getResponse().getLocation());
+		assertEquals("2", id.getVersionIdPart());
+
+		Patient p = myPatientDao.read(id.toVersionless(), mySrd);
+		assertEquals("2", p.getIdElement().getVersionIdPart());
+		assertEquals("http://system", p.getIdentifierFirstRep().getSystem());
+		assertTrue(p.getActive());
 	}
 
 	/**
@@ -3164,7 +3352,8 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		mySystemDao.transaction(mySrd, inputBundle);
 		assertEquals(21, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 		assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
-		assertEquals(78, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
+		myCaptureQueriesListener.logInsertQueries();
+		assertEquals(7, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
 		assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
 
 		// Now run the transaction again - It should not need too many SELECTs
@@ -3201,6 +3390,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 		myCaptureQueriesListener.clear();
 		inputBundle = myReindexTestHelper.createTransactionBundleWith20Observation(true);
 		mySystemDao.transaction(mySrd, inputBundle);
+		myCaptureQueriesListener.logSelectQueries();
 		assertEquals(4, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
 		assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
 		assertEquals(0, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
@@ -3212,7 +3402,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 	/**
 	 * See the class javadoc before changing the counts in this test!
 	 */
-	@SuppressWarnings("unchecked")
 	@Test
 	public void testTriggerSubscription_Sync() throws Exception {
 		// Setup
@@ -3505,6 +3694,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 		myCaptureQueriesListener.clear();
 		Bundle outcome = mySystemDao.transaction(new SystemRequestDetails(), supplier.get());
+		myCaptureQueriesListener.logSelectQueries();
 		assertEquals(6, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		myCaptureQueriesListener.logInsertQueries();
 		assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ReferentialIntegrityTest.java

@@ -97,9 +97,9 @@ public class FhirResourceDaoR4ReferentialIntegrityTest extends BaseJpaR4Test {
 			// When
 			myPatientDao.create(p);
 			fail();
-		} catch (UnprocessableEntityException e) {
+		} catch (InvalidRequestException e) {
 			// Then: identify that it is the wrong resource type, since ref integrity is enabled
-			assertEquals(Msg.code(1095) + "Resource contains reference to unknown resource ID Organization/" + obsId.getIdPart(), e.getMessage());
+			assertEquals(Msg.code(1094) + "Resource Organization/" + obsId.getIdPart() + " not found, specified in path: Patient.managingOrganization", e.getMessage());
 		}
 
 		// Given: now disable referential integrity on write

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchIncludeTest.java

@@ -177,7 +177,7 @@ public class FhirResourceDaoR4SearchIncludeTest extends BaseJpaR4Test {
 		}
 
 		if (!theReverse && theMatchAll) {
-			SqlQuery searchForCanonicalReferencesQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(3);
+			SqlQuery searchForCanonicalReferencesQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(2);
 			// Make sure we have the right query - If this ever fails, maybe we have optimized the queries
 			// (or somehow made things worse) and the search for the canonical target is no longer the 4th
 			// SQL query

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -1731,65 +1731,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
-	@Test
-	public void testSearchByIdParam_QueryIsMinimal() {
-		// With only an _id parameter
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			params.add(PARAM_ID, new StringParam("DiagnosticReport/123"));
-			myCaptureQueriesListener.clear();
-			myDiagnosticReportDao.search(params).size();
-			List<SqlQuery> selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread();
-			assertThat(selectQueries).hasSize(1);
-
-			String sqlQuery = selectQueries.get(0).getSql(true, true).toLowerCase();
-			ourLog.info("SQL Query:\n{}", sqlQuery);
-			assertThat(countMatches(sqlQuery, "res_id = '123'")).as(sqlQuery).isEqualTo(1);
-			assertThat(countMatches(sqlQuery, "join")).as(sqlQuery).isEqualTo(0);
-			assertThat(countMatches(sqlQuery, "res_type = 'diagnosticreport'")).as(sqlQuery).isEqualTo(1);
-			assertThat(countMatches(sqlQuery, "res_deleted_at is null")).as(sqlQuery).isEqualTo(1);
-		}
-		// With an _id parameter and a standard search param
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			params.add(PARAM_ID, new StringParam("DiagnosticReport/123"));
-			params.add("code", new TokenParam("foo", "bar"));
-			myCaptureQueriesListener.clear();
-			myDiagnosticReportDao.search(params).size();
-			List<SqlQuery> selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread();
-			assertThat(selectQueries).hasSize(1);
-
-			String sqlQuery = selectQueries.get(0).getSql(true, true).toLowerCase();
-			ourLog.info("SQL Query:\n{}", sqlQuery);
-			assertThat(countMatches(sqlQuery, "res_id = '123'")).as(sqlQuery).isEqualTo(1);
-			assertThat(countMatches(sqlQuery, "join")).as(sqlQuery).isEqualTo(1);
-			assertThat(countMatches(sqlQuery, "hash_sys_and_value")).as(sqlQuery).isEqualTo(1);
-			assertThat(countMatches(sqlQuery, "res_type = 'diagnosticreport")).as(sqlQuery).isEqualTo(0); // could be 0
-			assertThat(countMatches(sqlQuery, "res_deleted_at")).as(sqlQuery).isEqualTo(0); // could be 0
-		}
-	}
-
-	@Test
-	public void testSearchByIdParamAndOtherSearchParam_QueryIsMinimal() {
-		SearchParameterMap params = new SearchParameterMap();
-		params.setLoadSynchronous(true);
-		params.add(PARAM_ID, new StringParam("DiagnosticReport/123"));
-		params.add(PARAM_ID, new StringParam("DiagnosticReport/123"));
-		myCaptureQueriesListener.clear();
-		myDiagnosticReportDao.search(params).size();
-		List<SqlQuery> selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread();
-		assertThat(selectQueries).hasSize(1);
-
-		String sqlQuery = selectQueries.get(0).getSql(true, true).toLowerCase();
-		ourLog.info("SQL Query:\n{}", sqlQuery);
-		assertThat(countMatches(sqlQuery, "res_id = '123'")).as(sqlQuery).isEqualTo(1);
-		assertThat(countMatches(sqlQuery, "join")).as(sqlQuery).isEqualTo(0);
-		assertThat(countMatches(sqlQuery, "res_type = 'diagnosticreport'")).as(sqlQuery).isEqualTo(1);
-		assertThat(countMatches(sqlQuery, "res_deleted_at is null")).as(sqlQuery).isEqualTo(1);
-	}
-
 	@Test
 	public void testSearchByIdParamAnd() {
 		IIdType id1;

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java

@@ -95,7 +95,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		mySearchCoordinatorSvcImpl = ProxyUtil.getSingletonTarget(mySearchCoordinatorSvc, SearchCoordinatorSvcImpl.class);
 		mySearchCoordinatorSvcImpl.setLoadingThrottleForUnitTests(null);
 		mySearchCoordinatorSvcImpl.setSyncSizeForUnitTests(QueryParameterUtils.DEFAULT_SYNC_SIZE);
-		myCaptureQueriesListener.setCaptureQueryStackTrace(true);
+//		myCaptureQueriesListener.setCaptureQueryStackTrace(true);
 		myStorageSettings.setAdvancedHSearchIndexing(false);
 	}
 
@@ -876,8 +876,11 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		String obs2id = myObservationDao.create(obs2).getId().getIdPart();
 		assertThat(obs2id).matches("^[0-9]+$");
 
-		// Search by ID where all IDs are forced IDs
+
+		// Search by ID where all IDs are forced IDs, and in two separate params
 		{
+			myMemoryCacheService.invalidateAllCaches();
+
 			SearchParameterMap map = SearchParameterMap.newSynchronous();
 			map.add("_id", new TokenParam("A"));
 			map.add("subject", new ReferenceParam("Patient/B"));
@@ -885,20 +888,20 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 			myCaptureQueriesListener.clear();
 			IBundleProvider outcome = myObservationDao.search(map, new SystemRequestDetails());
 			assertThat(outcome.getResources(0, 999)).hasSize(1);
+
 			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-
 			String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "rt1_0.res_type='observation'")).as(selectQuery).isEqualTo(1);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "rt1_0.fhir_id in ('a')")).as(selectQuery).isEqualTo(1);
-
+			assertThat(selectQuery).contains("where rt1_0.RES_TYPE='Patient' and rt1_0.FHIR_ID='B'");
 			selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "select t1.res_id from hfj_resource t1")).as(selectQuery).isEqualTo(1);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "t1.res_type='observation'")).as(selectQuery).isEqualTo(0);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "t1.res_deleted_at is null")).as(selectQuery).isEqualTo(0);
+			assertThat(selectQuery).contains("where (rt1_0.RES_TYPE='Observation' and rt1_0.FHIR_ID='A')");
+			assertEquals(4, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+
 		}
 
