Allow client assigned IDs to be purely numeric in JPA server if

configured to do so

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

@@ -82,6 +82,7 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.failedToCreateWithInvalidId=Can not
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.incorrectResourceType=Incorrect resource type detected for endpoint, found {0} but expected {1}
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.failedToCreateWithClientAssignedNumericId=Can not create resource with ID[{0}], no resource with this ID exists and clients may only assign IDs which contain at least one non-numeric character
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.failedToCreateWithClientAssignedId=Can not create resource with ID[{0}], ID must not be supplied on a create (POST) operation
+ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.failedToCreateWithClientAssignedIdNotAllowed=No resource exists on this server resource with ID[{0}], and client-assigned IDs are not enabled.
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidParameterChain=Invalid parameter chain: {0}
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidVersion=Version "{0}" is not valid for resource {1}
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.multipleParamsWithSameNameOneIsMissingTrue=This server does not know how to handle multiple "{0}" parameters where one has a value of :missing=true

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java

@@ -34,10 +34,7 @@ import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
 import ca.uhn.fhir.jpa.subscription.email.SubscriptionEmailInterceptor;
 import ca.uhn.fhir.jpa.subscription.resthook.SubscriptionRestHookInterceptor;
 import ca.uhn.fhir.jpa.subscription.websocket.SubscriptionWebsocketInterceptor;
-import org.hibernate.cfg.AvailableSettings;
 import org.hibernate.jpa.HibernatePersistenceProvider;
-import org.hibernate.query.criteria.LiteralHandlingMode;
-import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
@@ -57,7 +54,6 @@ import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
 import org.springframework.scheduling.config.ScheduledTaskRegistrar;
 
 import javax.annotation.Nonnull;
-import java.util.Map;
 import java.util.concurrent.ScheduledExecutorService;
 
 
@@ -92,44 +88,7 @@ public abstract class BaseConfig implements SchedulingConfigurer {
 	 * factory with HAPI FHIR customizations
 	 */
 	protected LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean() {
+		LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean();
-			@Override
-			public Map<String, Object> getJpaPropertyMap() {
-				Map<String, Object> retVal = super.getJpaPropertyMap();
-
-				if (!retVal.containsKey(AvailableSettings.CRITERIA_LITERAL_HANDLING_MODE)) {
-					retVal.put(AvailableSettings.CRITERIA_LITERAL_HANDLING_MODE, LiteralHandlingMode.BIND);
-				}
-
-				if (!retVal.containsKey(AvailableSettings.CONNECTION_HANDLING)) {
-					retVal.put(AvailableSettings.CONNECTION_HANDLING, PhysicalConnectionHandlingMode.DELAYED_ACQUISITION_AND_HOLD);
-				}
-
-				/*
-				 * Set some performance options
-				 */
-
-				if (!retVal.containsKey(AvailableSettings.STATEMENT_BATCH_SIZE)) {
-					retVal.put(AvailableSettings.STATEMENT_BATCH_SIZE, "30");
-				}
-
-				if (!retVal.containsKey(AvailableSettings.ORDER_INSERTS)) {
-					retVal.put(AvailableSettings.ORDER_INSERTS, "true");
-				}
-
-				if (!retVal.containsKey(AvailableSettings.ORDER_UPDATES)) {
-					retVal.put(AvailableSettings.ORDER_UPDATES, "true");
-				}
-
-				if (!retVal.containsKey(AvailableSettings.BATCH_VERSIONED_DATA)) {
-					retVal.put(AvailableSettings.BATCH_VERSIONED_DATA, "true");
-				}
-
-				return retVal;
-			}
-
-
-		};
 		configureEntityManagerFactory(retVal, fhirContext());
 		return retVal;
 	}

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

@@ -0,0 +1,51 @@
+package ca.uhn.fhir.jpa.config;
+
+import org.hibernate.cfg.AvailableSettings;
+import org.hibernate.query.criteria.LiteralHandlingMode;
+import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+
+import java.util.Map;
+
+/**
+ * This class is an extension of the Spring/Hibernate LocalContainerEntityManagerFactoryBean
+ * that sets some sensible default property values
+ */
+public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContainerEntityManagerFactoryBean {
+	@Override
+	public Map<String, Object> getJpaPropertyMap() {
+		Map<String, Object> retVal = super.getJpaPropertyMap();
+
+		if (!retVal.containsKey(AvailableSettings.CRITERIA_LITERAL_HANDLING_MODE)) {
+			retVal.put(AvailableSettings.CRITERIA_LITERAL_HANDLING_MODE, LiteralHandlingMode.BIND);
+		}
+
+		if (!retVal.containsKey(AvailableSettings.CONNECTION_HANDLING)) {
+			retVal.put(AvailableSettings.CONNECTION_HANDLING, PhysicalConnectionHandlingMode.DELAYED_ACQUISITION_AND_HOLD);
+		}
+
+		/*
+		 * Set some performance options
+		 */
+
+		if (!retVal.containsKey(AvailableSettings.STATEMENT_BATCH_SIZE)) {
+			retVal.put(AvailableSettings.STATEMENT_BATCH_SIZE, "30");
+		}
+
+		if (!retVal.containsKey(AvailableSettings.ORDER_INSERTS)) {
+			retVal.put(AvailableSettings.ORDER_INSERTS, "true");
+		}
+
+		if (!retVal.containsKey(AvailableSettings.ORDER_UPDATES)) {
+			retVal.put(AvailableSettings.ORDER_UPDATES, "true");
+		}
+
+		if (!retVal.containsKey(AvailableSettings.BATCH_VERSIONED_DATA)) {
+			retVal.put(AvailableSettings.BATCH_VERSIONED_DATA, "true");
+		}
+
+		return retVal;
+	}
+
+
+}

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

@@ -21,7 +21,6 @@ import java.util.Set;
 import java.util.StringTokenizer;
 import java.util.UUID;
 import java.util.concurrent.atomic.AtomicInteger;
-import java.util.stream.Collectors;
 
 import javax.annotation.PostConstruct;
 import javax.persistence.EntityManager;
@@ -37,6 +36,7 @@ import javax.persistence.criteria.Root;
 import javax.xml.stream.events.Characters;
 import javax.xml.stream.events.XMLEvent;
 
+import ca.uhn.fhir.jpa.dao.data.*;
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.NameValuePair;
@@ -81,21 +81,6 @@ import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
-import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTagDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamCoordsDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamDateDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamNumberDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamQuantityDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamStringDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamTokenDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
-import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
-import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.index.IndexingSupport;
 import ca.uhn.fhir.jpa.dao.index.ResourceIndexedSearchParams;
 import ca.uhn.fhir.jpa.entity.BaseHasResource;
@@ -176,7 +161,6 @@ import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
-import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@@ -261,6 +245,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	protected EntityManager myEntityManager;
 	@Autowired
 	protected IForcedIdDao myForcedIdDao;
+	@Autowired
+	protected ISearchResultDao mySearchResultDao;
 	@Autowired(required = false)
 	protected IFulltextSearchSvc myFulltextSearchSvc;
 	@Autowired()
@@ -319,10 +305,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		}
 	}
 
