Standardize on one Transactional annotation (#4130)

* Standardize on one Transactional annotation

* Add changelog

* Disable checkstyle rule

* Fix up transactions

* Test fixes

* Test cleanup

* License headers

* One more dep bump

* Resolve commit issue

* Test fixes

* Test fix

* Dep bump

* Fix

* Fix test

* Version bump

* Test fixes

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>6.2.0-PRE13-SNAPSHOT</version>
+		 <version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-batch/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>6.2.0-PRE13-SNAPSHOT</version>
+    <version>6.2.0-PRE15-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java

@@ -106,7 +106,7 @@ public class FhirServerConfig {
 
 	@Primary
 	@Bean
-	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
 		JpaTransactionManager retVal = new JpaTransactionManager();
 		retVal.setEntityManagerFactory(entityManagerFactory);
 		return retVal;

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java

@@ -102,7 +102,7 @@ public class FhirServerConfigDstu3 {
 
 	@Primary
 	@Bean
-	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
 		JpaTransactionManager retVal = new JpaTransactionManager();
 		retVal.setEntityManagerFactory(entityManagerFactory);
 		return retVal;

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigR4.java

@@ -102,7 +102,7 @@ public class FhirServerConfigR4 {
 
 	@Primary
 	@Bean
-	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
 		JpaTransactionManager retVal = new JpaTransactionManager();
 		retVal.setEntityManagerFactory(entityManagerFactory);
 		return retVal;

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4130-transaction-scope-cleanup.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 4130
+title: "A transaction scoping bug in Batch2 has been resolved, preventing a crash on Postgres. We have also
+   standardized on the Spring @Transactional annotation, and removed use of the equivalent javax.transaction 
+   annotation."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/changes.yaml

@@ -5,6 +5,11 @@
 (dependent HAPI modules listed in brackets):
 <ul>
 <li>Woodstox (Base): 6.2.5 -> 6.3.1</li>
+<li>Spring (JPA): 5.3.20 -> 5.3.23</li>
+<li>Postgresql JDBC (JPA): 42.4.1 -> 42.5.0</li>
+<li>H2 (JPA): 2.1.212 -> 2.1.214</li>
+<li>Caffeine (JPA): 2.9.1 -> 3.1.1</li>
+<li>Spring Boot (Boot): 2.6.7 -> 2.7.4</li>
 </ul>
 "
 

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaBatch2Config.java

@@ -30,6 +30,7 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Primary;
+import org.springframework.transaction.PlatformTransactionManager;
 
 @Configuration
 @Import({
@@ -38,14 +39,14 @@ import org.springframework.context.annotation.Primary;
 public class JpaBatch2Config extends BaseBatch2Config {
 
 	@Bean
-	public IJobPersistence batch2JobInstancePersister(IBatch2JobInstanceRepository theJobInstanceRepository, IBatch2WorkChunkRepository theWorkChunkRepository) {
+	public IJobPersistence batch2JobInstancePersister(IBatch2JobInstanceRepository theJobInstanceRepository, IBatch2WorkChunkRepository theWorkChunkRepository, PlatformTransactionManager theTransactionManager) {
-		return new JpaJobPersistenceImpl(theJobInstanceRepository, theWorkChunkRepository);
+		return new JpaJobPersistenceImpl(theJobInstanceRepository, theWorkChunkRepository, theTransactionManager);
 	}
 
 	@Primary
 	@Bean
-	public IJobPersistence batch2JobInstancePersisterWrapper(IBatch2JobInstanceRepository theJobInstanceRepository, IBatch2WorkChunkRepository theWorkChunkRepository) {
+	public IJobPersistence batch2JobInstancePersisterWrapper(IBatch2JobInstanceRepository theJobInstanceRepository, IBatch2WorkChunkRepository theWorkChunkRepository, PlatformTransactionManager theTransactionManager) {
-		IJobPersistence retVal = batch2JobInstancePersister(theJobInstanceRepository, theWorkChunkRepository);
+		IJobPersistence retVal = batch2JobInstancePersister(theJobInstanceRepository, theWorkChunkRepository, theTransactionManager);
 		// Avoid H2 synchronization issues caused by
 		// https://github.com/h2database/h2database/issues/1808
 		if ("true".equals(System.getProperty("unit_test_mode"))) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java

@@ -35,7 +35,6 @@ import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
 import ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity;
 import ca.uhn.fhir.jpa.util.JobInstanceUtil;
 import ca.uhn.fhir.model.api.PagingIterator;
-import ca.uhn.fhir.narrative.BaseThymeleafNarrativeGenerator;
 import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
@@ -44,9 +43,13 @@ import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
-import javax.transaction.Transactional;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.Iterator;
@@ -59,24 +62,29 @@ import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
-@Transactional(Transactional.TxType.REQUIRES_NEW)
 public class JpaJobPersistenceImpl implements IJobPersistence {
 	private static final Logger ourLog = LoggerFactory.getLogger(JpaJobPersistenceImpl.class);
 
 	private final IBatch2JobInstanceRepository myJobInstanceRepository;
 	private final IBatch2WorkChunkRepository myWorkChunkRepository;
+	private final TransactionTemplate myTxTemplate;
 
 	/**
 	 * Constructor
 	 */
-	public JpaJobPersistenceImpl(IBatch2JobInstanceRepository theJobInstanceRepository, IBatch2WorkChunkRepository theWorkChunkRepository) {
+	public JpaJobPersistenceImpl(IBatch2JobInstanceRepository theJobInstanceRepository, IBatch2WorkChunkRepository theWorkChunkRepository, PlatformTransactionManager theTransactionManager) {
 		Validate.notNull(theJobInstanceRepository);
 		Validate.notNull(theWorkChunkRepository);
 		myJobInstanceRepository = theJobInstanceRepository;
 		myWorkChunkRepository = theWorkChunkRepository;
+
+		// TODO: JA replace with HapiTransactionManager in megascale ticket
+		myTxTemplate = new TransactionTemplate(theTransactionManager);
+		myTxTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public String storeWorkChunk(BatchWorkChunk theBatchWorkChunk) {
 		Batch2WorkChunkEntity entity = new Batch2WorkChunkEntity();
 		entity.setId(UUID.randomUUID().toString());
@@ -94,6 +102,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public Optional<WorkChunk> fetchWorkChunkSetStartTimeAndMarkInProgress(String theChunkId) {
 		myWorkChunkRepository.updateChunkStatusForStart(theChunkId, new Date(), StatusEnum.IN_PROGRESS);
 		Optional<Batch2WorkChunkEntity> chunk = myWorkChunkRepository.findById(theChunkId);
@@ -101,6 +110,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public String storeNewInstance(JobInstance theInstance) {
 		Validate.isTrue(isBlank(theInstance.getInstanceId()));
 
@@ -120,18 +130,22 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 		return entity.getId();
 	}
 