 		// Search by ID where at least one ID is a numeric ID
 		{
+			myMemoryCacheService.invalidateAllCaches();
+
 			SearchParameterMap map = SearchParameterMap.newSynchronous();
 			map.add("_id", new TokenOrListParam(null, "A", obs2id));
 			myCaptureQueriesListener.clear();
@@ -906,20 +909,19 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 			assertEquals(2, outcome.size());
 			assertThat(outcome.getResources(0, 999)).hasSize(2);
 			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-			String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "select t0.res_id from hfj_resource t0")).as(selectQuery).isEqualTo(1);
-			// Because we included a non-forced ID, we need to verify the type
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_type = 'observation'")).as(selectQuery).isEqualTo(1);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_deleted_at is null")).as(selectQuery).isEqualTo(1);
+			String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
+			assertThat(selectQuery).contains("where (rt1_0.RES_TYPE='Observation' and rt1_0.FHIR_ID='A' or rt1_0.RES_ID='" + obs2id + "')");
+			assertEquals(3, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		}
 
-		// Delete the resource - There should only be one search performed because deleted resources will
-		//		be filtered out in the query that resolves forced ids to persistent ids
+		// Delete the resource
 		myObservationDao.delete(new IdType("Observation/A"));
 		myObservationDao.delete(new IdType("Observation/" + obs2id));
 
 		// Search by ID where all IDs are forced IDs
 		{
+			myMemoryCacheService.invalidateAllCaches();
+
 			SearchParameterMap map = SearchParameterMap.newSynchronous();
 			map.add("_id", new TokenParam("A"));
 			myCaptureQueriesListener.clear();
@@ -928,26 +930,9 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 			assertThat(outcome.getResources(0, 999)).isEmpty();
 			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
 
-			assertThat(myCaptureQueriesListener.getSelectQueriesForCurrentThread()).hasSize(1);
 			String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "rt1_0.res_type='observation'")).as(selectQuery).isEqualTo(1);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "rt1_0.fhir_id in ('a')")).as(selectQuery).isEqualTo(1);
-		}
-
-		// Search by ID where at least one ID is a numeric ID
-		{
-			SearchParameterMap map = SearchParameterMap.newSynchronous();
-			map.add("_id", new TokenOrListParam(null, "A", obs2id));
-			myCaptureQueriesListener.clear();
-			IBundleProvider outcome = myObservationDao.search(map, new SystemRequestDetails());
-			assertEquals(0, outcome.size());
-			assertThat(outcome.getResources(0, 999)).isEmpty();
-			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-			String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "select t0.res_id from hfj_resource t0")).as(selectQuery).isEqualTo(1);
-			// Because we included a non-forced ID, we need to verify the type
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_type = 'observation'")).as(selectQuery).isEqualTo(1);
-			assertThat(StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_deleted_at is null")).as(selectQuery).isEqualTo(1);
+			assertThat(selectQuery).contains("where (rt1_0.RES_TYPE='Observation' and rt1_0.FHIR_ID='A')");
+			assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		}
 
 	}
@@ -1248,7 +1233,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		myPatientDao.update(p).getId().toUnqualifiedVersionless();
 
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(4, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(3, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 		assertEquals(1, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 		assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
 		assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());

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

@@ -5,6 +5,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
 import ca.uhn.fhir.jpa.api.pid.StreamTemplate;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
@@ -1090,16 +1091,28 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		runInTransaction(() -> {
 			Patient p = new Patient();
-			p.setId(id);
+			p.setId(id.getIdPart());
 			p.setActive(true);
 			p.addName().setFamily("FAMILY");
-			myPatientDao.update(p);
+			IIdType update1Id = myPatientDao.update(p).getId();
+			assertEquals("2", update1Id.getVersionIdPart());
 
 			p = new Patient();
-			p.setId(id);
+			p.setId(id.getIdPart());
 			p.setActive(false);
 			p.addName().setFamily("FAMILY2");
-			myPatientDao.update(p);
+			IIdType update2Id = myPatientDao.update(p).getId();
+			assertEquals("3", update2Id.getVersionIdPart());
+			assertEquals(update1Id.getIdPart(), update2Id.getIdPart());
+		});
+
+		runInTransaction(()->{
+			List<ResourceTable> resourceTables = myResourceTableDao.findAll();
+			assertEquals(1, resourceTables.size());
+			assertEquals(2, resourceTables.get(0).getVersion());
+
+			List<ResourceHistoryTable> versions = myResourceHistoryTableDao.findAllVersionsForResourceIdInOrder(resourceTables.get(0).getResourceId());
+			assertThat(versions.stream().map(ResourceHistoryTable::getVersion).toList()).asList().containsExactly(1L, 2L, 3L);
 		});
 
 		assertEquals(1, myPatientDao.search(SearchParameterMap.newSynchronous("name", new StringParam("family2"))).size());
@@ -1193,62 +1206,29 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	}
 
-	@Test
-	public void testCreateWithIllegalReference() {
+	@ParameterizedTest
+	@ValueSource(booleans = {true, false})
+	public void testCreateWithIllegalReference_InvalidTypeForElement(boolean theClientAssignedId) {
+
 		Observation o1 = new Observation();
 		o1.getCode().addCoding().setSystem("foo").setCode("testChoiceParam01");
-		IIdType id1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
+		IIdType id1;
+		if (theClientAssignedId) {
+			o1.setId("testCreateWithIllegalReference");
+			id1 = myObservationDao.update(o1, mySrd).getId().toUnqualifiedVersionless();
+		} else {
+			id1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
+		}
 
 		try {
 			Patient p = new Patient();
-			p.getManagingOrganization().setReferenceElement(id1);
+			p.getManagingOrganization().setReference(id1.getValue());
 			myPatientDao.create(p, mySrd);
-			fail();
+			fail("");
 		} catch (UnprocessableEntityException e) {
 			assertEquals(Msg.code(931) + "Invalid reference found at path 'Patient.managingOrganization'. Resource type 'Observation' is not valid for this path", e.getMessage());
 		}
 
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReferenceElement(new IdType("Organization", id1.getIdPart()));
-			myPatientDao.create(p, mySrd);
-			fail();
-		} catch (UnprocessableEntityException e) {
-			assertEquals(Msg.code(1095) + "Resource contains reference to unknown resource ID Organization/" + id1.getIdPart(), e.getMessage());
-		}
-
-		// Now with a forced ID
-
-		o1 = new Observation();
-		o1.setId("testCreateWithIllegalReference");
-		o1.getCode().addCoding().setSystem("foo").setCode("testChoiceParam01");
-		id1 = myObservationDao.update(o1, mySrd).getId().toUnqualifiedVersionless();
-
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReferenceElement(id1);
-			myPatientDao.create(p, mySrd);
-			fail();
-		} catch (UnprocessableEntityException e) {
-			assertEquals(Msg.code(931) + "Invalid reference found at path 'Patient.managingOrganization'. Resource type 'Observation' is not valid for this path", e.getMessage());
-		}
-
-		try {
-			Patient p = new Patient();
-			p.getManagingOrganization().setReferenceElement(new IdType("Organization", id1.getIdPart()));
-			myPatientDao.create(p, mySrd);
-			fail();
-		} catch (InvalidRequestException e) {
-			assertEquals(Msg.code(1094) + "Resource Organization/testCreateWithIllegalReference not found, specified in path: Patient.managingOrganization", e.getMessage());
-		}
-
-		// Disable validation
-		myStorageSettings.setEnforceReferenceTargetTypes(false);
-		Patient p = new Patient();
-		p.getManagingOrganization().setReferenceElement(id1);
-		myPatientDao.create(p, mySrd);
-
-
 	}
 