-	protected void createForcedIdIfNeeded(ResourceTable theEntity, IIdType theId) {
+	/**
-		if (theId.isEmpty() == false && theId.hasIdPart()) {
+	 * Returns the newly created forced ID. If the entity already had a forced ID, or if
-			if (isValidPid(theId)) {
+	 * none was created, returns null.
-				return;
+	 */
+	protected ForcedId createForcedIdIfNeeded(ResourceTable theEntity, IIdType theId, boolean theCreateForPureNumericIds) {
+		if (theId.isEmpty() == false && theId.hasIdPart() && theEntity.getForcedId() == null) {
+			if (!theCreateForPureNumericIds && isValidPid(theId)) {
+				return null;
 			}
 
 			ForcedId fid = new ForcedId();
@@ -330,7 +320,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 			fid.setForcedId(theId.getIdPart());
 			fid.setResource(theEntity);
 			theEntity.setForcedId(fid);
+			return fid;
 		}
+
+		return null;
 	}
 
 	protected ExpungeOutcome doExpunge(String theResourceName, Long theResourceId, Long theVersion, ExpungeOptions theExpungeOptions) {
@@ -373,6 +366,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 				}
 			});
 
+			/*
+			 * Delete any search result cache entries pointing to the given resource
+			 */
+			if (resourceIds.getContent().size() > 0) {
+				txTemplate.execute(t -> {
+					mySearchResultDao.deleteByResourceIds(resourceIds.getContent());
+					return null;
+				});
+			}
+
 			/*
 			 * Delete historical versions
 			 */
@@ -416,6 +419,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 					}
 				}
 			});
+
 			for (Long next : historicalIds) {
 				txTemplate.execute(t -> {
 					expungeHistoricalVersion(next);
@@ -675,6 +679,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		return retVal;
 	}
 
+	@Override
 	public DaoConfig getConfig() {
 		return myConfig;
 	}
@@ -705,6 +710,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		}
 	}
 
+	@Override
 	@SuppressWarnings("unchecked")
 	public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
 		Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> resourceTypeToDao = getDaos();
@@ -886,6 +892,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		theProvider.setSearchCoordinatorSvc(mySearchCoordinatorSvc);
 	}
 
+	@Override
 	public boolean isLogicalReference(IIdType theId) {
 		Set<String> treatReferencesAsLogical = myConfig.getTreatReferencesAsLogical();
 		if (treatReferencesAsLogical != null) {
@@ -1461,11 +1468,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 
 	@Override
 	public Long translateForcedIdToPid(String theResourceName, String theResourceId) {
-		return translateForcedIdToPids(new IdDt(theResourceName, theResourceId), myForcedIdDao).get(0);
+		return translateForcedIdToPids(getConfig(), new IdDt(theResourceName, theResourceId), myForcedIdDao).get(0);
 	}
 
 	protected List<Long> translateForcedIdToPids(IIdType theId) {
-		return translateForcedIdToPids(theId, myForcedIdDao);
+		return translateForcedIdToPids(getConfig(), theId, myForcedIdDao);
 	}
 
 
@@ -1649,7 +1656,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 													boolean theForceUpdateVersion, RequestDetails theRequestDetails, ResourceTable theEntity, IIdType
 														theResourceId, IBaseResource theOldResource) {
 		// Notify interceptors
-		ActionRequestDetails requestDetails = null;
+		ActionRequestDetails requestDetails;
 		if (theRequestDetails != null) {
 			requestDetails = new ActionRequestDetails(theRequestDetails, theResource, theResourceId.getResourceType(), theResourceId);
 			notifyInterceptors(RestOperationTypeEnum.UPDATE, requestDetails);
@@ -1988,15 +1995,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 		return retVal;
 	}
 
-	protected static Long translateForcedIdToPid(String theResourceName, String theResourceId, IForcedIdDao
+	protected static Long translateForcedIdToPid(DaoConfig theDaoConfig, String theResourceName, String theResourceId, IForcedIdDao
 		theForcedIdDao) {
-		return translateForcedIdToPids(new IdDt(theResourceName, theResourceId), theForcedIdDao).get(0);
+		return translateForcedIdToPids(theDaoConfig, new IdDt(theResourceName, theResourceId), theForcedIdDao).get(0);
 	}
 
-	static List<Long> translateForcedIdToPids(IIdType theId, IForcedIdDao theForcedIdDao) {
+	static List<Long> translateForcedIdToPids(DaoConfig theDaoConfig, IIdType theId, IForcedIdDao theForcedIdDao) {
 		Validate.isTrue(theId.hasIdPart());
 
-		if (isValidPid(theId)) {
+		if (theDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY && isValidPid(theId)) {
 			return Collections.singletonList(theId.getIdPartAsLong());
 		} else {
 			List<ForcedId> forcedId;

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

@@ -53,16 +53,12 @@ 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;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
-import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
-import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import javax.annotation.Nonnull;
 import javax.annotation.PostConstruct;
 import javax.persistence.NoResultException;
 import javax.persistence.TypedQuery;
@@ -387,12 +383,26 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			}
 		}
 
+		boolean serverAssignedId;
 		if (isNotBlank(theResource.getIdElement().getIdPart())) {
-			if (isValidPid(theResource.getIdElement())) {
+			switch (myDaoConfig.getResourceClientIdStrategy()) {
-				throw new UnprocessableEntityException(
+				case NOT_ALLOWED:
-					"This server cannot create an entity with a user-specified numeric ID - Client should not specify an ID when creating a new resource, or should include at least one letter in the ID to force a client-defined ID");
+					throw new ResourceNotFoundException(
+						getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "failedToCreateWithClientAssignedIdNotAllowed", theResource.getIdElement().getIdPart()));
+				case ALPHANUMERIC:
+					if (theResource.getIdElement().isIdPartValidLong()) {
+						throw new InvalidRequestException(
+							getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "failedToCreateWithClientAssignedNumericId", theResource.getIdElement().getIdPart()));
+					}
+					createForcedIdIfNeeded(entity, theResource.getIdElement(), false);
+					break;
+				case ANY:
+					createForcedIdIfNeeded(entity, theResource.getIdElement(), true);
+					break;
 			}
-			createForcedIdIfNeeded(entity, theResource.getIdElement());
+			serverAssignedId = false;
+		} else {
+			serverAssignedId = true;
 		}
 
 		// Notify interceptors
@@ -413,8 +423,21 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		// Perform actual DB update
 		ResourceTable updatedEntity = updateEntity(theRequest, theResource, entity, null, thePerformIndexing, thePerformIndexing, theUpdateTime, false, thePerformIndexing);
-		theResource.setId(entity.getIdDt());
 