+	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public List<JobInstance> fetchInstancesByJobDefinitionIdAndStatus(String theJobDefinitionId, Set<StatusEnum> theRequestedStatuses, int thePageSize, int thePageIndex) {
 		PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.ASC, "myCreateTime");
 		return toInstanceList(myJobInstanceRepository.fetchInstancesByJobDefinitionIdAndStatus(theJobDefinitionId, theRequestedStatuses, pageRequest));
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public List<JobInstance> fetchInstancesByJobDefinitionId(String theJobDefinitionId, int thePageSize, int thePageIndex) {
 		PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.ASC, "myCreateTime");
 		return toInstanceList(myJobInstanceRepository.findInstancesByJobDefinitionId(theJobDefinitionId, pageRequest));
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public Page<JobInstance> fetchJobInstances(JobInstanceFetchRequest theRequest) {
 		PageRequest pageRequest = PageRequest.of(
 			theRequest.getPageStart(),
@@ -150,11 +164,13 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 
 	@Override
 	@Nonnull
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public Optional<JobInstance> fetchInstance(String theInstanceId) {
 		return myJobInstanceRepository.findById(theInstanceId).map(this::toInstance);
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public List<JobInstance> fetchInstances(FetchJobInstancesRequest theRequest, int thePage, int theBatchSize) {
 		String definitionId = theRequest.getJobDefinition();
 		String params = theRequest.getParameters();
@@ -182,6 +198,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public List<JobInstance> fetchInstances(int thePageSize, int thePageIndex) {
 		// default sort is myCreateTime Asc
 		PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.ASC, "myCreateTime");
@@ -189,6 +206,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public List<JobInstance> fetchRecentInstances(int thePageSize, int thePageIndex) {
 		PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.DESC, "myCreateTime");
 		return myJobInstanceRepository.findAll(pageRequest).stream().map(this::toInstance).collect(Collectors.toList());
@@ -203,11 +221,13 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public void markWorkChunkAsErroredAndIncrementErrorCount(String theChunkId, String theErrorMessage) {
 		myWorkChunkRepository.updateChunkStatusAndIncrementErrorCountForEndError(theChunkId, new Date(), theErrorMessage, StatusEnum.ERRORED);
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public Optional<WorkChunk> markWorkChunkAsErroredAndIncrementErrorCount(MarkWorkChunkAsErrorRequest theParameters) {
 		markWorkChunkAsErroredAndIncrementErrorCount(theParameters.getChunkId(), theParameters.getErrorMsg());
 		Optional<Batch2WorkChunkEntity> op = myWorkChunkRepository.findById(theParameters.getChunkId());
@@ -216,6 +236,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public void markWorkChunkAsFailed(String theChunkId, String theErrorMessage) {
 		String errorMessage;
 		if (theErrorMessage.length() > Batch2WorkChunkEntity.ERROR_MSG_MAX_LENGTH) {
@@ -228,11 +249,13 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public void markWorkChunkAsCompletedAndClearData(String theChunkId, int theRecordsProcessed) {
 		myWorkChunkRepository.updateChunkStatusAndClearDataForEndSuccess(theChunkId, new Date(), theRecordsProcessed, StatusEnum.COMPLETED);
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public void markWorkChunksWithStatusAndWipeData(String theInstanceId, List<String> theChunkIds, StatusEnum theStatus, String theErrorMsg) {
 		List<List<String>> listOfListOfIds = ListUtils.partition(theChunkIds, 100);
 		for (List<String> idList : listOfListOfIds) {
@@ -241,10 +264,14 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public void incrementWorkChunkErrorCount(String theChunkId, int theIncrementBy) {
 		myWorkChunkRepository.incrementWorkChunkErrorCount(theChunkId, theIncrementBy);
 	}
 
+	/**
+	 * Note: Not @Transactional because {@link #fetchChunks(String, boolean, int, int, Consumer)} starts a transaction
+	 */
 	@Override
 	public List<WorkChunk> fetchWorkChunksWithoutData(String theInstanceId, int thePageSize, int thePageIndex) {
 		ArrayList<WorkChunk> chunks = new ArrayList<>();
@@ -253,25 +280,35 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	private void fetchChunks(String theInstanceId, boolean theIncludeData, int thePageSize, int thePageIndex, Consumer<WorkChunk> theConsumer) {
+		myTxTemplate.executeWithoutResult(tx -> {
 			List<Batch2WorkChunkEntity> chunks = myWorkChunkRepository.fetchChunks(PageRequest.of(thePageIndex, thePageSize), theInstanceId);
 			for (Batch2WorkChunkEntity chunk : chunks) {
 				theConsumer.accept(toChunk(chunk, theIncludeData));
 			}
+		});
 	}
 
 	private void fetchChunksForStep(String theInstanceId, String theStepId, int thePageSize, int thePageIndex, Consumer<WorkChunk> theConsumer) {
+		myTxTemplate.executeWithoutResult(tx -> {
 			List<Batch2WorkChunkEntity> chunks = myWorkChunkRepository.fetchChunksForStep(PageRequest.of(thePageIndex, thePageSize), theInstanceId, theStepId);
 			for (Batch2WorkChunkEntity chunk : chunks) {
 				theConsumer.accept(toChunk(chunk, true));
 			}
+		});
 	}
 
 
+	/**
+	 * Note: Not @Transactional because the transaction happens in a lambda that's called outside of this method's scope
+	 */
 	@Override
 	public Iterator<WorkChunk> fetchAllWorkChunksIterator(String theInstanceId, boolean theWithData) {
 		return new PagingIterator<>((thePageIndex, theBatchSize, theConsumer) -> fetchChunks(theInstanceId, theWithData, theBatchSize, thePageIndex, theConsumer));
 	}
 
+	/**
+	 * Note: Not @Transactional because the transaction happens in a lambda that's called outside of this method's scope
+	 */
 	@Override
 	public Iterator<WorkChunk> fetchAllWorkChunksForStepIterator(String theInstanceId, String theStepId) {
 		return new PagingIterator<>((thePageIndex, theBatchSize, theConsumer) -> fetchChunksForStep(theInstanceId, theStepId, theBatchSize, thePageIndex, theConsumer));
@@ -284,6 +321,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	 * @return true if the status changed
 	 */
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public boolean updateInstance(JobInstance theInstance) {
 		// Separate updating the status so we have atomic information about whether the status is changing
 		int recordsChangedByStatusUpdate = myJobInstanceRepository.updateInstanceStatus(theInstance.getInstanceId(), theInstance.getStatus());
@@ -312,23 +350,27 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public void deleteInstanceAndChunks(String theInstanceId) {
 		myWorkChunkRepository.deleteAllForInstance(theInstanceId);
 		myJobInstanceRepository.deleteById(theInstanceId);
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public void deleteChunks(String theInstanceId) {
 		myWorkChunkRepository.deleteAllForInstance(theInstanceId);
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public boolean markInstanceAsCompleted(String theInstanceId) {
 		int recordsChanged = myJobInstanceRepository.updateInstanceStatus(theInstanceId, StatusEnum.COMPLETED);
 		return recordsChanged > 0;
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public JobOperationResultJson cancelInstance(String theInstanceId) {
 		int recordsChanged = myJobInstanceRepository.updateInstanceCancelled(theInstanceId, true);
 		String operationString = "Cancel job instance " + theInstanceId;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/DatabaseBlobBinaryStorageSvcImpl.java

@@ -39,7 +39,9 @@ import org.springframework.transaction.PlatformTransactionManager;
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.PersistenceContextType;
-import javax.transaction.Transactional;
+
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -61,7 +63,7 @@ public class DatabaseBlobBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {
 	private DaoConfig myDaoConfig;
 
 	@Override
-	@Transactional(Transactional.TxType.REQUIRED)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public StoredDetails storeBlob(IIdType theResourceId, String theBlobIdOrNull, String theContentType, InputStream theInputStream) throws IOException {
 
 		/*

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

@@ -46,10 +46,11 @@ import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Slice;
 import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.PostConstruct;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.Date;
 import java.util.Optional;
 
@@ -98,7 +99,7 @@ public class BulkDataExportJobSchedulingHelperImpl implements IBulkDataExportJob
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.NEVER)
+	@Transactional(propagation = Propagation.NEVER)
 	public synchronized void cancelAndPurgeAllJobs() {
 		myTxTemplate.execute(t -> {
 			ourLog.info("Deleting all files");
@@ -115,7 +116,7 @@ public class BulkDataExportJobSchedulingHelperImpl implements IBulkDataExportJob
 	 * This method is called by the scheduler to run a pass of the
 	 * generator
 	 */
-	@Transactional(value = Transactional.TxType.NEVER)
+	@Transactional(propagation = Propagation.NEVER)
 	@Override
 	public void purgeExpiredFiles() {
 		if (!myDaoConfig.isEnableTaskBulkExportJobExecution()) {

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

@@ -25,7 +25,7 @@ import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 
 @Service
 public class BulkExportCollectionFileDaoSvc {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java

@@ -49,11 +49,12 @@ import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Slice;
 import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
 import javax.annotation.PostConstruct;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
@@ -156,7 +157,7 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
 	/**
 	 * To be called by the job scheduler
 	 */
-	@Transactional(value = Transactional.TxType.NEVER)
+	@Transactional(propagation = Propagation.NEVER)
 	@Override
 	public ActivateJobResult activateNextReadyJob() {
 		if (!myDaoConfig.isEnableTaskBulkImportJobExecution()) {