 	@Test
@@ -2803,7 +2783,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 			myPatientDao.read(new IdType("Patient/9999999999999/_history/1"), mySrd);
 			fail();
 		} catch (ResourceNotFoundException e) {
-			assertEquals(Msg.code(1996) + "Resource Patient/9999999999999/_history/1 is not known", e.getMessage());
+			assertEquals(Msg.code(2001) + "Resource Patient/9999999999999 is not known", e.getMessage());
 		}
 
 	}

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -32,6 +32,7 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.OperationOutcomeUtil;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.validation.IValidatorModule;
+import ca.uhn.test.util.LogbackTestExtension;
 import ca.uhn.test.util.LogbackTestExtensionAssert;
 import ch.qos.logback.classic.Level;
 import org.apache.commons.io.IOUtils;
@@ -85,6 +86,7 @@ import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Nested;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.CsvSource;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -113,6 +115,10 @@ import static org.mockito.Mockito.when;
 
 public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ValidateTest.class);
+
+	@RegisterExtension
+	public LogbackTestExtension myLogbackTestExtension = new LogbackTestExtension();
+
 	@Autowired
 	private IValidatorModule myValidatorModule;
 	@Autowired

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java

@@ -169,9 +169,10 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 		List<SqlQuery> selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread();
 		assertEquals(1, selectQueries.size());
 		// Look up the referenced subject/patient
-		String sql = selectQueries.get(0).getSql(true, false).toLowerCase();
-		assertThat(sql).contains(" from hfj_resource ");
-		assertEquals(2, StringUtils.countMatches(selectQueries.get(0).getSql(true, false).toLowerCase(), "partition"));
+		String searchSql = selectQueries.get(0).getSql(true, false);
+		assertThat(searchSql).contains(" from HFJ_RESOURCE ");
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID from"), searchSql);
+		assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
 
 		runInTransaction(() -> {
 			List<ResourceLink> resLinks = myResourceLinkDao.findAll();
@@ -180,7 +181,6 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			assertEquals(obsId.getIdPartAsLong(), resLinks.get(0).getSourceResourcePid());
 			assertEquals(patientId.getIdPartAsLong(), resLinks.get(0).getTargetResourcePid());
 			assertEquals(myPartitionId, resLinks.get(0).getTargetResourcePartitionId().getPartitionId());
-			assertLocalDateFromDbMatches(myPartitionDate, resLinks.get(0).getTargetResourcePartitionId().getPartitionDate());
 		});
 	}
 
@@ -466,7 +466,6 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			assertEquals(myPartitionId, resourceLinks.get(0).getPartitionId().getPartitionId().intValue());
 			assertLocalDateFromDbMatches(myPartitionDate, resourceLinks.get(0).getPartitionId().getPartitionDate());
 			assertEquals(myPartitionId, resourceLinks.get(0).getTargetResourcePartitionId().getPartitionId().intValue());
-			assertLocalDateFromDbMatches(myPartitionDate, resourceLinks.get(0).getTargetResourcePartitionId().getPartitionDate());
 
 			// HFJ_RES_PARAM_PRESENT
 			List<SearchParamPresentEntity> presents = mySearchParamPresentDao.findAllForResource(resourceTable);
@@ -876,7 +875,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			IdType gotId1 = myPatientDao.read(patientId1, mySrd).getIdElement().toUnqualifiedVersionless();
 			assertEquals(patientId1, gotId1);
 
-			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
 
 			// Only the read columns should be used, no criteria use partition
@@ -888,7 +887,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			IdType gotId2 = myPatientDao.read(patientId2, mySrd).getIdElement().toUnqualifiedVersionless();
 			assertEquals(patientId2, gotId2);
 
-			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
 			ourLog.info("Search SQL:\n{}", searchSql);
 
 			// Only the read columns should be used, no criteria use partition
@@ -925,7 +924,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 				myPatientDao.read(patientIdNull, mySrd).getIdElement().toUnqualifiedVersionless();
 				fail();
 			} catch (ResourceNotFoundException e) {
-				assertThat(e.getMessage()).matches(Msg.code(1996) + "Resource Patient/[0-9]+ is not known");
+				assertThat(e.getMessage()).matches(Msg.code(2001) + "Resource Patient/[0-9]+ is not known");
 			}
 		}
 
@@ -936,7 +935,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 				myPatientDao.read(patientId2, mySrd).getIdElement().toUnqualifiedVersionless();
 				fail();
 			} catch (ResourceNotFoundException e) {
-				assertThat(e.getMessage()).matches(Msg.code(1996) + "Resource Patient/[0-9]+ is not known");
+				assertThat(e.getMessage()).matches(Msg.code(2001) + "Resource Patient/[0-9]+ is not known");
 			}
 		}
 	}
@@ -948,6 +947,8 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 		createPatient(withPartition(2), withActiveTrue());
 		IIdType patientId3 = createPatient(withPartition(3), withActiveTrue());
 
+		logAllResources();
+
 		// Two partitions - Found
 		{
 			myCaptureQueriesListener.clear();
@@ -957,22 +958,30 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			assertEquals(patientId1, gotId1);
 
 			// Only the read columns should be used, but no selectors on partition ID
-			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
-			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID,"), searchSql);
+			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
+			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID from"), searchSql);
 			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID in ("), searchSql);
+			assertEquals(2, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
 		}
 
 		// Two partitions including default - Found
 		{
 			myCaptureQueriesListener.clear();
 			myPartitionInterceptor.addReadPartition(RequestPartitionId.fromPartitionNames(PARTITION_1, JpaConstants.DEFAULT_PARTITION_NAME));
-			IdType gotId1 = myPatientDao.read(patientIdNull, mySrd).getIdElement().toUnqualifiedVersionless();
+			IdType gotId1;
+			try {
+				gotId1 = myPatientDao.read(patientIdNull, mySrd).getIdElement().toUnqualifiedVersionless();
+			} finally {
+				myCaptureQueriesListener.logSelectQueries();
+			}
 			assertEquals(patientIdNull, gotId1);
 
 			// Only the read columns should be used, but no selectors on partition ID
-			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
-			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID,"), searchSql);
+			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
+			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID from"), searchSql);
+			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID in ("), searchSql);
 			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID is null"), searchSql);
+			assertEquals(3, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
 		}
 
 		// Two partitions - Not Found
@@ -1010,10 +1019,15 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			IdType gotId1 = myPatientDao.read(patientId1, mySrd).getIdElement().toUnqualifiedVersionless();
 			assertEquals(patientId1, gotId1);
 
-			// Only the read columns should be used, but no selectors on partition ID
-			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+			String resolveIdentitySql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
+			assertEquals(1, StringUtils.countMatches(resolveIdentitySql, "PARTITION_ID from"), resolveIdentitySql);
+			assertEquals(1, StringUtils.countMatches(resolveIdentitySql, "PARTITION_ID in ("), resolveIdentitySql);
+			assertEquals(2, StringUtils.countMatches(resolveIdentitySql, "PARTITION_ID"), resolveIdentitySql);
+
+			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false);
 			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID,"), searchSql);
 			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID in ("), searchSql);
+			assertEquals(2, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
 		}
 
 		// Two partitions including default - Found
@@ -1025,7 +1039,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			assertEquals(patientIdNull, gotId1);
 
 			// Only the read columns should be used, but no selectors on partition ID
-			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
+			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, true);
 			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID,"), searchSql);
 			assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID is null"), searchSql);
 		}
@@ -1079,7 +1093,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 				myPatientDao.read(patientId1, mySrd).getIdElement().toUnqualifiedVersionless();
 				fail();
 			} catch (ResourceNotFoundException e) {
-				assertThat(e.getMessage()).matches(Msg.code(1996) + "Resource Patient/[0-9]+ is not known");
+				assertThat(e.getMessage()).matches(Msg.code(2001) + "Resource Patient/[0-9]+ is not known");
 			}
 		}
 	}
@@ -1269,6 +1283,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			IIdType gotId1 = searchOutcome.getResources(0, 1).get(0).getIdElement().toUnqualifiedVersionless();
 			assertEquals(patientId1, gotId1);
 