+		theResource.setId(entity.getIdDt());
+		if (serverAssignedId) {
+			switch (myDaoConfig.getResourceClientIdStrategy()) {
+				case NOT_ALLOWED:
+				case ALPHANUMERIC:
+					break;
+				case ANY:
+					ForcedId forcedId = createForcedIdIfNeeded(updatedEntity, theResource.getIdElement(), true);
+					if (forcedId != null) {
+						myForcedIdDao.save(forcedId);
+					}
+					break;
+			}
+		}
 
 		/*
 		 * If we aren't indexing (meaning we're probably executing a sub-operation within a transaction),
@@ -1231,10 +1254,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			try {
 				entity = readEntityLatestVersion(resourceId);
 			} catch (ResourceNotFoundException e) {
-				if (resourceId.isIdPartValidLong()) {
-					throw new InvalidRequestException(
-						getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "failedToCreateWithClientAssignedNumericId", theResource.getIdElement().getIdPart()));
-				}
 				return doCreate(theResource, null, thePerformIndexing, new Date(), theRequestDetails);
 			}
 		}
@@ -1325,12 +1344,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 	private void validateGivenIdIsAppropriateToRetrieveResource(IIdType theId, BaseHasResource entity) {
 		if (entity.getForcedId() != null) {
-			if (theId.isIdPartValidLong()) {
+			if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY) {
-				// This means that the resource with the given numeric ID exists, but it has a "forced ID", meaning that
+				if (theId.isIdPartValidLong()) {
-				// as far as the outside world is concerned, the given ID doesn't exist (it's just an internal pointer
+					// This means that the resource with the given numeric ID exists, but it has a "forced ID", meaning that
-				// to the
+					// as far as the outside world is concerned, the given ID doesn't exist (it's just an internal pointer
-				// forced ID)
+					// to the
-				throw new ResourceNotFoundException(theId);
+					// forced ID)
+					throw new ResourceNotFoundException(theId);
+				}
 			}
 		}
 	}

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

@@ -156,6 +156,7 @@ public class DaoConfig {
 	private List<Integer> mySearchPreFetchThresholds = Arrays.asList(500, 2000, -1);
 	private List<WarmCacheEntry> myWarmCacheEntries = new ArrayList<>();
 	private boolean myDisableHashBasedSearches;
+	private ClientIdStrategyEnum myResourceClientIdStrategy = ClientIdStrategyEnum.ALPHANUMERIC;
 
 	/**
 	 * Constructor
@@ -642,9 +643,39 @@ public class DaoConfig {
 		myResourceMetaCountHardLimit = theResourceMetaCountHardLimit;
 	}
 
+	/**
+	 * Controls the behaviour when a client-assigned ID is encountered, i.e. an HTTP PUT
+	 * on a resource ID that does not already exist in the database.
+	 * <p>
+	 * Default is {@link ClientIdStrategyEnum#ALPHANUMERIC}
+	 * </p>
+	 */
+	public ClientIdStrategyEnum getResourceClientIdStrategy() {
+		return myResourceClientIdStrategy;
+	}
+
+	/**
+	 * Controls the behaviour when a client-assigned ID is encountered, i.e. an HTTP PUT
+	 * on a resource ID that does not already exist in the database.
+	 * <p>
+	 * Default is {@link ClientIdStrategyEnum#ALPHANUMERIC}
+	 * </p>
+	 *
+	 * @param theResourceClientIdStrategy Must not be <code>null</code>
+	 */
+	public void setResourceClientIdStrategy(ClientIdStrategyEnum theResourceClientIdStrategy) {
+		Validate.notNull(theResourceClientIdStrategy, "theClientIdStrategy must not be null");
+		myResourceClientIdStrategy = theResourceClientIdStrategy;
+	}
+
 	/**
 	 * This setting configures the strategy to use in generating IDs for newly
 	 * created resources on the server. The default is {@link IdStrategyEnum#SEQUENTIAL_NUMERIC}.
+	 * <p>
+	 * This strategy is only used for server-assigned IDs, i.e. for HTTP POST
+	 * where the client is requesing that the server store a new resource and give
+	 * it an ID.
+	 * </p>
 	 */
 	public IdStrategyEnum getResourceServerIdStrategy() {
 		return myResourceServerIdStrategy;
@@ -653,8 +684,13 @@ public class DaoConfig {
 	/**
 	 * This setting configures the strategy to use in generating IDs for newly
 	 * created resources on the server. The default is {@link IdStrategyEnum#SEQUENTIAL_NUMERIC}.
+	 * <p>
+	 * This strategy is only used for server-assigned IDs, i.e. for HTTP POST
+	 * where the client is requesing that the server store a new resource and give
+	 * it an ID.
+	 * </p>
 	 *
-	 * @param theResourceIdStrategy The strategy. Must not be null.
+	 * @param theResourceIdStrategy The strategy. Must not be <code>null</code>.
 	 */
 	public void setResourceServerIdStrategy(IdStrategyEnum theResourceIdStrategy) {
 		Validate.notNull(theResourceIdStrategy, "theResourceIdStrategy must not be null");
@@ -1353,18 +1389,8 @@ public class DaoConfig {
 	 * given number.
 	 * </p>
 	 */
-	public void setSearchPreFetchThresholds(List<Integer> thePreFetchThresholds) {
+	public List<Integer> getSearchPreFetchThresholds() {
-		Validate.isTrue(thePreFetchThresholds.size() > 0, "thePreFetchThresholds must not be empty");
+		return mySearchPreFetchThresholds;
-		int last = 0;
-		for (Integer nextInteger : thePreFetchThresholds) {
-			int nextInt = nextInteger.intValue();
-			Validate.isTrue(nextInt > 0 || nextInt == -1, nextInt + " is not a valid prefetch threshold");
-			Validate.isTrue(nextInt != last, "Prefetch thresholds must be sequential");
-			Validate.isTrue(nextInt > last || nextInt == -1, "Prefetch thresholds must be sequential");
-			Validate.isTrue(last != -1, "Prefetch thresholds must be sequential");
-			last = nextInt;
-		}
-		mySearchPreFetchThresholds = thePreFetchThresholds;
 	}
 
 	/**
@@ -1380,8 +1406,18 @@ public class DaoConfig {
 	 * given number.
 	 * </p>
 	 */
-	public List<Integer> getSearchPreFetchThresholds() {
+	public void setSearchPreFetchThresholds(List<Integer> thePreFetchThresholds) {
-		return mySearchPreFetchThresholds;
+		Validate.isTrue(thePreFetchThresholds.size() > 0, "thePreFetchThresholds must not be empty");
+		int last = 0;
+		for (Integer nextInteger : thePreFetchThresholds) {
+			int nextInt = nextInteger.intValue();
+			Validate.isTrue(nextInt > 0 || nextInt == -1, nextInt + " is not a valid prefetch threshold");
+			Validate.isTrue(nextInt != last, "Prefetch thresholds must be sequential");
+			Validate.isTrue(nextInt > last || nextInt == -1, "Prefetch thresholds must be sequential");
+			Validate.isTrue(last != -1, "Prefetch thresholds must be sequential");
+			last = nextInt;
+		}
+		mySearchPreFetchThresholds = thePreFetchThresholds;
 	}
 