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

@@ -785,6 +785,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			if (!allDefs.contains(tag)) {
 				if (shouldDroppedTagBeRemovedOnUpdate(theRequest, tag)) {
 					theEntity.getTags().remove(tag);
+				} else if (HapiExtensions.EXT_SUBSCRIPTION_MATCHING_STRATEGY.equals(tag.getTag().getSystem())) {
+					theEntity.getTags().remove(tag);
 				}
 			}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java

@@ -54,7 +54,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
 import javax.annotation.PostConstruct;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;

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

@@ -55,7 +55,9 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nullable;
 import javax.annotation.PostConstruct;
-import javax.transaction.Transactional;
+
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
@@ -70,7 +72,7 @@ import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LO
  * validation resources (StructureDefinition, ValueSet, CodeSystem, etc.) from the resources
  * persisted in the JPA server.
  */
-@Transactional(value = Transactional.TxType.REQUIRED)
+@Transactional(propagation = Propagation.REQUIRED)
 public class JpaPersistedResourceValidationSupport implements IValidationSupport {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(JpaPersistedResourceValidationSupport.class);

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

@@ -20,8 +20,9 @@ package ca.uhn.fhir.jpa.dao.data;
  * #L%
  */
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 
-@Transactional(Transactional.TxType.MANDATORY)
+@Transactional(propagation = Propagation.MANDATORY)
 public interface IHapiFhirJpaRepository {
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -49,7 +49,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.Nonnull;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;

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

@@ -258,7 +258,8 @@ public class ResourceExpungeService implements IResourceExpungeService {
 		ourLog.info("Expunging current version of resource {}", resource.getIdDt().getValue());
 
 		deleteAllSearchParams(new ResourcePersistentId(resource.getResourceId()));
-		resource.getTags().clear();
+
+		myResourceTagDao.deleteByResourceId(resource.getId());
 
 		if (resource.getForcedId() != null) {
 			ForcedId forcedId = resource.getForcedId();

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.delete;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java

@@ -71,6 +71,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Slice;
 import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
@@ -84,7 +85,7 @@ import javax.persistence.criteria.Join;
 import javax.persistence.criteria.JoinType;
 import javax.persistence.criteria.Predicate;
 import javax.persistence.criteria.Root;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -450,7 +451,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.NEVER)
+	@Transactional(propagation = Propagation.NEVER)
 	public NpmPackage installPackage(PackageInstallationSpec theInstallationSpec) throws IOException {
 		Validate.notBlank(theInstallationSpec.getName(), "thePackageId must not be blank");
 		Validate.notBlank(theInstallationSpec.getVersion(), "thePackageVersion must not be blank");

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/PartitionLookupSvcImpl.java

@@ -42,7 +42,7 @@ import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.PostConstruct;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.List;
 import java.util.Optional;
 import java.util.concurrent.TimeUnit;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchCacheSvcImpl.java

@@ -41,9 +41,10 @@ import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Slice;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.time.Instant;
 import java.util.Collection;
 import java.util.Date;
@@ -87,7 +88,7 @@ public class DatabaseSearchCacheSvcImpl implements ISearchCacheSvc {
 		myCutoffSlack = theCutoffSlack;
 	}
 
-	@Transactional(Transactional.TxType.REQUIRED)
+	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public Search save(Search theSearch) {
 		Search newSearch = mySearchDao.save(theSearch);
@@ -95,7 +96,7 @@ public class DatabaseSearchCacheSvcImpl implements ISearchCacheSvc {
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.REQUIRED)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public Optional<Search> fetchByUuid(String theUuid) {
 		Validate.notBlank(theUuid);
 		return mySearchDao.findByUuidAndFetchIncludes(theUuid);
@@ -110,7 +111,7 @@ public class DatabaseSearchCacheSvcImpl implements ISearchCacheSvc {
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.NEVER)
+	@Transactional(propagation = Propagation.NEVER)
 	public Optional<Search> tryToMarkSearchAsInProgress(Search theSearch) {
 		ourLog.trace("Going to try to change search status from {} to {}", theSearch.getStatus(), SearchStatusEnum.LOADING);
 		try {
@@ -152,7 +153,7 @@ public class DatabaseSearchCacheSvcImpl implements ISearchCacheSvc {
 		return Optional.empty();
 	}
 
-	@Transactional(Transactional.TxType.NEVER)
+	@Transactional(propagation = Propagation.NEVER)
 	@Override
 	public void pollForStaleSearchesAndDeleteThem() {
 		if (!myDaoConfig.isExpireSearchResults()) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchResultCacheSvcImpl.java

@@ -30,7 +30,8 @@ import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Pageable;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.Collections;
 import java.util.List;
 
@@ -43,7 +44,7 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
 	private ISearchResultDao mySearchResultDao;
 
 	@Override
-	@Transactional(Transactional.TxType.REQUIRED)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public List<ResourcePersistentId> fetchResultPids(Search theSearch, int theFrom, int theTo) {
 		final Pageable page = toPage(theFrom, theTo);
 		if (page == null) {
@@ -60,7 +61,7 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.REQUIRED)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public List<ResourcePersistentId> fetchAllResultPids(Search theSearch) {
 		List<Long> retVal = mySearchResultDao.findWithSearchPidOrderIndependent(theSearch.getId());
 		ourLog.trace("fetchAllResultPids returned {} pids", retVal.size());
@@ -68,7 +69,7 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.REQUIRED)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public void storeResults(Search theSearch, List<ResourcePersistentId> thePreviouslyStoredResourcePids, List<ResourcePersistentId> theNewResourcePids) {
 		List<SearchResult> resultsToSave = Lists.newArrayList();
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java

@@ -52,6 +52,7 @@ import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Slice;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
 
@@ -61,7 +62,7 @@ import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.PersistenceContextType;
 import javax.persistence.Query;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.Collection;
 import java.util.Date;
 import java.util.List;
@@ -153,13 +154,13 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.REQUIRED)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public Long markAllResourcesForReindexing() {
 		return markAllResourcesForReindexing(null);
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.REQUIRED)
+	@Transactional(propagation = Propagation.REQUIRED)
 	public Long markAllResourcesForReindexing(String theType) {
 
 		String typeDesc;
@@ -201,7 +202,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 	}
 
 	@Override
-	@Transactional(Transactional.TxType.NEVER)
+	@Transactional(propagation = Propagation.NEVER)
 	public Integer runReindexingPass() {
 		if (myDaoConfig.isSchedulingDisabled() || !myDaoConfig.isEnableTaskPreExpandValueSets()) {
 			return null;

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

@@ -422,7 +422,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@Override
-	@Transactional
 	public ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull String theValueSetCanonicalUrl) {
 		ValueSet valueSet = fetchCanonicalValueSetFromCompleteContext(theValueSetCanonicalUrl);
 		if (valueSet == null) {
@@ -433,16 +432,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@Override
-	@Transactional(propagation = Propagation.REQUIRED)
 	public ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull ValueSet theValueSetToExpand) {
 		String filter = null;
 		if (theExpansionOptions != null) {
 			filter = theExpansionOptions.getFilter();
 		}
-		return expandValueSet(theExpansionOptions, theValueSetToExpand, ExpansionFilter.fromFilterString(filter));
+		return doExpandValueSet(theExpansionOptions, theValueSetToExpand, ExpansionFilter.fromFilterString(filter));
 	}
 
-	private ValueSet expandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, ExpansionFilter theFilter) {
+	private ValueSet doExpandValueSet(@Nullable ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, ExpansionFilter theFilter) {
 		ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSetToExpand, "ValueSet to expand can not be null");
 
 		ValueSetExpansionOptions expansionOptions = provideExpansionOptions(theExpansionOptions);
@@ -461,7 +459,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			accumulator.addParameter().setName("count").setValue(new IntegerType(count));
 		}
 
