Fix expunge transaction boundaries

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao;
  * 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.
@@ -58,7 +58,6 @@ import ca.uhn.fhir.util.*;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Charsets;
 import com.google.common.collect.ArrayListMultimap;
-import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 import com.google.common.hash.HashFunction;
 import com.google.common.hash.Hashing;
@@ -227,6 +226,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	}
 
 	protected ExpungeOutcome doExpunge(String theResourceName, Long theResourceId, Long theVersion, ExpungeOptions theExpungeOptions) {
+		TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
 
 		if (!getConfig().isExpungeEnabled()) {
 			throw new MethodNotAllowedException("$expunge is not enabled on this server");
@@ -245,32 +245,39 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			/*
 			 * Delete historical versions of deleted resources
 			 */
-			Pageable page = new PageRequest(0, remainingCount.get());
+			Pageable page = PageRequest.of(0, remainingCount.get());
-			Slice<Long> resourceIds;
+			Slice<Long> resourceIds = txTemplate.execute(t -> {
-			if (theResourceId != null) {
+				if (theResourceId != null) {
-				resourceIds = myResourceTableDao.findIdsOfDeletedResourcesOfType(page, theResourceId, theResourceName);
+					return myResourceTableDao.findIdsOfDeletedResourcesOfType(page, theResourceId, theResourceName);
-			} else {
-				if (theResourceName != null) {
-					resourceIds = myResourceTableDao.findIdsOfDeletedResourcesOfType(page, theResourceName);
 				} else {
-					resourceIds = myResourceTableDao.findIdsOfDeletedResources(page);
+					if (theResourceName != null) {
+						return myResourceTableDao.findIdsOfDeletedResourcesOfType(page, theResourceName);
+					} else {
+						return myResourceTableDao.findIdsOfDeletedResources(page);
+					}
 				}
-			}
+			});
 			for (Long next : resourceIds) {
-				expungeHistoricalVersionsOfId(next, remainingCount);
+				txTemplate.execute(t -> {
-				if (remainingCount.get() <= 0) {
+					expungeHistoricalVersionsOfId(next, remainingCount);
-					return toExpungeOutcome(theExpungeOptions, remainingCount);
+					if (remainingCount.get() <= 0) {
-				}
+						return toExpungeOutcome(theExpungeOptions, remainingCount);
+					}
+					return null;
+				});
 			}
 
 			/*
 			 * Delete current versions of deleted resources
 			 */
 			for (Long next : resourceIds) {
-				expungeCurrentVersionOfResource(next);
+				txTemplate.execute(t -> {
-				if (remainingCount.get() <= 0) {
+					expungeCurrentVersionOfResource(next);
-					return toExpungeOutcome(theExpungeOptions, remainingCount);
+					if (remainingCount.get() <= 0) {
-				}
+						return toExpungeOutcome(theExpungeOptions, remainingCount);
+					}
+					return null;
+				});
 			}
 
 		}
@@ -280,22 +287,26 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			/*
 			 * Delete historical versions of non-deleted resources
 			 */
-			Pageable page = new PageRequest(0, remainingCount.get());
+			Pageable page = PageRequest.of(0, remainingCount.get());
-			Slice<Long> historicalIds;
+			Slice<Long> historicalIds = txTemplate.execute(t -> {
-			if (theResourceId != null && theVersion != null) {
+				if (theResourceId != null && theVersion != null) {
-				historicalIds = toSlice(myResourceHistoryTableDao.findForIdAndVersion(theResourceId, theVersion));
+					return toSlice(myResourceHistoryTableDao.findForIdAndVersion(theResourceId, theVersion));
-			} else {
-				if (theResourceName != null) {
-					historicalIds = myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResources(page, theResourceName);
 				} else {
-					historicalIds = myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResources(page);
+					if (theResourceName != null) {
+						return myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResources(page, theResourceName);
+					} else {
+						return myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResources(page);
+					}
 				}
-			}
+			});
 			for (Long next : historicalIds) {
-				expungeHistoricalVersion(next);
+				txTemplate.execute(t -> {
-				if (remainingCount.decrementAndGet() <= 0) {
+					expungeHistoricalVersion(next);
-					return toExpungeOutcome(theExpungeOptions, remainingCount);
+					if (remainingCount.decrementAndGet() <= 0) {
-				}
+						return toExpungeOutcome(theExpungeOptions, remainingCount);
+					}
+					return null;
+				});
 			}
 
 		}
@@ -704,58 +715,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		return retVal;
 	}
 