 	/**
@@ -1429,6 +1465,36 @@ public class DaoConfig {
 		UUID
 	}
 
+	public enum ClientIdStrategyEnum {
+		/**
+		 * Clients are not allowed to supply IDs for resources that do not
+		 * already exist
+		 */
+		NOT_ALLOWED,
+
+		/**
+		 * Clients may supply IDs but these IDs are not permitted to be purely
+		 * numeric. In other words, values such as "A", "A1" and "000A" would be considered
+		 * valid but "123" would not.
+		 * <p><b>This is the default setting.</b></p>
+		 */
+		ALPHANUMERIC,
+
+		/**
+		 * Clients may supply any ID including purely numeric IDs. Note that this setting should
+		 * only be set on an empty database, or on a database that has always had this setting
+		 * set as it causes a "forced ID" to be used for all resources.
+		 * <p>
+		 * Note that if you use this setting, it is highly recommended that you also
+		 * set the {@link #setResourceServerIdStrategy(IdStrategyEnum) ResourceServerIdStrategy}
+		 * to {@link IdStrategyEnum#UUID} in order to avoid any potential for conflicts. Otherwise
+		 * a database sequence will be used to generate IDs and these IDs can conflict with
+		 * client-assigned numeric IDs.
+		 * </P>
+		 */
+		ANY
+	}
+
 	private static void validateTreatBaseUrlsAsLocal(String theUrl) {
 		Validate.notBlank(theUrl, "Base URL must not be null or empty");
 

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

@@ -67,6 +67,9 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 
 	private Boolean ourDisabled;
 
+	@Autowired
+	private DaoConfig myDaoConfig;
+
 	/**
 	 * Constructor
 	 */
@@ -222,7 +225,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 				StringParam idParm = (StringParam) idParam;
 				idParamValue = idParm.getValue();
 			}
-			pid = BaseHapiFhirDao.translateForcedIdToPid(theResourceName, idParamValue, myForcedIdDao);
+			pid = BaseHapiFhirDao.translateForcedIdToPid(myDaoConfig, theResourceName, idParamValue, myForcedIdDao);
 		}
 
 		Long referencingPid = pid;
@@ -275,7 +278,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 		if (contextParts.length != 3 || "Patient".equals(contextParts[0]) == false || "$everything".equals(contextParts[2]) == false) {
 			throw new InvalidRequestException("Invalid context: " + theContext);
 		}
-		Long pid = BaseHapiFhirDao.translateForcedIdToPid(contextParts[0], contextParts[1], myForcedIdDao);
+		Long pid = BaseHapiFhirDao.translateForcedIdToPid( myDaoConfig, contextParts[0], contextParts[1], myForcedIdDao);
 
 		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
 

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

@@ -1600,7 +1600,7 @@ public class SearchBuilder implements ISearchBuilder {
 
 			if (myParams.get(IAnyResource.SP_RES_ID) != null) {
 				StringParam idParm = (StringParam) myParams.get(IAnyResource.SP_RES_ID).get(0).get(0);
-				Long pid = BaseHapiFhirDao.translateForcedIdToPid(myResourceName, idParm.getValue(), myForcedIdDao);
+				Long pid = BaseHapiFhirDao.translateForcedIdToPid(myCallingDao.getConfig(), myResourceName, idParm.getValue(), myForcedIdDao);
 				if (myAlsoIncludePids == null) {
 					myAlsoIncludePids = new ArrayList<>(1);
 				}

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

@@ -46,11 +46,14 @@ public interface IResourceTableDao extends JpaRepository<ResourceTable, Long> {
 	@Query("SELECT t.myResourceType as type, COUNT(t.myResourceType) as count FROM ResourceTable t GROUP BY t.myResourceType")
 	List<Map<?, ?>> getResourceCounts();
 
+	@Query("SELECT t.myId FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high ORDER BY t.myUpdated DESC")
+	Slice<Long> findIdsOfResourcesWithinUpdatedRangeOrderedFromNewest(Pageable thePage, @Param("low") Date theLow, @Param("high") Date theHigh);
+
 	@Query("SELECT t.myId FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high ORDER BY t.myUpdated ASC")
-	Slice<Long> findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage,@Param("low") Date theLow, @Param("high")Date theHigh);
+	Slice<Long> findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage, @Param("low") Date theLow, @Param("high") Date theHigh);
 
 	@Query("SELECT t.myId FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high AND t.myResourceType = :restype ORDER BY t.myUpdated ASC")
-	Slice<Long> findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage,@Param("restype") String theResourceType, @Param("low") Date theLow, @Param("high")Date theHigh);
+	Slice<Long> findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage, @Param("restype") String theResourceType, @Param("low") Date theLow, @Param("high") Date theHigh);
 
 	@Modifying
 	@Query("UPDATE ResourceTable t SET t.myIndexStatus = :status WHERE t.myId = :id")

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

@@ -45,6 +45,10 @@ public interface ISearchResultDao  extends JpaRepository<SearchResult, Long> {
 	@Query(value="SELECT r.myId FROM SearchResult r WHERE r.mySearchPid = :search")
 	Slice<Long> findForSearch(Pageable thePage, @Param("search") Long theSearchPid);
 
+	@Modifying
+	@Query("DELETE FROM SearchResult s WHERE s.myResourcePid IN :ids")
+	void deleteByResourceIds(@Param("ids") List<Long> theContent);
+
 	@Modifying
 	@Query("DELETE FROM SearchResult s WHERE s.myId IN :ids")
 	void deleteByIds(@Param("ids") List<Long> theContent);

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

@@ -44,7 +44,7 @@ public interface IResourceReindexingSvc {
 	 * Does the same thing as {@link #runReindexingPass()} but makes sure to perform at
 	 * least one pass even if one is half finished
 	 */
-	Integer forceReindexingPass();
+	int forceReindexingPass();
 
 	/**
 	 * Cancels all running and future reindexing jobs. This is mainly intended

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

@@ -196,7 +196,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 	}
 
 	@Override
-	public Integer forceReindexingPass() {
+	public int forceReindexingPass() {
 		myIndexingLock.lock();
 		try {
 			return doReindexingPassInsideLock();
@@ -219,7 +219,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
 		expungeJobsMarkedAsDeleted();
 	}
 