+		myTxTemplate.executeWithoutResult(tx-> {
 			expandValueSetIntoAccumulator(theValueSetToExpand, theExpansionOptions, accumulator, theFilter, true);
+		});
 
 		if (accumulator.getTotalConcepts() != null) {
 			accumulator.setTotal(accumulator.getTotalConcepts());
@@ -506,7 +506,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			ourLog.debug("ValueSet is not present in terminology tables. Will perform in-memory expansion without parameters. {}", getValueSetInfo(theValueSetToExpand));
 			String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "valueSetExpandedUsingInMemoryExpansion", getValueSetInfo(theValueSetToExpand));
 			theAccumulator.addMessage(msg);
-			expandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter);
+			doExpandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter);
 			return;
 		}
 
@@ -517,7 +517,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		if (termValueSet.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
 			String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "valueSetNotYetExpanded", getValueSetInfo(theValueSetToExpand), termValueSet.getExpansionStatus().name(), termValueSet.getExpansionStatus().getDescription());
 			theAccumulator.addMessage(msg);
-			expandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter);
+			doExpandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter);
 			return;
 		}
 
@@ -734,13 +734,16 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	}
 
 	@Override
-	@Transactional(propagation = Propagation.REQUIRED)
 	public void expandValueSet(ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
-		expandValueSet(theExpansionOptions, theValueSetToExpand, theValueSetCodeAccumulator, ExpansionFilter.NO_FILTER);
+		doExpandValueSet(theExpansionOptions, theValueSetToExpand, theValueSetCodeAccumulator, ExpansionFilter.NO_FILTER);
 	}
 
+	/**
+	 * Note: Not transactional because specific calls within this method
+	 * get executed in a transaction
+	 */
 	@SuppressWarnings("ConstantConditions")
-	private void expandValueSet(ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator, @Nonnull ExpansionFilter theExpansionFilter) {
+	private void doExpandValueSet(ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator, @Nonnull ExpansionFilter theExpansionFilter) {
 		Set<String> addedCodes = new HashSet<>();
 
 		StopWatch sw = new StopWatch();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java

@@ -8,6 +8,7 @@ import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
+import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.ValidateUtil;
 import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
@@ -22,6 +23,7 @@ import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.annotation.Transactional;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR4.java

@@ -19,7 +19,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
 
 import javax.annotation.Nonnull;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 
 /*
  * #%L
@@ -58,7 +58,6 @@ public class TermReadSvcR4 extends BaseTermReadSvcImpl implements ITermReadSvcR4
 		super.expandValueSet(theExpansionOptions, valueSetToExpand, theValueSetCodeAccumulator);
 	}
 
-	@Transactional(dontRollbackOn = {ExpansionTooCostlyException.class})
 	@Override
 	public IValidationSupport.ValueSetExpansionOutcome expandValueSet(ValidationSupportContext theValidationSupportContext, ValueSetExpansionOptions theExpansionOptions, @Nonnull IBaseResource theValueSetToExpand) {
 		ValueSet expanded = super.expandValueSet(theExpansionOptions, (ValueSet) theValueSetToExpand);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java

@@ -8,7 +8,6 @@ import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
-import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
 import ca.uhn.fhir.util.ValidateUtil;
 import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
@@ -20,11 +19,9 @@ import org.hl7.fhir.r5.model.CodeableConcept;
 import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.PlatformTransactionManager;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
-import javax.transaction.Transactional;
 
 /*
  * #%L
@@ -50,11 +47,8 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
 
 	@Autowired
 	private DaoRegistry myDaoRegistry;
-	@Autowired
-	private PlatformTransactionManager myTransactionManager;
 
 	@Override
-	@Transactional(dontRollbackOn = {ExpansionTooCostlyException.class})
 	public ValueSetExpansionOutcome expandValueSet(ValidationSupportContext theValidationSupportContext, ValueSetExpansionOptions theExpansionOptions, @Nonnull IBaseResource theValueSetToExpand) {
 		ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
 		org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(theExpansionOptions,

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

@@ -31,7 +31,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.ValueSet;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.List;
 
 /**

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

@@ -20,7 +20,7 @@ import org.hl7.fhir.r4.model.ValueSet;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImplTest.java

@@ -19,6 +19,7 @@ import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
+import org.springframework.transaction.PlatformTransactionManager;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -47,6 +48,8 @@ class JpaJobPersistenceImplTest {
 	IBatch2JobInstanceRepository myJobInstanceRepository;
 	@Mock
 	IBatch2WorkChunkRepository myWorkChunkRepository;
+	@Mock
+	PlatformTransactionManager myTxManager;
 	@InjectMocks
 	JpaJobPersistenceImpl mySvc;
 

hapi-fhir-jpaserver-cql/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -39,7 +39,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 import javax.annotation.Nonnull;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;

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

@@ -32,7 +32,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 import javax.annotation.Nonnull;
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.Collection;
 import java.util.List;
 import java.util.stream.Collectors;

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

@@ -37,7 +37,7 @@ import org.slf4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.ArrayList;
 import java.util.List;
 

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvcTest.java

@@ -80,7 +80,7 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
 		List<Long> expectedExpandedPids = mdmLinks.stream().map(MdmLink::getSourcePid).collect(Collectors.toList());
 
 		//SUT
-		List<MdmPidTuple> lists = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(new ResourcePersistentId(mdmLinks.get(0).getSourcePid()), MdmMatchResultEnum.MATCH);
+		List<MdmPidTuple> lists = runInTransaction(()->myMdmLinkDao.expandPidsBySourcePidAndMatchResult(new ResourcePersistentId(mdmLinks.get(0).getSourcePid()), MdmMatchResultEnum.MATCH));
 
 		assertThat(lists, hasSize(10));
 

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

@@ -32,6 +32,7 @@ import static org.mockito.Mockito.when;
 
 @ExtendWith(MockitoExtension.class)
 class MdmLinkCreateSvcImplTest {
+	@SuppressWarnings("unused")
 	@Spy
 	FhirContext myFhirContext = FhirContext.forR4();
 	@Mock
@@ -71,7 +72,7 @@ class MdmLinkCreateSvcImplTest {
 	}
 
 	@BeforeEach
-	private void setup() {
+	public void setup() {
 		ResourcePersistentId goldenId = new ResourcePersistentId(1L);
 		ResourcePersistentId sourceId = new ResourcePersistentId(2L);
 		when(myIdHelperService.getPidOrThrowException(any()))

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-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>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java

@@ -37,15 +37,15 @@ import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import org.hl7.fhir.instance.model.api.IIdType;
 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.mockito.internal.util.collections.ListUtil;
+import org.simplejavamail.internal.util.ListUtil;
 
 import java.util.List;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.contains;
@@ -312,12 +312,12 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu
 		myGroupDao.create(g);
 
 		assertThat(myResourceLinkDao.findAll(), empty());
-		assertThat(ListUtil.filter(myResourceIndexedSearchParamTokenDao.findAll(), new ListUtil.Filter<ResourceIndexedSearchParamToken>() {
+		List<ResourceIndexedSearchParamToken> tokens = myResourceIndexedSearchParamTokenDao
-			@Override
+			.findAll()
-			public boolean isOut(ResourceIndexedSearchParamToken object) {
+			.stream()
-				return !object.getResourceType().equals("Group") || object.isMissing();
+			.filter(object -> !(!object.getResourceType().equals("Group") || object.isMissing()))
-			}
+			.collect(Collectors.toList());
-		}), empty());
+		assertThat(tokens, empty());
 	}
 
 	@Test

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ConceptMapTest.java

@@ -106,7 +106,7 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
 	public void testConceptMapFindTermConceptMapByUrl() {
 
 		Pageable page = PageRequest.of(0, 1);
-		List<TermConceptMap> theExpConceptMapList = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByMostRecentUpdate(page, CM_URL);
+		List<TermConceptMap> theExpConceptMapList = runInTransaction(()->myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByMostRecentUpdate(page, CM_URL));
 		assertEquals(1, theExpConceptMapList.size());
 		assertEquals(CM_URL, theExpConceptMapList.get(0).getUrl());
 
@@ -125,8 +125,8 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
 		myConceptMapDao.create(theConceptMap1);
 		myConceptMapDao.create(theConceptMap2);
 