-
-	@SuppressWarnings("unchecked")
-	public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
-		Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> resourceTypeToDao = getDaos();
-		IFhirResourceDao<R> dao = (IFhirResourceDao<R>) resourceTypeToDao.get(theType);
-		return dao;
-	}
-
-	protected IFhirResourceDao<?> getDaoOrThrowException(Class<? extends IBaseResource> theClass) {
-		IFhirResourceDao<? extends IBaseResource> retVal = getDao(theClass);
-		if (retVal == null) {
-			List<String> supportedResourceTypes = getDaos()
-				.keySet()
-				.stream()
-				.map(t->myContext.getResourceDefinition(t).getName())
-				.sorted()
-				.collect(Collectors.toList());
-			throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName() + " - Can handle: " + supportedResourceTypes);
-		}
-		return retVal;
-	}
-
-
-	private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> getDaos() {
-		if (myResourceTypeToDao == null) {
-			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> resourceTypeToDao = new HashMap<>();
-
-			Map<String, IFhirResourceDao> daos = myApplicationContext.getBeansOfType(IFhirResourceDao.class, false, false);
-
-			String[] beanNames = myApplicationContext.getBeanNamesForType(IFhirResourceDao.class);
-
-			for (IFhirResourceDao<?> next : daos.values()) {
-				resourceTypeToDao.put(next.getResourceType(), next);
-			}
-
-			if (this instanceof IFhirResourceDao<?>) {
-				IFhirResourceDao<?> thiz = (IFhirResourceDao<?>) this;
-				resourceTypeToDao.put(thiz.getResourceType(), thiz);
-			}
-
-			myResourceTypeToDao = resourceTypeToDao;
-		}
-
-		return Collections.unmodifiableMap(myResourceTypeToDao);
-	}
-
-	@PostConstruct
-	public void startClearCaches() {
-		myResourceTypeToDao = null;
-	}
-
-
 	protected Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource) {
 		return mySearchParamExtractor.extractSearchParamCoords(theEntity, theResource);
 	}
@@ -958,18 +917,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		return myConfig;
 	}
 
-	@Override
-	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
-		/*
-		 * We do a null check here because Smile's module system tries to
-		 * initialize the application context twice if two modules depend on
-		 * the persistence module. The second time sets the dependency's appctx.
-		 */
-		if (myApplicationContext == null) {
-			myApplicationContext = theApplicationContext;
-		}
-	}
-
 	public void setConfig(DaoConfig theConfig) {
 		myConfig = theConfig;
 	}
@@ -996,6 +943,50 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		}
 	}
 
+	@SuppressWarnings("unchecked")
+	public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
+		Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> resourceTypeToDao = getDaos();
+		IFhirResourceDao<R> dao = (IFhirResourceDao<R>) resourceTypeToDao.get(theType);
+		return dao;
+	}
+
+	protected IFhirResourceDao<?> getDaoOrThrowException(Class<? extends IBaseResource> theClass) {
+		IFhirResourceDao<? extends IBaseResource> retVal = getDao(theClass);
+		if (retVal == null) {
+			List<String> supportedResourceTypes = getDaos()
+				.keySet()
+				.stream()
+				.map(t -> myContext.getResourceDefinition(t).getName())
+				.sorted()
+				.collect(Collectors.toList());
+			throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName() + " - Can handle: " + supportedResourceTypes);
+		}
+		return retVal;
+	}
+
+	private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> getDaos() {
+		if (myResourceTypeToDao == null) {
+			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> resourceTypeToDao = new HashMap<>();
+
+			Map<String, IFhirResourceDao> daos = myApplicationContext.getBeansOfType(IFhirResourceDao.class, false, false);
+
+			String[] beanNames = myApplicationContext.getBeanNamesForType(IFhirResourceDao.class);
+
+			for (IFhirResourceDao<?> next : daos.values()) {
+				resourceTypeToDao.put(next.getResourceType(), next);
+			}
+
+			if (this instanceof IFhirResourceDao<?>) {
+				IFhirResourceDao<?> thiz = (IFhirResourceDao<?>) this;
+				resourceTypeToDao.put(thiz.getResourceType(), thiz);
+			}
+
+			myResourceTypeToDao = resourceTypeToDao;
+		}
+
+		return Collections.unmodifiableMap(myResourceTypeToDao);
+	}
+
 	public IResourceIndexedCompositeStringUniqueDao getResourceIndexedCompositeStringUniqueDao() {
 		return myResourceIndexedCompositeStringUniqueDao;
 	}
@@ -1537,6 +1528,18 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		return retVal;
 	}
 