-	private Integer runReindexJobs() {
+	private int runReindexJobs() {
 		Collection<ResourceReindexJobEntity> jobs = myTxTemplate.execute(t -> myReindexJobDao.findAll(PageRequest.of(0, 10), false));
 		assert jobs != null;
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java

@@ -31,7 +31,7 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
 		myCodeSystemDao.create(cs, mySrd);
 
 		myResourceReindexingSvc.markAllResourcesForReindexing();
-		int outcome = myResourceReindexingSvc.runReindexingPass();
+		int outcome = myResourceReindexingSvc.forceReindexingPass();
 		assertNotEquals(-1, outcome); // -1 means there was a failure
 		
 		myTermSvc.saveDeferred();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java

@@ -3,7 +3,9 @@ package ca.uhn.fhir.jpa.dao.r4;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
+import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.*;
 import org.junit.After;
@@ -11,12 +13,14 @@ import org.junit.AfterClass;
 import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.dao.DataIntegrityViolationException;
+import org.springframework.data.domain.PageRequest;
 
 import java.io.IOException;
+import java.util.Date;
 
 import static org.hamcrest.Matchers.*;
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
-import static org.junit.Assert.assertThat;
 
 public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
 	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4CreateTest.class);
@@ -24,6 +28,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
 	@After
 	public void afterResetDao() {
 		myDaoConfig.setResourceServerIdStrategy(new DaoConfig().getResourceServerIdStrategy());
+		myDaoConfig.setResourceClientIdStrategy(new DaoConfig().getResourceClientIdStrategy());
 	}
 
 	@Test
@@ -69,6 +74,134 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testCreateWithClientAssignedIdDisallowed() {
+		myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.NOT_ALLOWED);
+
+		Patient p = new Patient();
+		p.setId("AAA");
+		p.addName().setFamily("FAM");
+		try {
+			myPatientDao.update(p);
+			fail();
+		} catch (ResourceNotFoundException e) {
+			assertEquals("No resource exists on this server resource with ID[AAA], and client-assigned IDs are not enabled.", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testCreateWithClientAssignedIdPureNumeric() {
+		myDaoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.SEQUENTIAL_NUMERIC);
+		myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.ANY);
+
+		// Create a server assigned ID
+		Patient p = new Patient();
+		p.setActive(true);
+		IIdType id0 = myPatientDao.create(p).getId();
+		long firstClientAssignedId = id0.getIdPartAsLong();
+		long newId = firstClientAssignedId + 2L;
+
+		// Read it back
+		p = myPatientDao.read(new IdType("Patient/" + firstClientAssignedId));
+		assertEquals(true, p.getActive());
+
+		// Not create a client assigned numeric ID
+		p = new Patient();
+		p.setId("Patient/" + newId);
+		p.addName().setFamily("FAM");
+		IIdType id1 = myPatientDao.update(p).getId();
+
+		assertEquals(Long.toString(newId), id1.getIdPart());
+		assertEquals("1", id1.getVersionIdPart());
+
+		p = myPatientDao.read(id1);
+		assertEquals("FAM", p.getNameFirstRep().getFamily());
+
+		// Update it
+		p = new Patient();
+		p.setId("Patient/" + newId);
+		p.addName().setFamily("FAM2");
+		id1 = myPatientDao.update(p).getId();
+
+		assertEquals(Long.toString(newId), id1.getIdPart());
+		assertEquals("2", id1.getVersionIdPart());
+
+		p = myPatientDao.read(id1);
+		assertEquals("FAM2", p.getNameFirstRep().getFamily());
+
+		// Try to create another server-assigned. This should fail since we have a
+		// a conflict.
+		p = new Patient();
+		p.setActive(false);
+		try {
+			myPatientDao.create(p).getId();
+			fail();
+		} catch (DataIntegrityViolationException e) {
+			// good
+		}
+
+		ourLog.info("ID0: {}", id0);
+		ourLog.info("ID1: {}", id1);
+	}
+
+	@Test
+	public void testCreateWithClientAssignedIdPureNumericServerIdUuid() {
+		myDaoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);
+		myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.ANY);
+
+		// Create a server assigned ID
+		Patient p = new Patient();
+		p.setActive(true);
+		IIdType id0 = myPatientDao.create(p).getId();
+
+		// Read it back
+		p = myPatientDao.read(id0.toUnqualifiedVersionless());
+		assertEquals(true, p.getActive());
+
+		// Pick an ID that was already used as an internal PID
+		Long newId = runInTransaction(() -> myResourceTableDao.findIdsOfResourcesWithinUpdatedRangeOrderedFromNewest(
+			PageRequest.of(0, 1),
+			DateUtils.addDays(new Date(), -1),
+			DateUtils.addDays(new Date(), 1)
+		).getContent().get(0));
+
+		// Not create a client assigned numeric ID
+		p = new Patient();
+		p.setId("Patient/" + newId);
+		p.addName().setFamily("FAM");
+		IIdType id1 = myPatientDao.update(p).getId();
+
+		assertEquals(Long.toString(newId), id1.getIdPart());
+		assertEquals("1", id1.getVersionIdPart());
+
+		// Read it back
+		p = myPatientDao.read(id1);
+		assertEquals("FAM", p.getNameFirstRep().getFamily());
+
+		// Update it
+		p = new Patient();
+		p.setId("Patient/" + newId);
+		p.addName().setFamily("FAM2");
+		id1 = myPatientDao.update(p).getId();
+
+		assertEquals(Long.toString(newId), id1.getIdPart());
+		assertEquals("2", id1.getVersionIdPart());
+
+		p = myPatientDao.read(id1);
+		assertEquals("FAM2", p.getNameFirstRep().getFamily());
+
+		// Try to create another server-assigned. This should fail since we have a
+		// a conflict.
+		p = new Patient();
+		p.setActive(false);
+		IIdType id2 = myPatientDao.create(p).getId();
+
+		ourLog.info("ID0: {}", id0);
+		ourLog.info("ID1: {}", id1);
+		ourLog.info("ID2: {}", id2);
+	}
+
+
 	@Test
 	public void testTransactionCreateWithUuidResourceStrategy() {
 		myDaoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);

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

@@ -146,8 +146,8 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 
 		mySearchParameterDao.create(fooSp, mySrd);
 
-		assertEquals(1, myResourceReindexingSvc.forceReindexingPass().intValue());
+		assertEquals(1, myResourceReindexingSvc.forceReindexingPass());
-		assertEquals(0, myResourceReindexingSvc.forceReindexingPass().intValue());
+		assertEquals(0, myResourceReindexingSvc.forceReindexingPass());
 
 	}
 

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

@@ -182,7 +182,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		});
 
 		myResourceReindexingSvc.markAllResourcesForReindexing();
-		myResourceReindexingSvc.runReindexingPass();
+		myResourceReindexingSvc.forceReindexingPass();
 
 		runInTransaction(() -> {
 			Optional<ResourceTable> tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong());
@@ -225,7 +225,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		});
 
 		myResourceReindexingSvc.markAllResourcesForReindexing();
-		myResourceReindexingSvc.runReindexingPass();
+		myResourceReindexingSvc.forceReindexingPass();
 
 		runInTransaction(() -> {
 			Optional<ResourceTable> tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong());