-		Optional<TermConceptMap> theExpConceptMapV1 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v1");
+		Optional<TermConceptMap> theExpConceptMapV1 = runInTransaction(()->myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v1"));
-		Optional<TermConceptMap> theExpConceptMapV2 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v2");
+		Optional<TermConceptMap> theExpConceptMapV2 = runInTransaction(()->myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v2"));
 
 		assertTrue(theExpConceptMapV1.isPresent());
 		assertEquals(theUrl, theExpConceptMapV1.get().getUrl());
@@ -138,7 +138,7 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
 
 		// should return the latest one which is v2
 		Pageable page = PageRequest.of(0, 1);
-		List<TermConceptMap> theExpSecondOne = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByMostRecentUpdate(page, theUrl);
+		List<TermConceptMap> theExpSecondOne = runInTransaction(()->myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByMostRecentUpdate(page, theUrl));
 
 		assertEquals(1, theExpSecondOne.size());
 		assertEquals(theUrl, theExpSecondOne.get(0).getUrl());
@@ -158,7 +158,7 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
 		myConceptMapDao.create(theConceptMap1);
 		myConceptMapDao.create(theConceptMap2);
 
-		Optional<TermConceptMap> theExpConceptMapV1 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v1");
+		Optional<TermConceptMap> theExpConceptMapV1 = runInTransaction(()->myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v1"));
 
 		assertTrue(theExpConceptMapV1.isPresent());
 		assertEquals(theUrl, theExpConceptMapV1.get().getUrl());
@@ -166,7 +166,7 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
 
 		// should return the latest one which in this case is not versioned
 		Pageable page = PageRequest.of(0, 1);
-		List<TermConceptMap> theExpSecondOne = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByMostRecentUpdate(page, theUrl);
+		List<TermConceptMap> theExpSecondOne = runInTransaction(()->myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByMostRecentUpdate(page, theUrl));
 
 		assertEquals(1, theExpSecondOne.size());
 		assertEquals(theUrl, theExpSecondOne.get(0).getUrl());

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValueSetMultiVersionTest.java

@@ -83,9 +83,9 @@ public class FhirResourceDaoDstu3ValueSetMultiVersionTest extends BaseJpaDstu3Te
 	public void testCreateVersionedValueSets() {
 		Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
 
-		assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(3, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
 
-		Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
+		Optional<TermValueSet> optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET));
 		assertTrue(optionalTermValueSet.isPresent());
 		Long nullVersion_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.NULL).getEntity()).getId();
 		assertNotNull(nullVersion_resid);
@@ -93,7 +93,7 @@ public class FhirResourceDaoDstu3ValueSetMultiVersionTest extends BaseJpaDstu3Te
 		assertEquals(nullVersion_resid, optionalTermValueSet.get().getResource().getId());
 		assertEquals("ValueSet_noVersion", optionalTermValueSet.get().getName());
 
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1"));
 		assertTrue(optionalTermValueSet.isPresent());
 		Long v1Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V1).getEntity()).getId();
 		assertNotNull(v1Version_resid);
@@ -101,7 +101,7 @@ public class FhirResourceDaoDstu3ValueSetMultiVersionTest extends BaseJpaDstu3Te
 		assertEquals(v1Version_resid, optionalTermValueSet.get().getResource().getId());
 		assertEquals("ValueSet_v1", optionalTermValueSet.get().getName());
 
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2"));
 		assertTrue(optionalTermValueSet.isPresent());
 		Long v2Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V2).getEntity()).getId();
 		assertNotNull(v2Version_resid);
@@ -115,15 +115,15 @@ public class FhirResourceDaoDstu3ValueSetMultiVersionTest extends BaseJpaDstu3Te
 	public void testUpdateVersionedValueSets() {
 		Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
 
-		assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(3, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
 
-		TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
+		TermValueSet termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version")));
 		assertEquals("ValueSet_noVersion", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1")));
 		assertEquals("ValueSet_v1", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
 		assertEquals("ValueSet_v2", termValueSet.getName());
 
 		// Update ValueSets
@@ -143,21 +143,21 @@ public class FhirResourceDaoDstu3ValueSetMultiVersionTest extends BaseJpaDstu3Te
 		Long v2Version_resid = ((ResourceTable)v2Version_update_outcome.getEntity()).getId();
 
 		// Verify that ValueSets were updated.
-		assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(3, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version")));
 		assertNotNull(nullVersion_resid);
 		assertNotNull(termValueSet.getResource());
 		assertEquals(nullVersion_resid, termValueSet.getResource().getId());
 		assertEquals("ValueSet_noVersion_updated", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1")));
 		assertNotNull(v1Version_resid);
 		assertNotNull(termValueSet.getResource());
 		assertEquals(v1Version_resid, termValueSet.getResource().getId());
 		assertEquals("ValueSet_v1_updated", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
 		assertNotNull(v2Version_resid);
 		assertNotNull(termValueSet.getResource());
 		assertEquals(v2Version_resid, termValueSet.getResource().getId());
@@ -169,53 +169,53 @@ public class FhirResourceDaoDstu3ValueSetMultiVersionTest extends BaseJpaDstu3Te
 	public void testDeleteVersionedValueSets() {
 		Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
 
-		assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(3, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
 
-		TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
+		TermValueSet termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version")));
 		assertEquals("ValueSet_noVersion", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1")));
 		assertEquals("ValueSet_v1", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
 		assertEquals("ValueSet_v2", termValueSet.getName());
 
 		// Delete ValueSets
 		myValueSetDao.delete(myValueSets.get(ValueSetVersions.NULL).getResource().getIdElement());
-		assertEquals(2, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(2, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
-		Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
+		Optional<TermValueSet> optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		assertNotNull(myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1")));
+		assertNotNull(runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"))));
-		assertNotNull(myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
+		assertNotNull(runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"))));
 
 		myValueSetDao.delete(myValueSets.get(ValueSetVersions.V1).getResource().getIdElement());
-		assertEquals(1, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(1, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1"));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2"));
 		if (!optionalTermValueSet.isPresent()) {
 			fail("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2");
 		}
 
 		myValueSetDao.delete(myValueSets.get(ValueSetVersions.V2).getResource().getIdElement());
-		assertEquals(0, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(0, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1"));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2"));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}

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

@@ -322,7 +322,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
 
 		loadAndPersistCodeSystemAndValueSet();
 		myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
-		Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
+		Slice<TermValueSet> page = runInTransaction(()->myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED));
 		assertEquals(2, page.getContent().size());
 
 		// Verify v1 ValueSet
@@ -418,7 +418,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
 		loadAndPersistCodeSystemAndValueSet();
 		myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
 
-		Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
+		Slice<TermValueSet> page = runInTransaction(()->myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED));
 		assertEquals(2, page.getContent().size());
 
 		// Validate ValueSet v1
@@ -585,7 +585,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
 		loadAndPersistCodeSystemAndValueSet();
 		myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
 
-		Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
+		Slice<TermValueSet> page = runInTransaction(()->myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED));
 		assertEquals(2, page.getContent().size());
 
 		// Check expansion of multi-versioned ValueSet with version 1

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/batch2/JobInstanceRepositoryTest.java

@@ -26,34 +26,33 @@ public class JobInstanceRepositoryTest extends BaseJpaR4Test {
 	private IBatch2JobInstanceRepository myJobInstanceRepository;
 	@Autowired
 	private IJobPersistence myJobPersistenceSvc;
-	private String myParams = "{\"param1\":\"value1\"}";
+	private static final String PARAMS = "{\"param1\":\"value1\"}";
-	private String myJobDefinitionId = "my-job-def-id";
+	private static final String JOB_DEFINITION_ID = "my-job-def-id";
-	private String myInstanceId = "abc-123";
+	private static final String INSTANCE_ID = "abc-123";
 