+	@Override
+	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
+		/*
+		 * We do a null check here because Smile's module system tries to
+		 * initialize the application context twice if two modules depend on
+		 * the persistence module. The second time sets the dependency's appctx.
+		 */
+		if (myApplicationContext == null) {
+			myApplicationContext = theApplicationContext;
+		}
+	}
+
 	private void setUpdatedTime(Collection<? extends BaseResourceIndexedSearchParam> theParams, Date theUpdateTime) {
 		for (BaseResourceIndexedSearchParam nextSearchParam : theParams) {
 			nextSearchParam.setUpdated(theUpdateTime);
@@ -1593,6 +1596,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		return false;
 	}
 
+	@PostConstruct
+	public void startClearCaches() {
+		myResourceTypeToDao = null;
+	}
+
 	private ExpungeOutcome toExpungeOutcome(ExpungeOptions theExpungeOptions, AtomicInteger theRemainingCount) {
 		return new ExpungeOutcome()
 			.setDeletedCount(theExpungeOptions.getLimit() - theRemainingCount.get());
@@ -1648,13 +1656,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 
 		// get preload the tagList
 		Collection<? extends BaseTag> myTagList;
-		
+
 		if (theTagList == null)
 			myTagList = theEntity.getTags();
 		else
 			myTagList = theTagList;
-		
+
-		
+
 		/*
 		 * Use the appropriate custom type if one is specified in the context
 		 */
@@ -1746,7 +1754,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			return theResourceType + '/' + theId.toString();
 		}
 	}
-	
+
 	@SuppressWarnings("unchecked")
 	protected ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, ResourceTable
 		theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,

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

@@ -50,6 +50,7 @@ import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
 import ca.uhn.fhir.util.*;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.r4.model.InstantType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Required;
 import org.springframework.lang.NonNull;
@@ -517,6 +518,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.NEVER)
 	public ExpungeOutcome expunge(IIdType theId, ExpungeOptions theExpungeOptions) {
 		BaseHasResource entity = readEntity(theId);
 		if (theId.hasVersionIdPart()) {
@@ -532,6 +534,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	@Override
+	@Transactional(propagation = Propagation.NEVER)
 	public ExpungeOutcome expunge(ExpungeOptions theExpungeOptions) {
 		ourLog.info("Beginning TYPE[{}] expunge operation", getResourceName());
 
@@ -856,14 +859,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		T retVal = toResource(myResourceType, entity, null, null, false);
 
-		IPrimitiveType<Date> deleted;
+		if (entity.getDeleted() != null) {
-		if (retVal instanceof IResource) {
+			throw new ResourceGoneException("Resource was deleted at " + new InstantType(entity.getDeleted()).getValueAsString());
-			deleted = ResourceMetadataKeyEnum.DELETED_AT.get((IResource) retVal);
-		} else {
-			deleted = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) retVal);
-		}
-		if (deleted != null && !deleted.isEmpty()) {
-			throw new ResourceGoneException("Resource was deleted at " + deleted.getValueAsString());
 		}
 
 		ourLog.debug("Processed read on {} in {}ms", theId.getValue(), w.getMillisAndRestart());

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -20,27 +20,17 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.ForeignKey;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToOne;
-import javax.persistence.SequenceGenerator;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
-
 import org.hibernate.annotations.ColumnDefault;
 
+import javax.persistence.*;
+
 //@formatter:off
 @Entity()
 @Table(name = "HFJ_FORCED_ID", uniqueConstraints = {
 	@UniqueConstraint(name = "IDX_FORCEDID_RESID", columnNames = {"RESOURCE_PID"}),
-	@UniqueConstraint(name = "IDX_FORCEDID_TYPE_RESID", columnNames = {"RESOURCE_TYPE", "RESOURCE_PID"})
+	@UniqueConstraint(name = "IDX_FORCEDID_TYPE_RESID", columnNames = {"RESOURCE_TYPE", "RESOURCE_PID"}),
-}, indexes= {
+	@UniqueConstraint(name = "IDX_FORCEDID_TYPE_FID", columnNames = {"RESOURCE_TYPE", "FORCED_ID"})
+}, indexes = {
 	@Index(name = "IDX_FORCEDID_TYPE_FORCEDID", columnList = "RESOURCE_TYPE,FORCED_ID"),
 })
 //@formatter:on
@@ -57,11 +47,11 @@ public class ForcedId {
 	@Column(name = "PID")
 	private Long myId;
 
-	@JoinColumn(name = "RESOURCE_PID", nullable = false, updatable = false, foreignKey=@ForeignKey(name="FK_FORCEDID_RESOURCE"))
+	@JoinColumn(name = "RESOURCE_PID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_FORCEDID_RESOURCE"))
 	@OneToOne()
 	private ResourceTable myResource;
 