+			myCaptureQueriesListener.logSelectQueries();
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
 			ourLog.info("Search SQL:\n{}", searchSql);
 
@@ -1321,6 +1336,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			IIdType gotId1 = searchOutcome.getResources(0, 1).get(0).getIdElement().toUnqualifiedVersionless();
 			assertEquals(patientId1, gotId1);
 
+			myCaptureQueriesListener.logSelectQueries();
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
 			ourLog.info("Search SQL:\n{}", searchSql);
 
@@ -1380,9 +1396,8 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			ourLog.info("Search SQL:\n{}", searchSql);
 
 			// Only the read columns should be used, no criteria use partition
-			assertThat(searchSql).as(searchSql).contains("PARTITION_ID IN ('1')");
-			assertThat(StringUtils.countMatches(searchSql, "PARTITION_ID,")).as(searchSql).isEqualTo(1);
-			assertThat(StringUtils.countMatches(searchSql, "PARTITION_DATE")).as(searchSql).isEqualTo(1);
+			assertThat(searchSql).as(searchSql).contains("PARTITION_ID = '1'");
+			assertThat(StringUtils.countMatches(searchSql, "PARTITION_ID")).as(searchSql).isEqualTo(2);
 		}
 
 		// Read in null Partition
@@ -1430,20 +1445,13 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 			assertEquals(1, searchOutcome.size());
 			IIdType gotId1 = searchOutcome.getResources(0, 1).get(0).getIdElement().toUnqualifiedVersionless();
 			assertEquals(patientId1, gotId1);
+			myCaptureQueriesListener.logSelectQueries();
 
-			// First SQL resolves the forced ID
+			// Performs the search
 			String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false).toUpperCase();
 			ourLog.info("Search SQL:\n{}", searchSql);
-			assertThat(searchSql).as(searchSql).contains("PARTITION_ID IN ('1')");
-			assertThat(StringUtils.countMatches(searchSql, "PARTITION_ID,")).as(searchSql).isEqualTo(1);
-			assertThat(StringUtils.countMatches(searchSql, "PARTITION_DATE")).as(searchSql).isEqualTo(1);
-
-			// Second SQL performs the search
-
-			searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(1).getSql(true, false).toUpperCase();
-			ourLog.info("Search SQL:\n{}", searchSql);
+			assertThat(searchSql).as(searchSql).contains("FROM HFJ_RESOURCE ");
 			assertThat(searchSql).as(searchSql).contains("PARTITION_ID = '1'");
-			assertThat(StringUtils.countMatches(searchSql, "PARTITION_ID")).as(searchSql).isEqualTo(3);
 		}
 
 		// Read in null Partition
@@ -2096,9 +2104,8 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 
 		String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
 		ourLog.info("Search SQL:\n{}", searchSql);
-		assertThat(searchSql).as(searchSql).contains("PARTITION_ID in ('1')");
-		assertThat(StringUtils.countMatches(searchSql, "PARTITION_ID,")).as(searchSql).isEqualTo(1);
-		assertThat(StringUtils.countMatches(searchSql, "PARTITION_DATE")).as(searchSql).isEqualTo(1);
+		assertThat(searchSql).as(searchSql).contains("PARTITION_ID = '1'");
+		assertThat(StringUtils.countMatches(searchSql, "PARTITION_ID")).as(searchSql).isEqualTo(2);
 	}
 
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/interceptor/PatientCompartmentEnforcingInterceptorTest.java

@@ -43,20 +43,25 @@ public class PatientCompartmentEnforcingInterceptorTest extends BaseResourceProv
 		myPartitionSettings.setDefaultPartitionId(ALTERNATE_DEFAULT_ID);
 	}
 
+	@Override
 	@AfterEach
-	public void after() {
+	public void after() throws Exception {
+		super.after();
 		myInterceptorRegistry.unregisterInterceptor(myPatientIdPartitionInterceptor);
 		myInterceptorRegistry.unregisterInterceptor(myForceOffsetSearchModeInterceptor);
 		myInterceptorRegistry.unregisterInterceptor(mySvc);
 
 		myPartitionSettings.setPartitioningEnabled(false);
-		myPartitionSettings.setUnnamedPartitionMode(new PartitionSettings().isUnnamedPartitionMode());
-		myPartitionSettings.setDefaultPartitionId(new PartitionSettings().getDefaultPartitionId());
+		PartitionSettings defaultPartitionSettings = new PartitionSettings();
+		myPartitionSettings.setUnnamedPartitionMode(defaultPartitionSettings.isUnnamedPartitionMode());
+		myPartitionSettings.setDefaultPartitionId(defaultPartitionSettings.getDefaultPartitionId());
+		myPartitionSettings.setAllowReferencesAcrossPartitions(defaultPartitionSettings.getAllowReferencesAcrossPartitions());
 	}
 
 
 	@Test
 	public void testUpdateResource_whenCrossingPatientCompartment_throws() {
+		myPartitionSettings.setAllowReferencesAcrossPartitions(PartitionSettings.CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
 		createPatientA();
 		createPatientB();
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptorTest.java

@@ -188,9 +188,8 @@ public class PatientIdPartitionInterceptorTest extends BaseResourceProviderR4Tes
 		Patient patient = myPatientDao.read(new IdType("Patient/A"), mySrd);
 		assertTrue(patient.getActive());
 		myCaptureQueriesListener.logSelectQueries();
-		assertThat(myCaptureQueriesListener.getSelectQueries()).hasSize(3);
-		assertThat(myCaptureQueriesListener.getSelectQueries().get(0).getSql(false, false)).contains("rt1_0.PARTITION_ID in (?)");
-		assertThat(myCaptureQueriesListener.getSelectQueries().get(1).getSql(false, false)).contains("where rt1_0.PARTITION_ID=? and rt1_0.RES_ID=?");
+		assertThat(myCaptureQueriesListener.getSelectQueries()).hasSize(2);
+		assertThat(myCaptureQueriesListener.getSelectQueries().get(0).getSql(false, false)).contains("rt1_0.PARTITION_ID=?");
 	}
 
 	@Test
@@ -223,9 +222,8 @@ public class PatientIdPartitionInterceptorTest extends BaseResourceProviderR4Tes
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
 
 		List<SqlQuery> selectQueriesForCurrentThread = myCaptureQueriesListener.getSelectQueriesForCurrentThread();
-		assertEquals(4, selectQueriesForCurrentThread.size());
-		assertThat(selectQueriesForCurrentThread.get(0).getSql(false, false)).contains("PARTITION_ID in (?)");
-		assertThat(selectQueriesForCurrentThread.get(1).getSql(false, false)).contains("PARTITION_ID=");
+		assertEquals(3, selectQueriesForCurrentThread.size());
+		assertThat(selectQueriesForCurrentThread.get(0).getSql(false, false)).contains("PARTITION_ID=?");
 	}
 
 
@@ -237,9 +235,8 @@ public class PatientIdPartitionInterceptorTest extends BaseResourceProviderR4Tes
 		IBundleProvider outcome = myPatientDao.search(SearchParameterMap.newSynchronous("_id", new TokenParam("A")), mySrd);
 		assertEquals(1, outcome.size());
 		myCaptureQueriesListener.logSelectQueries();
-		assertThat(myCaptureQueriesListener.getSelectQueries()).hasSize(3);
-		assertThat(myCaptureQueriesListener.getSelectQueries().get(0).getSql(false, false)).contains("rt1_0.PARTITION_ID in (?)");
-		assertThat(myCaptureQueriesListener.getSelectQueries().get(1).getSql(false, false)).contains("t0.PARTITION_ID = ?");
+		assertThat(myCaptureQueriesListener.getSelectQueries()).hasSize(2);
+		assertThat(myCaptureQueriesListener.getSelectQueries().get(0).getSql(false, false)).contains("PARTITION_ID = ?");
 	}
 