 	@Test
 	public void testSearchByJobParamsAndStatuses_SingleStatus() {
 		Set<StatusEnum> statuses = Set.of(StatusEnum.IN_PROGRESS);
-		List<Batch2JobInstanceEntity> instancesByJobIdParamsAndStatus = myJobInstanceRepository.findInstancesByJobIdParamsAndStatus(myJobDefinitionId, myParams, statuses, PageRequest.of(0, 10));
+		List<Batch2JobInstanceEntity> instancesByJobIdParamsAndStatus = runInTransaction(()->myJobInstanceRepository.findInstancesByJobIdParamsAndStatus(JOB_DEFINITION_ID, PARAMS, statuses, PageRequest.of(0, 10)));
 		assertThat(instancesByJobIdParamsAndStatus, hasSize(1));
 	}
 
 	@Test
 	public void testSearchByJobParamsAndStatuses_MultiStatus() {
 		Set<StatusEnum> statuses = Set.of(StatusEnum.IN_PROGRESS, StatusEnum.COMPLETED);
-		List<Batch2JobInstanceEntity> instances = myJobInstanceRepository.findInstancesByJobIdParamsAndStatus(myJobDefinitionId, myParams, statuses, PageRequest.of(0, 10));
+		List<Batch2JobInstanceEntity> instances = runInTransaction(()->myJobInstanceRepository.findInstancesByJobIdParamsAndStatus(JOB_DEFINITION_ID, PARAMS, statuses, PageRequest.of(0, 10)));
 		assertThat(instances, hasSize(2));
 	}
 
 	@Test
 	public void testSearchByJobParamsWithoutStatuses() {
-		List<Batch2JobInstanceEntity> instances = myJobInstanceRepository.findInstancesByJobIdAndParams(myJobDefinitionId, myParams, PageRequest.of(0, 10));
+		List<Batch2JobInstanceEntity> instances = runInTransaction(()->myJobInstanceRepository.findInstancesByJobIdAndParams(JOB_DEFINITION_ID, PARAMS, PageRequest.of(0, 10)));
 		assertThat(instances, hasSize(4));
-
 	}
 
 	@Test
 	public void testServiceLogicIsCorrectWhenNoStatusesAreUsed() {
-		FetchJobInstancesRequest request = new FetchJobInstancesRequest(myJobDefinitionId, myParams);
+		FetchJobInstancesRequest request = new FetchJobInstancesRequest(JOB_DEFINITION_ID, PARAMS);
 		List<JobInstance> jobInstances = myJobPersistenceSvc.fetchInstances(request, 0, 1000);
 		assertThat(jobInstances, hasSize(4));
 	}
@@ -61,7 +60,7 @@ public class JobInstanceRepositoryTest extends BaseJpaR4Test {
 	@Test
 	public void testServiceLogicIsCorrectWithStatuses() {
 		//Given
-		FetchJobInstancesRequest request = new FetchJobInstancesRequest(myJobDefinitionId, myParams, StatusEnum.IN_PROGRESS, StatusEnum.COMPLETED);
+		FetchJobInstancesRequest request = new FetchJobInstancesRequest(JOB_DEFINITION_ID, PARAMS, StatusEnum.IN_PROGRESS, StatusEnum.COMPLETED);
 
 		//When
 		List<JobInstance> jobInstances = myJobPersistenceSvc.fetchInstances(request, 0, 1000);
@@ -71,38 +70,38 @@ public class JobInstanceRepositoryTest extends BaseJpaR4Test {
 	}
 
 	@BeforeEach
-	private void beforeEach() {
+	public void beforeEach() {
 		//Create in-progress job.
 		Batch2JobInstanceEntity instance= new Batch2JobInstanceEntity();
-		instance.setId(myInstanceId);
+		instance.setId(INSTANCE_ID);
 		instance.setStatus(StatusEnum.IN_PROGRESS);
 		instance.setCreateTime(new Date());
-		instance.setDefinitionId(myJobDefinitionId);
+		instance.setDefinitionId(JOB_DEFINITION_ID);
-		instance.setParams(myParams);
+		instance.setParams(PARAMS);
 		myJobInstanceRepository.save(instance);
 
 		Batch2JobInstanceEntity completedInstance = new Batch2JobInstanceEntity();
-		completedInstance.setId(myInstanceId + "-2");
+		completedInstance.setId(INSTANCE_ID + "-2");
 		completedInstance.setStatus(StatusEnum.COMPLETED);
 		completedInstance.setCreateTime(new Date());
-		completedInstance.setDefinitionId(myJobDefinitionId);
+		completedInstance.setDefinitionId(JOB_DEFINITION_ID);
-		completedInstance.setParams(myParams);
+		completedInstance.setParams(PARAMS);
 		myJobInstanceRepository.save(completedInstance);
 
 		Batch2JobInstanceEntity cancelledInstance = new Batch2JobInstanceEntity();
-		cancelledInstance.setId(myInstanceId + "-3");
+		cancelledInstance.setId(INSTANCE_ID + "-3");
 		cancelledInstance.setStatus(StatusEnum.CANCELLED);
 		cancelledInstance.setCreateTime(new Date());
-		cancelledInstance.setDefinitionId(myJobDefinitionId);
+		cancelledInstance.setDefinitionId(JOB_DEFINITION_ID);
-		cancelledInstance.setParams(myParams);
+		cancelledInstance.setParams(PARAMS);
 		myJobInstanceRepository.save(cancelledInstance);
 
 		Batch2JobInstanceEntity failedInstance = new Batch2JobInstanceEntity();
-		failedInstance.setId(myInstanceId + "-4");
+		failedInstance.setId(INSTANCE_ID + "-4");
 		failedInstance.setStatus(StatusEnum.FAILED);
 		failedInstance.setCreateTime(new Date());
-		failedInstance.setDefinitionId(myJobDefinitionId);
+		failedInstance.setDefinitionId(JOB_DEFINITION_ID);
-		failedInstance.setParams(myParams);
+		failedInstance.setParams(PARAMS);
 		myJobInstanceRepository.save(failedInstance);
 	}
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java

@@ -64,7 +64,6 @@ import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.mockito.ArgumentCaptor;
-import org.mockito.internal.util.collections.ListUtil;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@@ -690,12 +689,12 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 
 		runInTransaction(() -> {
 			assertThat(myResourceLinkDao.findAll(), empty());
-			assertThat(ListUtil.filter(myResourceIndexedSearchParamTokenDao.findAll(), new ListUtil.Filter<ResourceIndexedSearchParamToken>() {
+			List<ResourceIndexedSearchParamToken> tokens = myResourceIndexedSearchParamTokenDao
-				@Override
+				.findAll()
-				public boolean isOut(ResourceIndexedSearchParamToken object) {
+				.stream()
-					return !object.getResourceType().equals("Group") || object.isMissing();
+				.filter(object -> !(!object.getResourceType().equals("Group") || object.isMissing()))
-				}
+				.collect(Collectors.toList());
-			}), empty());
+			assertThat(tokens, empty());
 		});
 	}
 

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

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
 import ca.uhn.fhir.jpa.provider.r4.BaseResourceProviderR4Test;
+import ca.uhn.fhir.jpa.test.config.TestR4Config;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
@@ -42,6 +43,13 @@ import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
+/**
+ * Note that some tests in this class use the {@link ThreadSafeResourceDeleterSvc}
+ * which uses {@link org.springframework.transaction.annotation.Propagation#REQUIRES_NEW}
+ * propagation and therefore needs at least 2 connections free in the pool. Since the
+ * test config randomizes the number of connections available, these tests
+ * only run if more than one connection is going to be available.
+ */
 public class CascadingDeleteInterceptorTest extends BaseResourceProviderR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CascadingDeleteInterceptorTest.class);
@@ -187,6 +195,10 @@ public class CascadingDeleteInterceptorTest extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testDeleteCascading() throws IOException {
+		if (TestR4Config.getMaxThreads() == 1) {
+			return; // See class javadoc for explanation
+		}
+
 		createResources();
 
 		ourRestServer.getInterceptorService().registerInterceptor(myDeleteInterceptor);
@@ -211,6 +223,10 @@ public class CascadingDeleteInterceptorTest extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testDeleteCascadingWithOverridePathBasedReferentialIntegrityForDeletesInterceptorAlsoRegistered() throws IOException {
+		if (TestR4Config.getMaxThreads() == 1) {
+			return; // See class javadoc for explanation
+		}
+
 		ourRestServer.getInterceptorService().registerInterceptor(myOverridePathBasedReferentialIntegrityForDeletesInterceptor);
 		try {
 
