/*
 * #%L
 * HAPI FHIR JPA Server
 * %%
 * Copyright (C) 2014 - 2025 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%
 */
package ca.uhn.fhir.jpa.dao;

import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.api.IJobPartitionProvider;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.executor.InterceptorService;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictUtil;
import ca.uhn.fhir.jpa.interceptor.PatientCompartmentEnforcingInterceptor;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.model.entity.BaseTag;
import ca.uhn.fhir.jpa.model.entity.EntityIndexStatusEnum;
import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
import ca.uhn.fhir.jpa.model.entity.IdAndPartitionId;
import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryProvenanceEntity;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.TagDefinition;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
import ca.uhn.fhir.jpa.search.ResourceSearchUrlSvc;
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.update.UpdateParameters;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.StorageResponseCodeEnum;
import ca.uhn.fhir.model.dstu2.resource.BaseResource;
import ca.uhn.fhir.model.dstu2.resource.ListResource;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.HistorySearchDateRangeParam;
import ca.uhn.fhir.rest.server.IPagingProvider;
import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
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;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.util.ReflectionUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ValidationOptions;
import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.annotations.VisibleForTesting;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import jakarta.annotation.PostConstruct;
import jakarta.persistence.LockModeType;
import jakarta.persistence.NoResultException;
import jakarta.persistence.TypedQuery;
import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.function.TriFunction;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseMetaType;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.data.domain.Sort;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionSynchronization;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.UUID;
import java.util.concurrent.Callable;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import java.util.stream.Stream;

import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
import static java.util.Objects.isNull;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends BaseHapiFhirDao<T>
                implements IFhirResourceDao<T> {

        public static final String BASE_RESOURCE_NAME = "resource";
        private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);

        @Autowired
        protected IInterceptorBroadcaster myInterceptorBroadcaster;

        @Autowired
        protected PlatformTransactionManager myPlatformTransactionManager;

        @Autowired(required = false)
        protected IFulltextSearchSvc mySearchDao;

        @Autowired
        protected HapiTransactionService myTransactionService;

        @Autowired
        private MatchResourceUrlService<JpaPid> myMatchResourceUrlService;

        @Autowired
        private SearchBuilderFactory<JpaPid> mySearchBuilderFactory;

        @Autowired
        private DaoRegistry myDaoRegistry;

        @Autowired
        private IRequestPartitionHelperSvc myRequestPartitionHelperService;

        @Autowired
        private IJobPartitionProvider myJobPartitionProvider;

        @Autowired
        private MatchUrlService myMatchUrlService;

        @Autowired
        private IDeleteExpungeJobSubmitter myDeleteExpungeJobSubmitter;

        @Autowired
        private IJobCoordinator myJobCoordinator;

        @Autowired
        private IResourceHistoryProvenanceDao myResourceHistoryProvenanceDao;

        private IInstanceValidatorModule myInstanceValidator;
        private String myResourceName;
        private Class<T> myResourceType;

        @Autowired
        private PersistedJpaBundleProviderFactory myPersistedJpaBundleProviderFactory;

        @Autowired
        private MemoryCacheService myMemoryCacheService;

        private TransactionTemplate myTxTemplate;

        @Autowired
        private ResourceSearchUrlSvc myResourceSearchUrlSvc;

        @Autowired
        private IFhirSystemDao<?, ?> mySystemDao;