-	@Column(name = "RESOURCE_PID", nullable = false, updatable = false, insertable=false)
+	@Column(name = "RESOURCE_PID", nullable = false, updatable = false, insertable = false)
 	private Long myResourcePid;
 
 	// This is updatable=true because it was added in 1.6 and needs to be set.. At some
@@ -81,39 +71,39 @@ public class ForcedId {
 		return myForcedId;
 	}
 
-	public ResourceTable getResource() {
-		return myResource;
-	}
-	
-	public Long getResourcePid() {
-		if (myResourcePid==null) {
-			return myResource.getId();
-		}
-		return myResourcePid;
-	}
-
-	public String getResourceType() {
-		return myResourceType;
-	}
-
 	public void setForcedId(String theForcedId) {
 		myForcedId = theForcedId;
 	}
 
+	public ResourceTable getResource() {
+		return myResource;
+	}
+
 	public void setResource(ResourceTable theResource) {
 		myResource = theResource;
 	}
 
-	public void setResourcePid(Long theResourcePid) {
+	public Long getResourcePid() {
-		myResourcePid = theResourcePid;
+		if (myResourcePid == null) {
+			return myResource.getId();
+		}
+		return myResourcePid;
 	}
 
 	public void setResourcePid(ResourceTable theResourcePid) {
 		myResource = theResourcePid;
 	}
 
+	public String getResourceType() {
+		return myResourceType;
+	}
+
 	public void setResourceType(String theResourceType) {
 		myResourceType = theResourceType;
 	}
 
+	public void setResourcePid(Long theResourcePid) {
+		myResourcePid = theResourcePid;
+	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -170,6 +170,12 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myPatientDaoR4")
 	protected IFhirResourceDaoPatient<Patient> myPatientDao;
 	@Autowired
+	protected IResourceTableDao myResourceTableDao;
+	@Autowired
+	protected IResourceHistoryTableDao myResourceHistoryTableDao;
+	@Autowired
+	protected IForcedIdDao myForcedIdDao;
+	@Autowired
 	@Qualifier("myCoverageDaoR4")
 	protected IFhirResourceDao<Coverage> myCoverageDao;
 	@Autowired
@@ -188,10 +194,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myResourceProvidersR4")
 	protected Object myResourceProviders;
 	@Autowired
-	protected IResourceTableDao myResourceTableDao;
-	@Autowired
-	protected IResourceHistoryTableDao myResourceHistoryTableDao;
-	@Autowired
 	protected IResourceTagDao myResourceTagDao;
 	@Autowired
 	protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@@ -284,7 +286,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 
 	@Before
 	public void beforeFlushFT() {
-		runInTransaction(()->{
+		runInTransaction(() -> {
 			FullTextEntityManager ftem = Search.getFullTextEntityManager(myEntityManager);
 			ftem.purgeAll(ResourceTable.class);
 			ftem.purgeAll(ResourceIndexedSearchParamString.class);
@@ -315,6 +317,11 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 		return myFhirCtx;
 	}
 
+	@Override
+	protected PlatformTransactionManager getTxManager() {
+		return myTxManager;
+	}
+
 	protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
 		InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
 		if (stream == null) {
@@ -325,11 +332,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 		return newJsonParser.parseResource(type, string);
 	}
 
-	@Override
-	protected PlatformTransactionManager getTxManager() {
-		return myTxManager;
-	}
-
 	@AfterClass
 	public static void afterClassClearContextBaseJpaR4Test() throws Exception {
 		ourValueSetDao.purgeCaches();

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

@@ -2,19 +2,27 @@ package ca.uhn.fhir.jpa.provider.r4;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.util.ExpungeOptions;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
+import org.hamcrest.Matchers;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
 
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.not;
 import static org.junit.Assert.*;
 
 public class ExpungeR4Test extends BaseResourceProviderR4Test {
@@ -58,11 +66,8 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 		getDao(theId).read(theId);
 	}
 
-	@Override
-	@Before
-	public void before() throws Exception {
-		super.before();
 
+	public void createStandardPatients() {
 		Patient p = new Patient();
 		p.setId("PT-ONEVERSION");
 		p.getMeta().addTag().setSystem("http://foo").setCode("bar");
@@ -105,7 +110,6 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 		o.setStatus(Observation.ObservationStatus.FINAL);
 		myDeletedObservationId = myObservationDao.create(o).getId();
 		myDeletedObservationId = myObservationDao.delete(myDeletedObservationId).getId();
-
 	}
 
 	private IFhirResourceDao<?> getDao(IIdType theId) {
@@ -126,6 +130,8 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testExpungeInstanceOldVersionsAndDeleted() {
+		createStandardPatients();
+
 		Patient p = new Patient();
 		p.setId("PT-TWOVERSION");
 		p.getMeta().addTag().setSystem("http://foo").setCode("bar");
@@ -151,8 +157,35 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 		assertGone(myDeletedObservationId);
 	}
 