 	@Test
@@ -352,9 +349,9 @@ public class PatientIdPartitionInterceptorTest extends BaseResourceProviderR4Tes
 		IBundleProvider outcome = myOrganizationDao.history(new IdType("Organization/C"), null, null, null, mySrd);
 		myCaptureQueriesListener.logSelectQueries();
 		assertEquals(2, outcome.size());
-		assertThat(myCaptureQueriesListener.getSelectQueries()).hasSize(3);
-		assertThat(myCaptureQueriesListener.getSelectQueries().get(0).getSql(false, false)).contains("PARTITION_ID in ");
-		assertThat(myCaptureQueriesListener.getSelectQueries().get(1).getSql(false, false)).contains("PARTITION_ID=");
+		assertThat(myCaptureQueriesListener.getSelectQueries()).hasSize(2);
+		assertThat(myCaptureQueriesListener.getSelectQueries().get(0).getSql(false, false)).contains("PARTITION_ID=?");
+		assertThat(myCaptureQueriesListener.getSelectQueries().get(1).getSql(false, false)).contains("PARTITION_ID in (?)");
 	}
 
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ConsentInterceptorResourceProviderR4IT.java

@@ -137,6 +137,7 @@ public class ConsentInterceptorResourceProviderR4IT extends BaseResourceProvider
 
 		myInterceptorRegistry.unregisterInterceptor(myBinaryStorageInterceptor);
 	}
+
 	@Test
 	public void testSearchAndBlockSomeWithReject() {
 		create50Observations();
@@ -960,7 +961,12 @@ public class ConsentInterceptorResourceProviderR4IT extends BaseResourceProvider
 			String fhirType = theResource.fhirType();
 			IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(fhirType);
 			String currentTransactionName = TransactionSynchronizationManager.getCurrentTransactionName();
-			dao.read(theResource.getIdElement());
+			try {
+				dao.read(theResource.getIdElement());
+			} catch (ResourceNotFoundException e) {
+				// this is expected, the resource isn't saved in the DB yet. But it shouldn't
+				// be an NPE, only a ResourceNotFoundException
+			}
 			return ConsentOutcome.PROCEED;
 		}
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantServerR4Test.java

@@ -531,7 +531,8 @@ public class MultitenantServerR4Test extends BaseMultitenantResourceProviderR4Te
 			myPatientDao.update((Patient) patientA, requestDetails);
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals(Msg.code(2079) + "Resource " + ((Patient) patientA).getResourceType() + "/" + ((Patient) patientA).getIdElement().getIdPart() + " is not known", e.getMessage());
+			String idPart = ((Patient) patientA).getIdElement().getIdPart();
+			assertThat(e.getMessage()).contains("HAPI-0960: Can not create resource with ID[" + idPart + "]");
 		}
 	}
 

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

@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.util.SqlQueryList;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.util.BundleUtil;
+import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
@@ -39,7 +40,7 @@ public class ResourceProviderRevIncludeTest extends BaseResourceProviderR4Test {
 
 
 
-	class SqlCapturingInterceptor {
+	static class SqlCapturingInterceptor {
 		SqlQueryList queryList = null;
 		@Hook(Pointcut.JPA_PERFTRACE_RAW_SQL)
 		public void trackRequest(RequestDetails theRequestDetails, SqlQueryList theQueryList) {
@@ -89,7 +90,7 @@ public class ResourceProviderRevIncludeTest extends BaseResourceProviderR4Test {
 		Bundle bundle = myClient.search()
 			.forResource(Patient.class)
 			.count(200)
-			.where(Patient.RES_ID.exactly().codes(pid.getIdPart()))
+			.where(IAnyResource.RES_ID.exactly().codes(pid.getIdPart()))
 			.revInclude(new Include("CareTeam:subject:Group").setRecurse(true))
 //			.revInclude(new Include("CareTeam:subject:Group"))
 			.revInclude(new Include("Group:member:Patient"))
@@ -128,7 +129,7 @@ public class ResourceProviderRevIncludeTest extends BaseResourceProviderR4Test {
 					}
 					break;
 				default:
-					ourLog.warn(type + " found but not expected");
+					ourLog.warn("{} found but not expected", type);
 			}
 
 			if (patientFound && groupFound && careTeamFound && detectedIssueFound) {
@@ -144,7 +145,7 @@ public class ResourceProviderRevIncludeTest extends BaseResourceProviderR4Test {
 		assertEquals(methodName, patient.getName().get(0).getFamily());
 
 		//Ensure that the revincludes are included in the query list of the sql trace.
-		//TODO GGG/KHS reduce this to something less than 6 by smarter iterating and getting the resource types earlier when needed.
+		//TODO GGG/KHS reduce this to something less than 5 by smarter iterating and getting the resource types earlier when needed.
 		assertThat(sqlCapturingInterceptor.getQueryList()).hasSize(5);
 		myInterceptorRegistry.unregisterInterceptor(sqlCapturingInterceptor);
 	}
@@ -166,7 +167,7 @@ public class ResourceProviderRevIncludeTest extends BaseResourceProviderR4Test {
 		// DetectedIssue?_id=123&_include=DetectedIssue:author&_revinclude=PractitionerRole:practitioner
 		Bundle bundle = myClient.search()
 			.forResource(DetectedIssue.class)
-			.where(DetectedIssue.RES_ID.exactly().codes(detectedIssueId.getIdPart()))
+			.where(IAnyResource.RES_ID.exactly().codes(detectedIssueId.getIdPart()))
 			.include(new Include("DetectedIssue:author"))
 			.revInclude(new Include("PractitionerRole:practitioner").setRecurse(true))
 			.returnBundle(Bundle.class)

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java

@@ -292,11 +292,11 @@ public class GiantTransactionPerfTest {
 
 		ourLog.info("Merges:\n * " + myEntityManager.myMergeCount.stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
 
-		assertThat(myEntityManager.myPersistCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList())).containsExactly("ResourceTable");
+		assertThat(myEntityManager.myPersistCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList())).containsExactly("ResourceTable", "ResourceHistoryTable");
 		assertThat(myEntityManager.myMergeCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList())).containsExactlyInAnyOrder("ResourceTable", "ResourceIndexedSearchParamToken", "ResourceIndexedSearchParamToken");
 		assertEquals(1, myEntityManager.myFlushCount);
 		assertEquals(1, myResourceVersionSvc.myGetVersionMap);
-		assertEquals(1, myResourceHistoryTableDao.mySaveCount);
+		assertEquals(0, myResourceHistoryTableDao.mySaveCount);
 	}
 
 	@Test
@@ -632,12 +632,12 @@ public class GiantTransactionPerfTest {
 
 		@Override
 		public FlushModeType getFlushMode() {
-			throw new UnsupportedOperationException();
+			return FlushModeType.AUTO;
 		}
 
 		@Override
 		public void setFlushMode(FlushModeType flushMode) {
-			throw new UnsupportedOperationException();
+			// ignore
 		}
 
 		@Override

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/subscription/async/AsyncSubscriptionMessageSubmissionIT.java

@@ -17,6 +17,7 @@ import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionMatcherInterc
 import ca.uhn.fhir.jpa.subscription.submit.interceptor.SynchronousSubscriptionMatcherInterceptor;
 import ca.uhn.fhir.jpa.test.util.StoppableSubscriptionDeliveringRestHookSubscriber;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.test.util.LogbackTestExtension;
 import ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.spi.ILoggingEvent;
 import com.fasterxml.jackson.core.JsonProcessingException;
@@ -28,6 +29,7 @@ import org.hl7.fhir.r4.model.Subscription;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -48,6 +50,9 @@ import static org.junit.jupiter.api.Assertions.assertFalse;
 public class AsyncSubscriptionMessageSubmissionIT extends BaseSubscriptionsR4Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(AsyncSubscriptionMessageSubmissionIT.class);
 
+	@RegisterExtension
+	public LogbackTestExtension myLogbackTestExtension = new LogbackTestExtension(AsyncResourceModifiedSubmitterSvc.class);
+
 	@SpyBean
 	IResourceModifiedConsumer myResourceModifiedConsumer;
 

hapi-fhir-jpaserver-test-r4b/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-r5/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirSystemDaoTransactionR5Test.java