        @Nullable
        public static <T extends IBaseResource> T invokeStoragePreShowResources(
                        IInterceptorBroadcaster theInterceptorBroadcaster, RequestDetails theRequest, T retVal) {
                IInterceptorBroadcaster compositeBroadcaster =
                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(theInterceptorBroadcaster, theRequest);
                if (compositeBroadcaster.hasHooks(Pointcut.STORAGE_PRESHOW_RESOURCES)) {
                        SimplePreResourceShowDetails showDetails = new SimplePreResourceShowDetails(retVal);
                        HookParams params = new HookParams()
                                        .add(IPreResourceShowDetails.class, showDetails)
                                        .add(RequestDetails.class, theRequest)
                                        .addIfMatchesType(ServletRequestDetails.class, theRequest);
                        compositeBroadcaster.callHooks(Pointcut.STORAGE_PRESHOW_RESOURCES, params);
                        //noinspection unchecked
                        retVal = (T) showDetails.getResource(
                                        0); // TODO GGG/JA : getting resource 0 is interesting. We apparently allow null values in the list.
                        // Should we?
                        return retVal;
                } else {
                        return retVal;
                }
        }

        public static void invokeStoragePreAccessResources(
                        IInterceptorBroadcaster theInterceptorBroadcaster,
                        RequestDetails theRequest,
                        IIdType theId,
                        IBaseResource theResource) {
                IInterceptorBroadcaster compositeBroadcaster =
                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(theInterceptorBroadcaster, theRequest);
                if (compositeBroadcaster.hasHooks(Pointcut.STORAGE_PREACCESS_RESOURCES)) {
                        SimplePreResourceAccessDetails accessDetails = new SimplePreResourceAccessDetails(theResource);
                        HookParams params = new HookParams()
                                        .add(IPreResourceAccessDetails.class, accessDetails)
                                        .add(RequestDetails.class, theRequest)
                                        .addIfMatchesType(ServletRequestDetails.class, theRequest);
                        compositeBroadcaster.callHooks(Pointcut.STORAGE_PREACCESS_RESOURCES, params);
                        if (accessDetails.isDontReturnResourceAtIndex(0)) {
                                throw new ResourceNotFoundException(Msg.code(1995) + "Resource " + theId + " is not known");
                        }
                }
        }

        @Override
        protected HapiTransactionService getTransactionService() {
                return myTransactionService;
        }

        @VisibleForTesting
        public void setTransactionService(HapiTransactionService theTransactionService) {
                myTransactionService = theTransactionService;
        }

        @Override
        protected MatchResourceUrlService getMatchResourceUrlService() {
                return myMatchResourceUrlService;
        }

        @Override
        protected IStorageResourceParser getStorageResourceParser() {
                return myJpaStorageResourceParser;
        }

        @Override
        protected IDeleteExpungeJobSubmitter getDeleteExpungeJobSubmitter() {
                return myDeleteExpungeJobSubmitter;
        }

        /**
         * @deprecated Use {@link #create(T, RequestDetails)} instead
         */
        @Override
        public DaoMethodOutcome create(final T theResource) {
                return create(theResource, null, true, null, new TransactionDetails());
        }

        @Override
        public DaoMethodOutcome create(final T theResource, RequestDetails theRequestDetails) {
                return create(theResource, null, true, theRequestDetails, new TransactionDetails());
        }

        /**
         * @deprecated Use {@link #create(T, String, RequestDetails)} instead
         */
        @Override
        public DaoMethodOutcome create(final T theResource, String theIfNoneExist) {
                return create(theResource, theIfNoneExist, null);
        }

        @Override
        public DaoMethodOutcome create(final T theResource, String theIfNoneExist, RequestDetails theRequestDetails) {
                return create(theResource, theIfNoneExist, true, theRequestDetails, new TransactionDetails());
        }

        @Override
        public DaoMethodOutcome create(
                        T theResource,
                        String theIfNoneExist,
                        boolean thePerformIndexing,
                        RequestDetails theRequestDetails,
                        @Nonnull TransactionDetails theTransactionDetails) {
                RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineCreatePartitionForRequest(
                                theRequestDetails, theResource, getResourceName());
                return myTransactionService
                                .withRequest(theRequestDetails)
                                .withTransactionDetails(theTransactionDetails)
                                .withRequestPartitionId(requestPartitionId)
                                .execute(tx -> doCreateForPost(
                                                theResource,
                                                theIfNoneExist,
                                                thePerformIndexing,
                                                theTransactionDetails,
                                                theRequestDetails,
                                                requestPartitionId));
        }