+	@Test
+	public void testExpungeAllVersionsDeletesRow() {
+		// Create then delete
+		Patient p = new Patient();
+		p.setId("TEST");
+		p.getMeta().addTag().setSystem("http://foo").setCode("bar");
+		p.setActive(true);
+		p.addName().setFamily("FOO");
+		myPatientDao.update(p).getId();
+		myPatientDao.delete(new IdType("Patient/TEST"));
+
+		runInTransaction(()-> assertThat(myResourceTableDao.findAll(), not(empty())));
+		runInTransaction(()-> assertThat(myResourceHistoryTableDao.findAll(), not(empty())));
+		runInTransaction(()-> assertThat(myForcedIdDao.findAll(), not(empty())));
+
+		myPatientDao.expunge(new ExpungeOptions()
+			.setExpungeDeletedResources(true)
+			.setExpungeOldVersions(true));
+
+		runInTransaction(()-> assertThat(myResourceTableDao.findAll(), empty()));
+		runInTransaction(()-> assertThat(myResourceHistoryTableDao.findAll(), empty()));
+		runInTransaction(()-> assertThat(myForcedIdDao.findAll(), empty()));
+
+	}
+
+
 	@Test
 	public void testExpungeInstanceVersionCurrentVersion() {
+		createStandardPatients();
 
 		try {
 			myPatientDao.expunge(myTwoVersionPatientId.withVersion("2"), new ExpungeOptions()
@@ -166,6 +199,8 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testExpungeInstanceVersionOldVersionsAndDeleted() {
+		createStandardPatients();
+
 		Patient p = new Patient();
 		p.setId("PT-TWOVERSION");
 		p.getMeta().addTag().setSystem("http://foo").setCode("bar");
@@ -193,6 +228,8 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testExpungeSystemOldVersionsAndDeleted() {
+		createStandardPatients();
+
 		mySystemDao.expunge(new ExpungeOptions()
 			.setExpungeDeletedResources(true)
 			.setExpungeOldVersions(true));
@@ -212,6 +249,8 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testExpungeTypeDeletedResources() {
+		createStandardPatients();
+
 		myPatientDao.expunge(new ExpungeOptions()
 			.setExpungeDeletedResources(true)
 			.setExpungeOldVersions(false));
@@ -231,6 +270,8 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testExpungeTypeOldVersions() {
+		createStandardPatients();
+
 		myPatientDao.expunge(new ExpungeOptions()
 			.setExpungeDeletedResources(false)
 			.setExpungeOldVersions(true));
@@ -251,6 +292,8 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testExpungeSystemEverything() {
+		createStandardPatients();
+
 		mySystemDao.expunge(new ExpungeOptions()
 			.setExpungeEverything(true));
 
@@ -270,6 +313,8 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 
 	@Test
 	public void testExpungeTypeOldVersionsAndDeleted() {
+		createStandardPatients();
+
 		myPatientDao.expunge(new ExpungeOptions()
 			.setExpungeDeletedResources(true)
 			.setExpungeOldVersions(true));

hapi-fhir-jpaserver-uhnfhirtest/derby_maintenance.txt

@@ -144,3 +144,5 @@ drop index IDX_SP_TOKEN_UNQUAL;
 
    16919 | public             | hfj_spidx_token             |   5.5205e+07 | 24763842560 | 17233928192 |        8192 |  7529906176 | 23 GB      | 16 GB      | 8192 bytes | 7181 MB
 
+drop index IDX_FORCEDID_TYPE_FORCEDID;
+create index IDX_FORCEDID_TYPE_FID;

src/changes/changes.xml

@@ -95,6 +95,19 @@
 				performance improvement on servers that are validating or executing FHIRPath repeatedly
 				under load. This module is used by default in the JPA server.
 			</action>
+			<action type="fix">
+				An index in the JPA server on the HFJ_FORCED_ID table was incorrectly
+				not marked as unique. This meant that under heavy load it was possible to
+				create two resources with the same client-assigned ID.
+			</action>
+			<action type="fix">
+				The JPA server 
+				<![CDATA[<code>$expunge</code>]]>
+				operation deleted components of an individual resource record in 
+				separate database transactions, meaning that if an operation failed 
+				unexpectedly resources could be left in a weird state. This has been
+				corrected.
+			</action>
 		</release>
 		<release version="3.4.0" date="2018-05-28">
 			<action type="add">