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

@@ -2,15 +2,14 @@ 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.SearchParameterMap;
-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.api.server.IBundleProvider;
 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.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Observation;
@@ -19,7 +18,8 @@ import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.List;
 
 import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.not;
@@ -168,17 +168,17 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 		myPatientDao.update(p).getId();
 		myPatientDao.delete(new IdType("Patient/TEST"));
 
-		runInTransaction(()-> assertThat(myResourceTableDao.findAll(), not(empty())));
+		runInTransaction(() -> assertThat(myResourceTableDao.findAll(), not(empty())));
-		runInTransaction(()-> assertThat(myResourceHistoryTableDao.findAll(), not(empty())));
+		runInTransaction(() -> assertThat(myResourceHistoryTableDao.findAll(), not(empty())));
-		runInTransaction(()-> assertThat(myForcedIdDao.findAll(), not(empty())));
+		runInTransaction(() -> assertThat(myForcedIdDao.findAll(), not(empty())));
 
 		myPatientDao.expunge(new ExpungeOptions()
 			.setExpungeDeletedResources(true)
 			.setExpungeOldVersions(true));
 
-		runInTransaction(()-> assertThat(myResourceTableDao.findAll(), empty()));
+		runInTransaction(() -> assertThat(myResourceTableDao.findAll(), empty()));
-		runInTransaction(()-> assertThat(myResourceHistoryTableDao.findAll(), empty()));
+		runInTransaction(() -> assertThat(myResourceHistoryTableDao.findAll(), empty()));
-		runInTransaction(()-> assertThat(myForcedIdDao.findAll(), empty()));
+		runInTransaction(() -> assertThat(myForcedIdDao.findAll(), empty()));
 
 	}
 
@@ -332,6 +332,61 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 		assertGone(myDeletedObservationId);
 	}
 
+	@Test
+	public void testExpungeEverythingWhereResourceInSearchResults() {
+		createStandardPatients();
+
+		IBundleProvider search = myPatientDao.search(new SearchParameterMap());
+		assertEquals(2, search.size().intValue());
+		search.getResources(0, 2);
+
+		runInTransaction(() -> {
+			assertEquals(2, mySearchResultDao.count());
+		});
+
+		mySystemDao.expunge(new ExpungeOptions()
+			.setExpungeEverything(true));
+
+		// Everything deleted
+		assertExpunged(myOneVersionPatientId);
+		assertExpunged(myTwoVersionPatientId.withVersion("1"));
+		assertExpunged(myTwoVersionPatientId.withVersion("2"));
+		assertExpunged(myDeletedPatientId.withVersion("1"));
+		assertExpunged(myDeletedPatientId);
+
+		// Everything deleted
+		assertExpunged(myOneVersionObservationId);
+		assertExpunged(myTwoVersionObservationId.withVersion("1"));
+		assertExpunged(myTwoVersionObservationId.withVersion("2"));
+		assertExpunged(myDeletedObservationId);
+	}
+
+	@Test
+	public void testExpungeDeletedWhereResourceInSearchResults() {
+		createStandardPatients();
+
+		IBundleProvider search = myPatientDao.search(new SearchParameterMap());
+		assertEquals(2, search.size().intValue());
+		List<IBaseResource> resources = search.getResources(0, 2);
+		myPatientDao.delete(resources.get(0).getIdElement());
+
+		runInTransaction(() -> {
+			assertEquals(2, mySearchResultDao.count());
+		});
+
+
+		mySystemDao.expunge(new ExpungeOptions()
+			.setExpungeDeletedResources(true));
+
+		// Everything deleted
+		assertExpunged(myOneVersionPatientId);
+		assertStillThere(myTwoVersionPatientId.withVersion("1"));
+		assertStillThere(myTwoVersionPatientId.withVersion("2"));
+		assertExpunged(myDeletedPatientId.withVersion("1"));
+		assertExpunged(myDeletedPatientId);
+
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/RestHookTestDstu3Test.java

@@ -24,6 +24,7 @@ import org.junit.*;
 
 import javax.servlet.http.HttpServletRequest;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 import static org.junit.Assert.assertEquals;
@@ -35,14 +36,14 @@ import static org.junit.Assert.fail;
 public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookTestDstu3Test.class);
-	private static List<Observation> ourCreatedObservations = Lists.newArrayList();
+	private static List<Observation> ourCreatedObservations = Collections.synchronizedList(Lists.newArrayList());
 	private static int ourListenerPort;
 	private static RestfulServer ourListenerRestServer;
 	private static Server ourListenerServer;
 	private static String ourListenerServerBase;
-	private static List<Observation> ourUpdatedObservations = Lists.newArrayList();
+	private static List<Observation> ourUpdatedObservations = Collections.synchronizedList(Lists.newArrayList());
-	private static List<String> ourContentTypes = new ArrayList<>();
+	private static List<String> ourContentTypes = Collections.synchronizedList(new ArrayList<>());
-	private List<IIdType> mySubscriptionIds = new ArrayList<>();
+	private List<IIdType> mySubscriptionIds = Collections.synchronizedList(new ArrayList<>());
 
 	@After
 	public void afterUnregisterRestHookListener() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test.java

@@ -1,4 +1,3 @@
-
 package ca.uhn.fhir.jpa.subscription;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -27,6 +26,7 @@ import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.junit.*;
 
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -34,13 +34,13 @@ import java.util.List;
  */
 public class RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test extends BaseResourceProviderDstu2Test {
 
-	private static List<Observation> ourCreatedObservations = Lists.newArrayList();
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test.class);
+	private static List<Observation> ourCreatedObservations = Collections.synchronizedList(Lists.newArrayList());
 	private static int ourListenerPort;
 	private static RestfulServer ourListenerRestServer;
 	private static Server ourListenerServer;
 	private static String ourListenerServerBase;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test.class);
+	private static List<Observation> ourUpdatedObservations = Collections.synchronizedList(Lists.newArrayList());
-	private static List<Observation> ourUpdatedObservations = Lists.newArrayList();
 
 	@After
 	public void afterUnregisterRestHookListener() {
@@ -142,7 +142,7 @@ public class RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test extends B
 		waitForSize(0, ourCreatedObservations);
 		waitForSize(3, ourUpdatedObservations);
 
-		ourClient.delete().resourceById(new IdDt("Subscription/"+ subscription2.getId())).execute();
+		ourClient.delete().resourceById(new IdDt("Subscription/" + subscription2.getId())).execute();
 
 		Observation observationTemp3 = sendObservation(code, "SNOMED-CT");
 