        @VisibleForTesting
        public void setRequestPartitionHelperService(IRequestPartitionHelperSvc theRequestPartitionHelperService) {
                myRequestPartitionHelperService = theRequestPartitionHelperService;
        }

        /**
         * Called for FHIR create (POST) operations
         */
        protected DaoMethodOutcome doCreateForPost(
                        T theResource,
                        String theIfNoneExist,
                        boolean thePerformIndexing,
                        TransactionDetails theTransactionDetails,
                        RequestDetails theRequestDetails,
                        RequestPartitionId theRequestPartitionId) {
                if (theResource == null) {
                        String msg = getContext().getLocalizer().getMessage(BaseStorageDao.class, "missingBody");
                        throw new InvalidRequestException(Msg.code(956) + msg);
                }

                if (isNotBlank(theResource.getIdElement().getIdPart())) {
                        if (getContext().getVersion().getVersion().isOlderThan(FhirVersionEnum.DSTU3)) {
                                String message = getMessageSanitized(
                                                "failedToCreateWithClientAssignedId",
                                                theResource.getIdElement().getIdPart());
                                throw new InvalidRequestException(
                                                Msg.code(957) + message, createErrorOperationOutcome(message, "processing"));
                        } else {
                                // As of DSTU3, ID and version in the body should be ignored for a create/update
                                theResource.setId("");
                        }
                }

                if (getStorageSettings().getResourceServerIdStrategy() == JpaStorageSettings.IdStrategyEnum.UUID) {
                        theResource.setId(UUID.randomUUID().toString());
                        theResource.setUserData(JpaConstants.RESOURCE_ID_SERVER_ASSIGNED, Boolean.TRUE);
                }

                return doCreateForPostOrPut(
                                theRequestDetails,
                                theResource,
                                theIfNoneExist,
                                true,
                                thePerformIndexing,
                                theRequestPartitionId,
                                RestOperationTypeEnum.CREATE,
                                theTransactionDetails);
        }

        /**
         * Called both for FHIR create (POST) operations (via {@link #doCreateForPost(IBaseResource, String, boolean, TransactionDetails, RequestDetails, RequestPartitionId)}
         * as well as for FHIR update (PUT) where we're doing a create-with-client-assigned-ID (via {@link #doUpdate(IBaseResource, String, boolean, boolean, RequestDetails, TransactionDetails, RequestPartitionId)}.
         */
        private DaoMethodOutcome doCreateForPostOrPut(
                        RequestDetails theRequest,
                        T theResource,
                        String theMatchUrl,
                        boolean theProcessMatchUrl,
                        boolean thePerformIndexing,
                        RequestPartitionId theRequestPartitionId,
                        RestOperationTypeEnum theOperationType,
                        TransactionDetails theTransactionDetails) {
                StopWatch w = new StopWatch();

                preProcessResourceForStorage(theResource);
                preProcessResourceForStorage(theResource, theRequest, theTransactionDetails, thePerformIndexing);

                ResourceTable entity = new ResourceTable();
                entity.setResourceType(toResourceName(theResource));
                entity.setPartitionId(PartitionablePartitionId.toStoragePartition(theRequestPartitionId, myPartitionSettings));
                entity.setCreatedByMatchUrl(theMatchUrl);
                entity.initializeVersion();

                if (isNotBlank(theMatchUrl) && theProcessMatchUrl) {
                        Set<JpaPid> match = myMatchResourceUrlService.processMatchUrl(
                                        theMatchUrl, myResourceType, theTransactionDetails, theRequest);
                        ourLog.trace("Resolving match URL {} found: {}", theMatchUrl, match);
                        if (match.size() > 1) {
                                String msg = getContext()
                                                .getLocalizer()
                                                .getMessageSanitized(
                                                                BaseStorageDao.class,
                                                                "transactionOperationWithMultipleMatchFailure",
                                                                "CREATE",
                                                                myResourceName,
                                                                theMatchUrl,
                                                                match.size());
                                throw new PreconditionFailedException(Msg.code(958) + msg);
                        } else if (match.size() == 1) {