@@ -221,8 +237,8 @@ public class CascadingDeleteInterceptorTest extends BaseResourceProviderR4Test {
 			HttpDelete delete = new HttpDelete(ourServerBase + "/" + myPatientId.getValue() + "?" + Constants.PARAMETER_CASCADE_DELETE + "=" + Constants.CASCADE_DELETE + "&_pretty=true");
 			delete.addHeader(Constants.HEADER_ACCEPT, Constants.CT_FHIR_JSON_NEW);
 			try (CloseableHttpResponse response = ourHttpClient.execute(delete)) {
-				assertEquals(200, response.getStatusLine().getStatusCode());
 				String deleteResponse = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
+				assertEquals(200, response.getStatusLine().getStatusCode(), deleteResponse);
 				ourLog.info("Response: {}", deleteResponse);
 				assertThat(deleteResponse, containsString("Cascaded delete to "));
 			}
@@ -284,6 +300,10 @@ public class CascadingDeleteInterceptorTest extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testDeleteCascadingByHeader() throws IOException {
+		if (TestR4Config.getMaxThreads() == 1) {
+			return; // See class javadoc for explanation
+		}
+
 		createResources();
 
 		ourRestServer.getInterceptorService().registerInterceptor(myDeleteInterceptor);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ExpungeR4Test.java

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
+import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
 import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
@@ -83,6 +84,7 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 	public void afterDisableExpunge() {
 		myDaoConfig.setExpungeEnabled(new DaoConfig().isExpungeEnabled());
 		myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
+		myDaoConfig.setTagStorageMode(new DaoConfig().getTagStorageMode());
 		myModelConfig.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
 
 		ourRestServer.getInterceptorService().unregisterInterceptorsIf(t -> t instanceof CascadingDeleteInterceptor);
@@ -588,6 +590,28 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 		assertExpunged(myDeletedObservationId);
 	}
 
+	@Test
+	public void testExpungeByTypeAndNoId_NonVersionedTags() {
+		myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.NON_VERSIONED);
+
+		Patient p = new Patient();
+		p.setId("PT-DELETED");
+		p.getMeta().addTag().setSystem("http://foo").setCode("bar");
+		p.setActive(true);
+		myDeletedPatientId = myPatientDao.update(p).getId();
+		myDeletedPatientId = myPatientDao.delete(myDeletedPatientId).getId();
+
+		myCaptureQueriesListener.clear();
+		myExpungeService.expunge("Patient", null, new ExpungeOptions().setExpungeDeletedResources(true), null);
+		myCaptureQueriesListener.logAllQueries();
+
+		assertExpunged(myDeletedPatientId.withVersion("2"));
+	}
+
+
+	@Autowired
+	private ExpungeService myExpungeService;
+
 	@Test
 	public void testExpungeDeletedWhereResourceInSearchResults() {
 		createStandardPatients();

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

@@ -690,7 +690,7 @@ public class MultitenantServerR4Test extends BaseMultitenantResourceProviderR4Te
 		}
 
 		@BeforeEach
-		private void setBulkDataExportProvider() {
+		public void setBulkDataExportProvider() {
 			ourRestServer.registerProvider(myProvider);
 		}
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionsR4Test.java

@@ -23,6 +23,7 @@ import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Subscription;
+import org.jetbrains.annotations.NotNull;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
@@ -115,12 +116,25 @@ public abstract class BaseSubscriptionsR4Test extends BaseResourceProviderR4Test
 	}
 
 	protected Subscription createSubscription(String theCriteria, String thePayload, Extension theExtension) {
+		String id = null;
+
+		return createSubscription(theCriteria, thePayload, theExtension, id);
+	}
+
+	@NotNull
+	protected Subscription createSubscription(String theCriteria, String thePayload, Extension theExtension, String id) {
 		Subscription subscription = newSubscription(theCriteria, thePayload);
 		if (theExtension != null) {
 			subscription.getChannel().addExtension(theExtension);
 		}
 
-		MethodOutcome methodOutcome = myClient.create().resource(subscription).execute();
+		MethodOutcome methodOutcome;
+		if (id != null) {
+			subscription.setId(id);
+			methodOutcome = myClient.update().resource(subscription).execute();
+		} else {
+			methodOutcome = myClient.create().resource(subscription).execute();
+		}
 		subscription.setId(methodOutcome.getId().getIdPart());
 		mySubscriptionIds.add(methodOutcome.getId());
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestR4Test.java

@@ -68,6 +68,37 @@ public class RestHookTestR4Test extends BaseSubscriptionsR4Test {
 		myDaoConfig.setTriggerSubscriptionsForNonVersioningChanges(new DaoConfig().isTriggerSubscriptionsForNonVersioningChanges());
 	}
 
+
+
+	/**
+	 * Make sure that if we delete a subscription, then reinstate it with a criteria
+	 * that changes the database mode we don't store both versioning modes
+	 */
+	@Test
+	public void testReuseSubscriptionIdWithDifferentDatabaseMode() throws Exception {
+		myDaoConfig.setTagStorageMode(DaoConfig.TagStorageModeEnum.NON_VERSIONED);
+
+		String payload = "application/fhir+json";
+		IdType id = createSubscription("Observation?_has:DiagnosticReport:result:identifier=foo|IDENTIFIER", payload, null, "sub").getIdElement().toUnqualifiedVersionless();
+		waitForActivatedSubscriptionCount(1);
+
+		Subscription subscription = mySubscriptionDao.read(id, mySrd);
+		assertEquals(1, subscription.getMeta().getTag().size());
+		assertEquals("DATABASE", subscription.getMeta().getTag().get(0).getCode());
+
+		mySubscriptionDao.delete(id, mySrd);
+		waitForActivatedSubscriptionCount(0);
+
+		payload = "application/fhir+json";
+		id = createSubscription("Observation?", payload, null, "sub").getIdElement().toUnqualifiedVersionless();
+		waitForActivatedSubscriptionCount(1);
+
+		subscription = mySubscriptionDao.read(id, mySrd);
+		assertEquals(1, subscription.getMeta().getTag().size());
+		assertEquals("IN_MEMORY", subscription.getMeta().getTag().get(0).getCode());
+	}
+
+
 	@Test
 	public void testRestHookSubscriptionApplicationFhirJson() throws Exception {
 		String payload = "application/fhir+json";

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5ValueSetMultiVersionTest.java

@@ -82,9 +82,9 @@ public class FhirResourceDaoR5ValueSetMultiVersionTest extends BaseJpaR5Test {
 	public void testCreateVersionedValueSets() {
 		Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
 
-		assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(3, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
 
-		Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
+		Optional<TermValueSet> optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET));
 		assertTrue(optionalTermValueSet.isPresent());
 		Long nullVersion_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.NULL).getEntity()).getId();
 		assertNotNull(nullVersion_resid);
@@ -92,7 +92,7 @@ public class FhirResourceDaoR5ValueSetMultiVersionTest extends BaseJpaR5Test {
 		assertEquals(nullVersion_resid, optionalTermValueSet.get().getResource().getId());
 		assertEquals("ValueSet_noVersion", optionalTermValueSet.get().getName());
 
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1"));
 		assertTrue(optionalTermValueSet.isPresent());
 		Long v1Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V1).getEntity()).getId();
 		assertNotNull(v1Version_resid);
@@ -100,7 +100,7 @@ public class FhirResourceDaoR5ValueSetMultiVersionTest extends BaseJpaR5Test {
 		assertEquals(v1Version_resid, optionalTermValueSet.get().getResource().getId());
 		assertEquals("ValueSet_v1", optionalTermValueSet.get().getName());
 
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2"));
 		assertTrue(optionalTermValueSet.isPresent());
 		Long v2Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V2).getEntity()).getId();
 		assertNotNull(v2Version_resid);
@@ -114,15 +114,15 @@ public class FhirResourceDaoR5ValueSetMultiVersionTest extends BaseJpaR5Test {
 	public void testUpdateVersionedValueSets() {
 		Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
 