@@ -215,7 +215,7 @@ public class RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test extends B
 		waitForSize(0, ourCreatedObservations);
 		waitForSize(3, ourUpdatedObservations);
 
-		ourClient.delete().resourceById(new IdDt("Subscription/"+ subscription2.getId())).execute();
+		ourClient.delete().resourceById(new IdDt("Subscription/" + subscription2.getId())).execute();
 
 		Observation observationTemp3 = sendObservation(code, "SNOMED-CT");
 
@@ -256,6 +256,28 @@ public class RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test extends B
 		Assert.assertFalse(observation2.getId().isEmpty());
 	}
 
+	public static class ObservationListener implements IResourceProvider {
+
+		@Create
+		public MethodOutcome create(@ResourceParam Observation theObservation) {
+			ourLog.info("Received Listener Create");
+			ourCreatedObservations.add(theObservation);
+			return new MethodOutcome(new IdDt("Observation/1"), true);
+		}
+
+		@Override
+		public Class<? extends IBaseResource> getResourceType() {
+			return Observation.class;
+		}
+
+		@Update
+		public MethodOutcome update(@ResourceParam Observation theObservation) {
+			ourLog.info("Received Listener Update");
+			ourUpdatedObservations.add(theObservation);
+			return new MethodOutcome(new IdDt("Observation/1"), false);
+		}
+
+	}
 
 	@BeforeClass
 	public static void startListenerServer() throws Exception {
@@ -284,27 +306,4 @@ public class RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test extends B
 		ourListenerServer.stop();
 	}
 
-	public static class ObservationListener implements IResourceProvider {
-
-		@Create
-		public MethodOutcome create(@ResourceParam Observation theObservation) {
-			ourLog.info("Received Listener Create");
-			ourCreatedObservations.add(theObservation);
-			return new MethodOutcome(new IdDt("Observation/1"), true);
-		}
-
-		@Override
-		public Class<? extends IBaseResource> getResourceType() {
-			return Observation.class;
-		}
-
-		@Update
-		public MethodOutcome update(@ResourceParam Observation theObservation) {
-			ourLog.info("Received Listener Update");
-			ourUpdatedObservations.add(theObservation);
-			return new MethodOutcome(new IdDt("Observation/1"), false);
-		}
-
-	}
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/RestHookTestWithInterceptorRegisteredToDaoConfigDstu3Test.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.subscription;
 
 import static org.junit.Assert.*;
 
+import java.util.Collections;
 import java.util.List;
 
 import org.eclipse.jetty.server.Server;
@@ -29,13 +30,13 @@ import ca.uhn.fhir.rest.server.RestfulServer;
  */
 public class RestHookTestWithInterceptorRegisteredToDaoConfigDstu3Test extends BaseResourceProviderDstu3Test {
 
-	private static List<Observation> ourCreatedObservations = Lists.newArrayList();
+	private static List<Observation> ourCreatedObservations = Collections.synchronizedList(Lists.newArrayList());
 	private static int ourListenerPort;
 	private static RestfulServer ourListenerRestServer;
 	private static Server ourListenerServer;
 	private static String ourListenerServerBase;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookTestWithInterceptorRegisteredToDaoConfigDstu3Test.class);
-	private static List<Observation> ourUpdatedObservations = Lists.newArrayList();
+	private static List<Observation> ourUpdatedObservations = Collections.synchronizedList(Lists.newArrayList());
 
 	@Override
 	protected boolean shouldLogClient() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/r4/RestHookActivatesPreExistingSubscriptionsR4Test.java

@@ -23,10 +23,12 @@ import org.slf4j.LoggerFactory;
 
 import javax.servlet.http.HttpServletRequest;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 public class RestHookActivatesPreExistingSubscriptionsR4Test extends BaseResourceProviderR4Test {
 
@@ -35,9 +37,9 @@ public class RestHookActivatesPreExistingSubscriptionsR4Test extends BaseResourc
 	private static RestfulServer ourListenerRestServer;
 	private static String ourListenerServerBase;
 	private static Server ourListenerServer;
-	private static List<Observation> ourUpdatedObservations = Lists.newArrayList();
+	private static List<Observation> ourUpdatedObservations = Collections.synchronizedList(Lists.newArrayList());
-	private static List<String> ourContentTypes = new ArrayList<>();
+	private static List<String> ourContentTypes = Collections.synchronizedList(new ArrayList<>());
-	private static List<String> ourHeaders = new ArrayList<>();
+	private static List<String> ourHeaders = Collections.synchronizedList(new ArrayList<>());
 
 	@After
 	public void afterResetSubscriptionActivatingInterceptor() {
@@ -123,33 +125,6 @@ public class RestHookActivatesPreExistingSubscriptionsR4Test extends BaseResourc
 		}
 	}
 
-	@BeforeClass
-	public static void startListenerServer() throws Exception {
-		ourListenerPort = PortUtil.findFreePort();
-		ourListenerRestServer = new RestfulServer(FhirContext.forR4());
-		ourListenerServerBase = "http://localhost:" + ourListenerPort + "/fhir/context";
-
-		ObservationListener obsListener = new ObservationListener();
-		ourListenerRestServer.setResourceProviders(obsListener);
-
-		ourListenerServer = new Server(ourListenerPort);
-
-		ServletContextHandler proxyHandler = new ServletContextHandler();
-		proxyHandler.setContextPath("/");
-
-		ServletHolder servletHolder = new ServletHolder();
-		servletHolder.setServlet(ourListenerRestServer);
-		proxyHandler.addServlet(servletHolder, "/fhir/context/*");
-
-		ourListenerServer.setHandler(proxyHandler);
-		ourListenerServer.start();
-	}
-
-	@AfterClass
-	public static void stopListenerServer() throws Exception {
-		ourListenerServer.stop();
-	}
-
 	public static class ObservationListener implements IResourceProvider {
 
 
@@ -181,4 +156,31 @@ public class RestHookActivatesPreExistingSubscriptionsR4Test extends BaseResourc
 
 	}
 
+	@BeforeClass
+	public static void startListenerServer() throws Exception {
+		ourListenerPort = PortUtil.findFreePort();
+		ourListenerRestServer = new RestfulServer(FhirContext.forR4());
+		ourListenerServerBase = "http://localhost:" + ourListenerPort + "/fhir/context";
+
+		ObservationListener obsListener = new ObservationListener();
+		ourListenerRestServer.setResourceProviders(obsListener);
+
+		ourListenerServer = new Server(ourListenerPort);
+
+		ServletContextHandler proxyHandler = new ServletContextHandler();
+		proxyHandler.setContextPath("/");
+
+		ServletHolder servletHolder = new ServletHolder();
+		servletHolder.setServlet(ourListenerRestServer);
+		proxyHandler.addServlet(servletHolder, "/fhir/context/*");
+
+		ourListenerServer.setHandler(proxyHandler);
+		ourListenerServer.start();
+	}
+
+	@AfterClass
+	public static void stopListenerServer() throws Exception {
+		ourListenerServer.stop();
+	}
+
 }