                                /*
                                 * Ok, so we've found a single PID that matches the conditional URL.
                                 * That's good, there are two possibilities below.
                                 */

                                JpaPid pid = match.iterator().next();
                                if (theTransactionDetails.getDeletedResourceIds().contains(pid)) {

                                        /*
                                         * If the resource matching the given match URL has already been
                                         * deleted within this transaction. This is a really rare case, since
                                         * it means the client has performed a FHIR transaction with both
                                         * a delete and a create on the same conditional URL. This is rare
                                         * but allowed, and means that it's now ok to create a new one resource
                                         * matching the conditional URL since we'll be deleting any existing
                                         * index rows on the existing resource as a part of this transaction.
                                         * We can also un-resolve the previous match URL in the TransactionDetails
                                         * since we'll resolve it to the new resource ID below
                                         */

                                        myMatchResourceUrlService.unresolveMatchUrl(theTransactionDetails, getResourceName(), theMatchUrl);

                                } else {

                                        /*
                                         * This is the normal path where the conditional URL matched exactly
                                         * one resource, so we won't be creating anything but instead
                                         * just returning the existing ID. We now have a PID for the matching
                                         * resource, but we haven't loaded anything else (e.g. the forced ID
                                         * or the resource body aren't yet loaded from the DB). We're going to
                                         * return a LazyDaoOutcome with two lazy loaded providers for loading the
                                         * entity and the forced ID since we can avoid these extra SQL loads
                                         * unless we know we're actually going to use them. For example, if
                                         * the client has specified "Prefer: return=minimal" then we won't be
                                         * needing the load the body.
                                         */

                                        Supplier<LazyDaoMethodOutcome.EntityAndResource> entitySupplier = () -> myTxTemplate.execute(tx -> {
                                                ResourceTable foundEntity = myEntityManager.find(ResourceTable.class, pid);
                                                IBaseResource resource = myJpaStorageResourceParser.toResource(foundEntity, false);
                                                theResource.setId(resource.getIdElement().getValue());
                                                return new LazyDaoMethodOutcome.EntityAndResource(foundEntity, resource);
                                        });
                                        Supplier<IIdType> idSupplier = () -> myTxTemplate.execute(tx -> {
                                                IIdType retVal = myIdHelperService.translatePidIdToForcedId(myFhirContext, myResourceName, pid);
                                                if (!retVal.hasVersionIdPart()) {
                                                        Long version = myMemoryCacheService.getIfPresent(
                                                                        MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getId());
                                                        if (version == null) {
                                                                version = myResourceTableDao.findCurrentVersionByPid(pid);
                                                                if (version != null) {
                                                                        myMemoryCacheService.putAfterCommit(
                                                                                        MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION,
                                                                                        pid.getId(),
                                                                                        version);
                                                                }
                                                        }
                                                        if (version != null) {
                                                                retVal = myFhirContext
                                                                                .getVersion()
                                                                                .newIdType()
                                                                                .setParts(
                                                                                                retVal.getBaseUrl(),
                                                                                                retVal.getResourceType(),
                                                                                                retVal.getIdPart(),
                                                                                                Long.toString(version));
                                                        }
                                                }
                                                return retVal;
                                        });