@@ -2,12 +2,20 @@ package ca.uhn.fhir.jpa.dao.r5;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermConceptMap;
+import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.BundleBuilder;
 import jakarta.annotation.Nonnull;
 import org.hl7.fhir.r5.model.BooleanType;
 import org.hl7.fhir.r5.model.Bundle;
+import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.CodeType;
+import org.hl7.fhir.r5.model.ConceptMap;
+import org.hl7.fhir.r5.model.Enumerations;
 import org.hl7.fhir.r5.model.IdType;
 import org.hl7.fhir.r5.model.Observation;
 import org.hl7.fhir.r5.model.Parameters;
@@ -15,6 +23,7 @@ import org.hl7.fhir.r5.model.Patient;
 import org.hl7.fhir.r5.model.Quantity;
 import org.hl7.fhir.r5.model.Reference;
 import org.hl7.fhir.r5.model.UriType;
+import org.hl7.fhir.r5.model.ValueSet;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -22,14 +31,17 @@ import org.junit.jupiter.params.provider.CsvSource;
 import org.junit.jupiter.params.provider.ValueSource;
 
 import java.io.IOException;
+import java.util.List;
 import java.util.UUID;
 
 import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.assertj.core.api.Assertions.assertThat;
-import static org.junit.jupiter.api.Assertions.fail;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.Mockito.when;
 
 public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
@@ -363,21 +375,21 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 		myCaptureQueriesListener.logSelectQueries();
 		if (theTargetAlreadyExists) {
 			if (theResourceChanges) {
-				assertEquals(6, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+				assertEquals(5, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 				assertEquals(1, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 				assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 			} else {
-				assertEquals(6, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+				assertEquals(5, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 				assertEquals(0, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 				assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 			}
 		} else {
 			if (theResourceChanges) {
-				assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+				assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 				assertEquals(7, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 				assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 			} else {
-				assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+				assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 				assertEquals(7, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
 				assertEquals(0, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
 			}
@@ -488,14 +500,14 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 		assertNull(outcome.getEntry().get(0).getResponse().getLocation());
 		assertEquals("204 No Content", outcome.getEntry().get(0).getResponse().getStatus());
-		assertThat(outcome.getEntry().get(1).getResponse().getLocation()).endsWith("_history/2");
+		assertThat(outcome.getEntry().get(1).getResponse().getLocation()).endsWith("_history/3");
 		assertEquals("201 Created", outcome.getEntry().get(1).getResponse().getStatus());
 
 		logAllResources();
 		logAllResourceVersions();
 
 		actual = myPatientDao.read(resourceId, mySrd);
-		assertEquals("2", actual.getIdElement().getVersionIdPart());
+		assertEquals("3", actual.getIdElement().getVersionIdPart());
 		assertEquals("http://foo", actual.getIdentifierFirstRep().getSystem());
 		assertEquals("http://tag", actual.getMeta().getTagFirstRep().getSystem());
 
@@ -505,11 +517,11 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 		assertNull(outcome.getEntry().get(0).getResponse().getLocation());
 		assertEquals("204 No Content", outcome.getEntry().get(0).getResponse().getStatus());
-		assertThat(outcome.getEntry().get(1).getResponse().getLocation()).endsWith("_history/3");
+		assertThat(outcome.getEntry().get(1).getResponse().getLocation()).endsWith("_history/5");
 		assertEquals("201 Created", outcome.getEntry().get(1).getResponse().getStatus());
 
 		actual = myPatientDao.read(resourceId, mySrd);
-		assertEquals("3", actual.getIdElement().getVersionIdPart());
+		assertEquals("5", actual.getIdElement().getVersionIdPart());
 		assertEquals("http://foo", actual.getIdentifierFirstRep().getSystem());
 		assertEquals("http://tag", actual.getMeta().getTagFirstRep().getSystem());
 	}
@@ -525,7 +537,6 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 	}
 
 
-
 	@Test
 	public void testConditionalDeleteAndConditionalUpdateOnSameResource_MultipleMatchesAlreadyExist() {
 
@@ -558,7 +569,7 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 
 		// First pass (resource doesn't already exist)
 
-		outcome = mySystemDao.transaction(mySrd, createBundleWithConditionalDeleteAndConditionalCreateOnSameResource(myFhirContext));
+		outcome = mySystemDao.transaction(mySrd, createBundleWithConditionalDeleteAndConditionalCreateOnSameResource(myFhirContext, "FAMILY-0"));
 		assertNull(outcome.getEntry().get(0).getResponse().getLocation());
 		assertEquals("204 No Content", outcome.getEntry().get(0).getResponse().getStatus());
 		assertThat(outcome.getEntry().get(1).getResponse().getLocation()).endsWith("_history/1");
@@ -569,23 +580,26 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 		assertEquals("1", actual.getIdElement().getVersionIdPart());
 		assertEquals("http://foo", actual.getIdentifierFirstRep().getSystem());
 		assertEquals("http://tag", actual.getMeta().getTagFirstRep().getSystem());
+		assertEquals("FAMILY-0", actual.getNameFirstRep().getFamily());
 
 		// Second pass (resource already exists)
 
 		myCaptureQueriesListener.clear();
-		outcome = mySystemDao.transaction(mySrd, createBundleWithConditionalDeleteAndConditionalCreateOnSameResource(myFhirContext));
+		outcome = mySystemDao.transaction(mySrd, createBundleWithConditionalDeleteAndConditionalCreateOnSameResource(myFhirContext, "FAMILY-1"));
 		myCaptureQueriesListener.logUpdateQueries();
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 		assertNull(outcome.getEntry().get(0).getResponse().getLocation());
 		assertEquals("204 No Content", outcome.getEntry().get(0).getResponse().getStatus());
 		assertThat(outcome.getEntry().get(1).getResponse().getLocation()).endsWith("_history/1");
 		assertEquals("201 Created", outcome.getEntry().get(1).getResponse().getStatus());
+		resourceId = new IdType(outcome.getEntry().get(1).getResponse().getLocation()).toUnqualifiedVersionless();
+		actual = myPatientDao.read(resourceId, mySrd);
+		assertEquals("FAMILY-1", actual.getNameFirstRep().getFamily());
 
 		logAllResources();
 		logAllResourceVersions();
 
 		IdType resourceId2 = new IdType(outcome.getEntry().get(1).getResponse().getLocation()).toUnqualifiedVersionless();
-		assertThat(resourceId2.getIdPart()).isNotEqualTo(resourceId.getIdPart());
 		actual = myPatientDao.read(resourceId2, mySrd);
 		assertEquals("1", actual.getIdElement().getVersionIdPart());
 		assertEquals("http://foo", actual.getIdentifierFirstRep().getSystem());
@@ -593,7 +607,7 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 
 		// Third pass (resource already exists)
 
-		outcome = mySystemDao.transaction(mySrd, createBundleWithConditionalDeleteAndConditionalCreateOnSameResource(myFhirContext));
+		outcome = mySystemDao.transaction(mySrd, createBundleWithConditionalDeleteAndConditionalCreateOnSameResource(myFhirContext, "FAMILY-2"));
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 		assertNull(outcome.getEntry().get(0).getResponse().getLocation());
 		assertEquals("204 No Content", outcome.getEntry().get(0).getResponse().getStatus());
@@ -606,6 +620,7 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 		assertEquals("1", actual.getIdElement().getVersionIdPart());
 		assertEquals("http://foo", actual.getIdentifierFirstRep().getSystem());
 		assertEquals("http://tag", actual.getMeta().getTagFirstRep().getSystem());
+		assertEquals("FAMILY-2", actual.getNameFirstRep().getFamily());
 	}
 
 	/**
@@ -632,22 +647,32 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 		assertEquals("http://foo", actual.getIdentifierFirstRep().getSystem());
 		assertEquals("http://tag", actual.getMeta().getTagFirstRep().getSystem());
 
+		logAllResources();
+		logAllResourceVersions();
+
 		// Second pass (resource already exists)
 
 		myCaptureQueriesListener.clear();
-		outcome = mySystemDao.transaction(mySrd, createBundleWithDeleteAndUpdateOnSameResource(myFhirContext));
+		try {
+			outcome = mySystemDao.transaction(mySrd, createBundleWithDeleteAndUpdateOnSameResource(myFhirContext));
+		} finally {
+			myCaptureQueriesListener.logInsertQueries();
+		}
 		myCaptureQueriesListener.logUpdateQueries();
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
 		assertEquals("Patient/P/_history/2", outcome.getEntry().get(0).getResponse().getLocation());
 		assertEquals("204 No Content", outcome.getEntry().get(0).getResponse().getStatus());
-		assertEquals("Patient/P/_history/2", outcome.getEntry().get(1).getResponse().getLocation());
+		assertEquals("Patient/P/_history/3", outcome.getEntry().get(1).getResponse().getLocation());
 		assertEquals("201 Created", outcome.getEntry().get(1).getResponse().getStatus());
 
 		logAllResources();
 		logAllResourceVersions();
 