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

@@ -27,6 +27,7 @@ import org.springframework.messaging.support.ExecutorSubscribableChannel;
 
 import javax.servlet.http.HttpServletRequest;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
 
@@ -41,15 +42,15 @@ import static org.junit.Assert.fail;
 public class RestHookTestR4Test extends BaseResourceProviderR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookTestDstu2Test.class);
-	private static List<Observation> ourCreatedObservations = Lists.newArrayList();
+	private static List<Observation> ourCreatedObservations = Collections.synchronizedList(Lists.newArrayList());
 	private static int ourListenerPort;
 	private static RestfulServer ourListenerRestServer;
 	private static Server ourListenerServer;
 	private static String ourListenerServerBase;
-	private static List<Observation> ourUpdatedObservations = Lists.newArrayList();
+	private static List<Observation> ourUpdatedObservations = Collections.synchronizedList(Lists.newArrayList());
-	private static List<String> ourContentTypes = new ArrayList<>();
+	private static List<String> ourContentTypes = Collections.synchronizedList(new ArrayList<>());
-	private static List<String> ourHeaders = new ArrayList<>();
+	private static List<String> ourHeaders = Collections.synchronizedList(new ArrayList<>());
-	private List<IIdType> mySubscriptionIds = new ArrayList<>();
+	private List<IIdType> mySubscriptionIds = Collections.synchronizedList(new ArrayList<>());
 	private CountingInterceptor myCountingInterceptor;
 
 	@After

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/r4/RestHookTestWithInterceptorRegisteredToDaoConfigR4Test.java

@@ -1,6 +1,7 @@
 
 package ca.uhn.fhir.jpa.subscription.r4;
 
+import java.util.Collections;
 import java.util.List;
 
 import org.eclipse.jetty.server.Server;
@@ -27,13 +28,13 @@ import ca.uhn.fhir.rest.server.RestfulServer;
  */
 public class RestHookTestWithInterceptorRegisteredToDaoConfigR4Test extends BaseResourceProviderR4Test {
 
-	private static List<Observation> ourCreatedObservations = Lists.newArrayList();
+	private static List<Observation> ourCreatedObservations = Collections.synchronizedList(Lists.newArrayList());
 	private static int ourListenerPort;
 	private static RestfulServer ourListenerRestServer;
 	private static Server ourListenerServer;
 	private static String ourListenerServerBase;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookTestWithInterceptorRegisteredToDaoConfigR4Test.class);
-	private static List<Observation> ourUpdatedObservations = Lists.newArrayList();
+	private static List<Observation> ourUpdatedObservations = Collections.synchronizedList(Lists.newArrayList());
 
 	@Override
 	protected boolean shouldLogClient() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/r4/RestHookWithEventDefinitionR4Test.java

@@ -13,6 +13,7 @@ import org.junit.Test;
 import org.slf4j.Logger;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -35,13 +36,13 @@ import java.util.List;
 public class RestHookWithEventDefinitionR4Test extends BaseResourceProviderR4Test {
 
 	private static final Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookWithEventDefinitionR4Test.class);
-	private static List<Observation> ourUpdatedObservations = Lists.newArrayList();
+	private static List<Observation> ourUpdatedObservations = Collections.synchronizedList(Lists.newArrayList());
-	private static List<String> ourContentTypes = new ArrayList<>();
+	private static List<String> ourContentTypes = Collections.synchronizedList(new ArrayList<>());
-	private static List<String> ourHeaders = new ArrayList<>();
+	private static List<String> ourHeaders = Collections.synchronizedList(new ArrayList<>());
-	private static List<Observation> ourCreatedObservations = Lists.newArrayList();
+	private static List<Observation> ourCreatedObservations = Collections.synchronizedList(Lists.newArrayList());
 	private String myPatientId;
 	private String mySubscriptionId;
-	private List<IIdType> mySubscriptionIds = new ArrayList<>();
+	private List<IIdType> mySubscriptionIds = Collections.synchronizedList(new ArrayList<>());
 
 	@Override
 	@After

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/ServerExceptionDstu3Test.java

@@ -83,15 +83,12 @@ public class ServerExceptionDstu3Test {
 		ourException = new InternalErrorException("Error", operationOutcome);
 
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=json");
-		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		try {
 			byte[] responseContentBytes = IOUtils.toByteArray(status.getEntity().getContent());
 			String responseContent = new String(responseContentBytes, Charsets.UTF_8);
 			ourLog.info(status.getStatusLine().toString());
 			ourLog.info(responseContent);
 			assertThat(responseContent, containsString("El nombre está vacío"));
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
 
 	}
@@ -105,16 +102,13 @@ public class ServerExceptionDstu3Test {
 		ourException = new AuthenticationException().addAuthenticateHeaderForRealm("REALM");
 
 		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
-		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
-		try {
 			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(status.getStatusLine().toString());
 			ourLog.info(responseContent);
 
 			assertEquals(401, status.getStatusLine().getStatusCode());
 			assertEquals("Basic realm=\"REALM\"", status.getFirstHeader("WWW-Authenticate").getValue());
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
 		}
 
 	}

pom.xml

@@ -2063,7 +2063,7 @@
 					</reportsDirectories>
 				</configuration>
 			</plugin>
-			<plugin>
+			<!--<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-project-info-reports-plugin</artifactId>
 				<version>3.0.0</version>
@@ -2078,7 +2078,7 @@
 						</reports>
 					</reportSet>
 				</reportSets>
-			</plugin>
+			</plugin>-->
 			<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-linkcheck-plugin</artifactId> <version>1.1</version> </plugin> -->
 		</plugins>
 	</reporting>

src/changes/changes.xml

@@ -147,6 +147,23 @@
 				The JPA server version migrator tool now runs in a multithreaded way, allowing it to
 				upgrade th database faster when migration tasks require data updates.
 			</action>
+			<action type="fix">
+				A bug in the JPA server was fixed: When a resource was previously deleted,
+				a transaction could not be posted that both restored the deleted resource but
+				also contained references to the now-restored resource.
+			</action>
+			<action type="fix">
+				The $expunge operation could sometimes fail to delete resources if a resource
+				to be deleted had recently been returned in a search result. This has been
+				corrected.
+			</action>
+			<action type="add">
+				A new setting has been added to the JPA Server DopConfig that controls the
+				behaviour when a client-assigned ID is encountered (i.e. the client performs
+				an HTTP PUT to a resource ID that doesn't already exist on the server). It is
+				now possible to disallow this action, to only allow alphanumeric IDs (the default
+				and only option previously) or allow any IDs including alphanumeric.
+			</action>
 		</release>
 
 		<release version="3.5.0" date="2018-09-17">