-		assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(3, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
 
-		TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
+		TermValueSet termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version")));
 		assertEquals("ValueSet_noVersion", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1")));
 		assertEquals("ValueSet_v1", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
 		assertEquals("ValueSet_v2", termValueSet.getName());
 
 		// Update ValueSets
@@ -142,21 +142,21 @@ public class FhirResourceDaoR5ValueSetMultiVersionTest extends BaseJpaR5Test {
 		Long v2Version_resid = ((ResourceTable)v2Version_update_outcome.getEntity()).getId();
 
 		// Verify that ValueSets were updated.
-		assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(3, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version")));
 		assertNotNull(nullVersion_resid);
 		assertNotNull(termValueSet.getResource());
 		assertEquals(nullVersion_resid, termValueSet.getResource().getId());
 		assertEquals("ValueSet_noVersion_updated", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1")));
 		assertNotNull(v1Version_resid);
 		assertNotNull(termValueSet.getResource());
 		assertEquals(v1Version_resid, termValueSet.getResource().getId());
 		assertEquals("ValueSet_v1_updated", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
 		assertNotNull(v2Version_resid);
 		assertNotNull(termValueSet.getResource());
 		assertEquals(v2Version_resid, termValueSet.getResource().getId());
@@ -168,50 +168,50 @@ public class FhirResourceDaoR5ValueSetMultiVersionTest extends BaseJpaR5Test {
 	public void testDeleteVersionedValueSets() {
 		Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
 
-		assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(3, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
 
-		TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
+		TermValueSet termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version")));
 		assertEquals("ValueSet_noVersion", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1")));
 		assertEquals("ValueSet_v1", termValueSet.getName());
 
-		termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
+		termValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
 		assertEquals("ValueSet_v2", termValueSet.getName());
 
 		// Delete ValueSets
 		myValueSetDao.delete(myValueSets.get(ValueSetVersions.NULL).getResource().getIdElement());
-		assertEquals(2, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(2, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
-		Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
+		Optional<TermValueSet> optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		assertNotNull(myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1")));
+		assertNotNull(runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"))));
-		assertNotNull(myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
+		assertNotNull(runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"))));
 
 		myValueSetDao.delete(myValueSets.get(ValueSetVersions.V1).getResource().getIdElement());
-		assertEquals(1, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(1, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1"));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		assertNotNull(myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2")));
+		assertNotNull(runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"))));
 
 		myValueSetDao.delete(myValueSets.get(ValueSetVersions.V2).getResource().getIdElement());
-		assertEquals(0, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
+		assertEquals(0, runInTransaction(()->myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size()));
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1"));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}
-		optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
+		optionalTermValueSet = runInTransaction(()->myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2"));
 		if (optionalTermValueSet.isPresent()) {
 			fail();
 		}

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetVersionedTest.java

@@ -303,7 +303,7 @@ public class ResourceProviderR5ValueSetVersionedTest extends BaseResourceProvide
 		loadAndPersistCodeSystemAndValueSet();
 		await().until(() -> clearDeferredStorageQueue());
 		myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
-		Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
+		Slice<TermValueSet> page = runInTransaction(()->myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED));
 		assertEquals(2, page.getContent().size());
 
 		// Verify v1 ValueSet
@@ -400,7 +400,7 @@ public class ResourceProviderR5ValueSetVersionedTest extends BaseResourceProvide
 		await().until(() -> clearDeferredStorageQueue());
 		myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
 
-		Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
+		Slice<TermValueSet> page = runInTransaction(()->myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED));
 		assertEquals(2, page.getContent().size());
 
 		// Validate ValueSet v1
@@ -568,7 +568,7 @@ public class ResourceProviderR5ValueSetVersionedTest extends BaseResourceProvide
 		await().until(() -> clearDeferredStorageQueue());
 		myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
 
-		Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
+		Slice<TermValueSet> page = runInTransaction(()->myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED));
 		assertEquals(2, page.getContent().size());
 
 		// Check expansion of multi-versioned ValueSet with version 1

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

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.test.config;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server Test Utilities
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import net.ttddyy.dsproxy.ExecutionInfo;
 import net.ttddyy.dsproxy.QueryInfo;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/CommonConfig.java

@@ -2,11 +2,13 @@ package ca.uhn.fhirtest.config;
 
 import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
+import ca.uhn.fhir.jpa.api.config.ThreadPoolFactoryConfig;
 import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
 import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
@@ -23,7 +25,8 @@ import org.springframework.context.annotation.Import;
 	SubscriptionProcessorConfig.class,
 	SubscriptionSubmitterConfig.class,
 	JpaBatch2Config.class,
-	Batch2JobsConfig.class
+	Batch2JobsConfig.class,
+	ThreadPoolFactoryConfig.class
 })
 public class CommonConfig {
 
@@ -53,6 +56,11 @@ public class CommonConfig {
 		return retVal;
 	}
 
+	@Bean
+	public IEmailSender emailSender() {
+		return new LoggingEmailSender();
+	}
+
 	/**
 	 * This is a joke
 	 * <p>

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/LoggingEmailSender.java

@@ -0,0 +1,15 @@
+package ca.uhn.fhirtest.config;
+
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailDetails;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class LoggingEmailSender implements IEmailSender {
+	private static final Logger ourLog = LoggerFactory.getLogger(LoggingEmailSender.class);
+
+	@Override
+	public void send(EmailDetails theDetails) {
+		ourLog.info("Not sending subscription email to: {}", theDetails.getTo());
+	}
+}

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -122,7 +122,7 @@ public class TestDstu2Config {
 
 	@Primary
 	@Bean
-	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
 		JpaTransactionManager retVal = new JpaTransactionManager();
 		retVal.setEntityManagerFactory(entityManagerFactory);
 		return retVal;

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -189,7 +189,7 @@ public class TestDstu3Config {
 
 	@Bean
 	@Primary
-	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
 		JpaTransactionManager retVal = new JpaTransactionManager();
 		retVal.setEntityManagerFactory(entityManagerFactory);
 		return retVal;

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -183,7 +183,7 @@ public class TestR4Config {
 
 	@Bean
 	@Primary
-	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
 		JpaTransactionManager retVal = new JpaTransactionManager();
 		retVal.setEntityManagerFactory(entityManagerFactory);
 		return retVal;

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java

@@ -190,7 +190,7 @@ public class TestR5Config {
 
 	@Bean
 	@Primary
-	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
 		JpaTransactionManager retVal = new JpaTransactionManager();
 		retVal.setEntityManagerFactory(entityManagerFactory);
 		return retVal;

hapi-fhir-server-mdm/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -34,6 +34,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.slf4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
 
 import javax.annotation.Nonnull;
 import java.util.HashSet;
@@ -42,6 +43,7 @@ import java.util.Set;
 import java.util.stream.Collectors;
 
 @Service
+@Transactional
 public class MdmLinkExpandSvc implements IMdmLinkExpandSvc {
 	private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
 

hapi-fhir-server-openapi/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-server/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/src/main/java/ca/uhn/fhir/spring/boot/autoconfigure/FhirAutoConfiguration.java

@@ -191,7 +191,7 @@ public class FhirAutoConfiguration {
 
 			@Bean
 			@Primary
-			public PlatformTransactionManager hapiTransactionManager() {
+			public PlatformTransactionManager transactionManager() {
 				return new JpaTransactionManager(emf);
 			}
 

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot-samples</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-spring-boot</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>hapi-fhir-spring-boot-samples</artifactId>

hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml

@@ -5,7 +5,7 @@
    <parent>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-deployable-pom</artifactId>
-      <version>6.2.0-PRE13-SNAPSHOT</version>
+      <version>6.2.0-PRE15-SNAPSHOT</version>
       <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
    </parent>
 

hapi-fhir-spring-boot/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-sql-migrate/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-storage-batch2-jobs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.2.0-PRE13-SNAPSHOT</version>
+		<version>6.2.0-PRE15-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>