-		actual = myPatientDao.read(resourceId, mySrd);
-		assertEquals("2", actual.getIdElement().getVersionIdPart());
+		assertThrows(ResourceGoneException.class, ()->myPatientDao.read(resourceId.withVersion("2"), mySrd));
+		actual = myPatientDao.read(resourceId.withVersion("3"), mySrd);
+		assertEquals("3", actual.getIdElement().getVersionIdPart());
+		actual = myPatientDao.read(resourceId.toVersionless(), mySrd);
+		assertEquals("3", actual.getIdElement().getVersionIdPart());
 		assertEquals("http://foo", actual.getIdentifierFirstRep().getSystem());
 		assertEquals("http://tag", actual.getMeta().getTagFirstRep().getSystem());
 
@@ -655,26 +680,47 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 
 		outcome = mySystemDao.transaction(mySrd, createBundleWithDeleteAndUpdateOnSameResource(myFhirContext));
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
-		assertEquals("Patient/P/_history/3", outcome.getEntry().get(0).getResponse().getLocation());
+		assertEquals("Patient/P/_history/4", outcome.getEntry().get(0).getResponse().getLocation());
 		assertEquals("204 No Content", outcome.getEntry().get(0).getResponse().getStatus());
-		assertEquals("Patient/P/_history/3", outcome.getEntry().get(1).getResponse().getLocation());
+		assertEquals("Patient/P/_history/5", outcome.getEntry().get(1).getResponse().getLocation());
 		assertEquals("201 Created", outcome.getEntry().get(1).getResponse().getStatus());
 
-		actual = myPatientDao.read(resourceId, mySrd);
-		assertEquals("3", actual.getIdElement().getVersionIdPart());
+		actual = myPatientDao.read(resourceId.withVersion("5"), mySrd);
+		assertEquals("5", actual.getIdElement().getVersionIdPart());
 		assertEquals("http://foo", actual.getIdentifierFirstRep().getSystem());
 		assertEquals("http://tag", actual.getMeta().getTagFirstRep().getSystem());
 
 
 	}
 
+	@Test
+	public void testDeleteThenConditionalCreateOnTheSameResource() {
+		// Create a patient
+		myPatientDao.update(createPatientWithIdentifierAndTag().setActive(true), mySrd);
+
+		// Transaction which deletes that patient by ID and then recreates it conditionally
+		BundleBuilder bb = new BundleBuilder(myFhirContext);
+		bb.addTransactionDeleteEntry(new IdType("Patient/P"));
+		bb.addTransactionUpdateEntry(createPatientWithIdentifierAndTag().setActive(false)).conditional("Patient?identifier=http://foo|bar");
+		Bundle outcome = mySystemDao.transaction(mySrd, bb.getBundleTyped());
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
+
+		assertThat(outcome.getEntry().get(0).getResponse().getLocation()).endsWith("_history/2");
+		assertThat(outcome.getEntry().get(1).getResponse().getLocation()).endsWith("_history/3");
+
+		// Verify
+		Patient patient = myPatientDao.read(new IdType("Patient/P"), mySrd);
+		assertFalse(patient.getActive());
+		assertEquals("3", patient.getIdElement().getVersionIdPart());
+	}
+
 
 	/**
 	 * See #5110
 	 */
 	@Test
 	public void testTransactionWithMissingSystem() {
-        BundleBuilder bb = new BundleBuilder(myFhirContext);
+		BundleBuilder bb = new BundleBuilder(myFhirContext);
 		Patient patient = new Patient();
 		patient.setId(IdType.newRandomUuid());
 
@@ -685,13 +731,149 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 
 		patient.addName().setText("Jane Doe");
 		bb.addTransactionCreateEntry(patient);
-        Bundle inputBundle = bb.getBundleTyped();
+		Bundle inputBundle = bb.getBundleTyped();
 
 		Bundle outputBundle = mySystemDao.transaction(mySrd, inputBundle);
 
 		assertThat(outputBundle.getEntry().get(0).getResponse().getLocation()).matches("Patient/[0-9]+/_history/1");
 	}
 
+	/**
+	 * Make sure we can successfully handle this in a transaction, including
+	 * creating the extra table rows for this resource type
+	 */
+	@Test
+	public void testCreateCodeSystem() {
+		CodeSystem cs = newDummyCodeSystem();
+
+		BundleBuilder bb = new BundleBuilder(myFhirContext);
+		bb.addTransactionCreateEntry(cs);
+
+		// Test
+		mySystemDao.transaction(mySrd, bb.getBundleTyped());
+
+		// Verify
+		runInTransaction(() -> {
+			List<TermCodeSystem> valueSets = myTermCodeSystemDao.findAll();
+			assertThat(valueSets).hasSize(1);
+		});
+	}
+
+	/**
+	 * Make sure we can successfully handle this in a transaction, including
+	 * creating the extra table rows for this resource type
+	 */
+	@Test
+	public void testCreateConceptMap() {
+		ConceptMap cm = newDummyConceptMap();
+
+		BundleBuilder bb = new BundleBuilder(myFhirContext);
+		bb.addTransactionCreateEntry(cm);
+
+		// Test
+		mySystemDao.transaction(mySrd, bb.getBundleTyped());
+
+		// Verify
+		runInTransaction(() -> {
+			List<TermConceptMap> valueSets = myTermConceptMapDao.findAll();
+			assertThat(valueSets).hasSize(1);
+		});
+	}
+
+	/**
+	 * Make sure we can successfully handle this in a transaction, including
+	 * creating the extra table rows for this resource type
+	 */
+	@Test
+	public void testCreateValueSet() {
+		ValueSet vs = newDummyValueSet();
+
+		BundleBuilder bb = new BundleBuilder(myFhirContext);
+		bb.addTransactionCreateEntry(vs);
+
+		// Test
+		mySystemDao.transaction(mySrd, bb.getBundleTyped());
+
+		// Verify
+		runInTransaction(() -> {
+			List<TermValueSet> valueSets = myTermValueSetDao.findAll();
+			assertThat(valueSets).hasSize(1);
+		});
+	}
+
+	/**
+	 * Two resources with the same URL in a single transaction
+	 * bundle should error gracefully
+	 */
+	@Test
+	public void testCreateDuplicateCodeSystem() {
+
+		BundleBuilder bb = new BundleBuilder(myFhirContext);
+		bb.addTransactionCreateEntry(newDummyCodeSystem());
+		bb.addTransactionCreateEntry(newDummyCodeSystem());
+
+		// Test
+		try {
+			mySystemDao.transaction(mySrd, bb.getBundleTyped());
+			fail();
+		} catch (UnprocessableEntityException e) {
+			// Verify
+			assertThat(e.getMessage()).contains("Can not create multiple CodeSystem resources with CodeSystem.url");
+		}
+
+	}
+
+	/**
+	 * Two resources with the same URL in a single transaction
+	 * bundle should error gracefully
+	 */
+	@Test
+	public void testCreateDuplicateValueSet() {
+
+		BundleBuilder bb = new BundleBuilder(myFhirContext);
+		bb.addTransactionCreateEntry(newDummyValueSet());
+		bb.addTransactionCreateEntry(newDummyValueSet());
+
+		// Test
+		try {
+			mySystemDao.transaction(mySrd, bb.getBundleTyped());
+			fail();
+		} catch (UnprocessableEntityException e) {
+			// Verify
+			assertThat(e.getMessage()).contains("Can not create multiple ValueSet resources with ValueSet.url");
+		}
+
+	}
+
+	@Nonnull
+	private static CodeSystem newDummyCodeSystem() {
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setVersion("1.2.3");
+		cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		cs.addConcept().setCode("HELLO");
+		return cs;
+	}
+
+	@Nonnull
+	private static ConceptMap newDummyConceptMap() {
+		ConceptMap cm = new ConceptMap();
+		cm.setUrl("http://foo");
+		cm.setVersion("1.2.3");
+		cm.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		return cm;
+	}
+
+	@Nonnull
+	private static ValueSet newDummyValueSet() {
+		ValueSet vs = new ValueSet();
+		vs.setUrl("http://foo");
+		vs.setVersion("1.2.3");
+		vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		vs.getCompose().addInclude().setSystem("http://hl7.org/fhir/administrative-gender");
+		return vs;
+	}
+
 
 	@Nonnull
 	private static Bundle createBundleWithConditionalDeleteAndConditionalUpdateOnSameResource(FhirContext theFhirContext) {
@@ -705,13 +887,14 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 	}
 
 	@Nonnull
-	private static Bundle createBundleWithConditionalDeleteAndConditionalCreateOnSameResource(FhirContext theFhirContext) {
+	private static Bundle createBundleWithConditionalDeleteAndConditionalCreateOnSameResource(FhirContext theFhirContext, String theFamilyName) {
 		// Build a new bundle each time we need it
 		BundleBuilder bb = new BundleBuilder(theFhirContext);
 		bb.addTransactionDeleteConditionalEntry("Patient?identifier=http://foo|bar");
 
 		Patient patient = createPatientWithIdentifierAndTag();
-		patient.setId((String)null);
+		patient.setId((String) null);
+		patient.getNameFirstRep().setFamily(theFamilyName);
 		bb.addTransactionCreateEntry(patient).conditional("Patient?identifier=http://foo|bar");
 		return bb.getBundleTyped();
 	}

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/UpliftedRefchainsAndChainedSortingR5Test.java

@@ -247,9 +247,9 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
 
 		// Verify SQL
 
-		// 1- Resolve resource forced IDs, and 2- Resolve Practitioner/PR1 reference
+		// 2- Resolve Practitioner/PR1 reference
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 
 		// Verify correct indexes are written
 
@@ -291,9 +291,9 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
 
 		// Verify SQL
 
-		// 1- Resolve resource forced IDs, and 2- Resolve Practitioner/PR1 reference
+		// 1- Resolve Practitioner/PR1 reference
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 
 		// Verify correct indexes are written
 
@@ -337,7 +337,7 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
 
 		// 1- Resolve resource forced IDs, and 2- Resolve Practitioner/PR1 reference
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(3, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(2, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 
 		// Verify correct indexes are written
 
@@ -382,7 +382,7 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
 
 		// 1- Resolve resource forced IDs, and 2- Resolve Practitioner/PR1 reference
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(9, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(8, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 
 		// Verify correct indexes are written
 
@@ -426,7 +426,7 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
 		// Verify SQL
 
 		// 1- Resolve resource forced IDs, and 2- Resolve Practitioner/PR1 reference
-		assertEquals(4, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(3, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 
 		// Verify correct indexes are written
 
@@ -476,7 +476,7 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
 		// Verify SQL
 
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
-		assertEquals(10, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
+		assertEquals(9, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
 
 		// Verify correct indexes are written
 

hapi-fhir-jpaserver-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java

@@ -566,9 +566,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 	@RegisterExtension
 	private final PreventDanglingInterceptorsExtension myPreventDanglingInterceptorsExtension = new PreventDanglingInterceptorsExtension(()-> myInterceptorRegistry);
 
-	@RegisterExtension
-	public LogbackTestExtension myLogbackTestExtension = new LogbackTestExtension();
-
 	@AfterEach()
 	@Order(0)
 	public void afterCleanupDao() {

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaTest.java

@@ -20,7 +20,9 @@
 package ca.uhn.fhir.jpa.test;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.ParserOptions;
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.interceptor.api.Pointcut;
@@ -158,6 +160,7 @@ import java.util.stream.Stream;
 import static ca.uhn.fhir.rest.api.Constants.HEADER_CACHE_CONTROL;
 import static ca.uhn.fhir.util.TestUtil.doRandomizeLocaleAndTimezone;
 import static java.util.stream.Collectors.joining;
+import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
 import static org.awaitility.Awaitility.await;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -398,9 +401,13 @@ public abstract class BaseJpaTest extends BaseTest {
 		JpaStorageSettings defaultConfig = new JpaStorageSettings();
 		myStorageSettings.setAdvancedHSearchIndexing(defaultConfig.isAdvancedHSearchIndexing());
 		myStorageSettings.setAllowContainsSearches(defaultConfig.isAllowContainsSearches());
+		myStorageSettings.setDeleteEnabled(defaultConfig.isDeleteEnabled());
 		myStorageSettings.setIncludeHashIdentityForTokenSearches(defaultConfig.isIncludeHashIdentityForTokenSearches());
 		myStorageSettings.setMaximumIncludesToLoadPerPage(defaultConfig.getMaximumIncludesToLoadPerPage());
+		myStorageSettings.getTreatBaseUrlsAsLocal().clear();
 
+		ParserOptions defaultParserOptions = new ParserOptions();
+		myFhirContext.getParserOptions().setStripVersionsFromReferences(defaultParserOptions.isStripVersionsFromReferences());
 	}
 
 	@AfterEach
@@ -938,7 +945,10 @@ public abstract class BaseJpaTest extends BaseTest {
 			dao.read(theId, mySrd);
 			fail("");
 		} catch (ResourceNotFoundException e) {
-			// good
+			assertThat(e.getMessage()).containsAnyOf(
+				Msg.code(1996) + "Resource " + theId.toUnqualifiedVersionless().getValue() + " is not known",
+				Msg.code(2001) + "Resource " + theId.toUnqualifiedVersionless().getValue() + " is not known"
+			);
 		}
 	}
 }

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-server-cds-hooks/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-server-mdm/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.6-SNAPSHOT</version>
+		<version>7.7.7-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/svc/MdmSurvivorshipSvcImpl.java

@@ -24,7 +24,9 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
+import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
 import ca.uhn.fhir.mdm.api.IMdmLinkQuerySvc;
 import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
@@ -40,6 +42,7 @@ import ca.uhn.fhir.util.TerserUtil;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.springframework.data.domain.Page;
 
 import java.util.ArrayList;
@@ -153,12 +156,15 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
 		Page<MdmLinkJson> linksQuery = myMdmLinkQuerySvc.queryLinks(searchParameters, theMdmTransactionContext);
 
 		// we want it ordered
-		List<String> sourceIds = new ArrayList<>();
+		List<IIdType> sourceIds = new ArrayList<>();
 		linksQuery.forEach(link -> {
 			String sourceId = link.getSourceId();
-			// we want only the id part, not the resource type
-			sourceId = sourceId.replace(resourceType + "/", "");
-			sourceIds.add(sourceId);
+			if (!sourceId.contains("/")) {
+				sourceId = resourceType + "/" + sourceId;
+			}
+			IIdType id = myFhirContext.getVersion().newIdType();
+			id.setValue(sourceId);
+			sourceIds.add(id);
 		});
 		Map<String, IResourcePersistentId> sourceIdToPid = new HashMap<>();
 		if (!sourceIds.isEmpty()) {
@@ -166,15 +172,19 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
 			myTransactionService
 					.withRequest(new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.allPartitions()))
 					.execute(() -> {
-						Map<String, ? extends IResourcePersistentId> ids =
-								myIIdHelperService.resolveResourcePersistentIds(
-										RequestPartitionId.allPartitions(), resourceType, sourceIds);
-						sourceIdToPid.putAll(ids);
+						Map<IIdType, ? extends IResourceLookup<?>> ids = myIIdHelperService.resolveResourceIdentities(
+								RequestPartitionId.allPartitions(),
+								sourceIds,
+								ResolveIdentityMode.includeDeleted().cacheOk());
+						for (Map.Entry<IIdType, ? extends IResourceLookup<?>> entry : ids.entrySet()) {
+							sourceIdToPid.put(
+									entry.getKey().getIdPart(), entry.getValue().getPersistentId());
+						}
 					});
 		}
 
 		return sourceIds.stream().map(id -> {
-			IResourcePersistentId<?> pid = sourceIdToPid.get(id);
+			IResourcePersistentId<?> pid = sourceIdToPid.get(id.getIdPart());
 			return dao.readByPid(pid);
 		});
 	}