                                        DaoMethodOutcome outcome = toMethodOutcomeLazy(theRequest, pid, entitySupplier, idSupplier)
                                                        .setCreated(false)
                                                        .setNop(true);
                                        StorageResponseCodeEnum responseCode =
                                                        StorageResponseCodeEnum.SUCCESSFUL_CREATE_WITH_CONDITIONAL_MATCH;
                                        String msg = getContext()
                                                        .getLocalizer()
                                                        .getMessageSanitized(
                                                                        BaseStorageDao.class,
                                                                        "successfulCreateConditionalWithMatch",
                                                                        w.getMillisAndRestart(),
                                                                        UrlUtil.sanitizeUrlPart(theMatchUrl));
                                        outcome.setOperationOutcome(createInfoOperationOutcome(msg, responseCode));
                                        return outcome;
                                }
                        }
                }

                boolean isClientAssignedId = storeNonPidResourceId(theResource, entity);

                HookParams hookParams;

                // Notify interceptor for accepting/rejecting client assigned ids
                if (isClientAssignedId) {
                        hookParams = new HookParams().add(IBaseResource.class, theResource).add(RequestDetails.class, theRequest);
                        doCallHooks(theTransactionDetails, theRequest, Pointcut.STORAGE_PRESTORAGE_CLIENT_ASSIGNED_ID, hookParams);
                }

                // Interceptor call: STORAGE_PRESTORAGE_RESOURCE_CREATED
                hookParams = new HookParams()
                                .add(IBaseResource.class, theResource)
                                .add(RequestDetails.class, theRequest)
                                .addIfMatchesType(ServletRequestDetails.class, theRequest)
                                .add(RequestPartitionId.class, theRequestPartitionId)
                                .add(TransactionDetails.class, theTransactionDetails);
                doCallHooks(theTransactionDetails, theRequest, Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED, hookParams);

                if (isClientAssignedId) {
                        validateResourceIdCreation(theResource, theRequest);
                }

                if (theMatchUrl != null) {
                        // Note: We actually create the search URL below by calling enforceMatchUrlResourceUniqueness
                        // since we can't do that until we know the assigned PID, but we set this flag up here
                        // because we need to set it before we persist the ResourceTable entity in order to
                        // avoid triggering an extra DB update
                        entity.setSearchUrlPresent(true);
                }

                // Perform actual DB update
                // this call will also update the metadata
                ResourceTable updatedEntity = updateEntity(
                                theRequest,
                                theResource,
                                entity,
                                null,
                                thePerformIndexing,
                                false,
                                theTransactionDetails,
                                false,
                                thePerformIndexing);

                // Store the resource forced ID if necessary
                JpaPid jpaPid = updatedEntity.getPersistentId();

                // Populate the resource with its actual final stored ID from the entity
                theResource.setId(entity.getIdDt());

                // Pre-cache the resource ID
                jpaPid.setAssociatedResourceId(entity.getIdType(myFhirContext));
                String fhirId = entity.getFhirId();
                assert fhirId != null;
                myIdHelperService.addResolvedPidToFhirIdAfterCommit(
                                jpaPid, theRequestPartitionId, getResourceName(), fhirId, null);
                theTransactionDetails.addResolvedResourceId(jpaPid.getAssociatedResourceId(), jpaPid);
                theTransactionDetails.addResolvedResource(jpaPid.getAssociatedResourceId(), theResource);

                // Pre-cache the match URL, and create an entry in the HFJ_RES_SEARCH_URL table to
                // protect against concurrent writes to the same conditional URL
                if (theMatchUrl != null) {
                        myResourceSearchUrlSvc.enforceMatchUrlResourceUniqueness(getResourceName(), theMatchUrl, updatedEntity);
                        myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theMatchUrl, jpaPid);
                }

                // Update the version/last updated in the resource so that interceptors get
                // the correct version
                // TODO - the above updateEntity calls updateResourceMetadata
                //              Maybe we don't need this call here?
                myJpaStorageResourceParser.updateResourceMetadata(entity, theResource);

                // Populate the PID in the resource so it is available to hooks
                addPidToResource(entity, theResource);

                // Notify JPA interceptors
                if (!updatedEntity.isUnchangedInCurrentOperation()) {
                        hookParams = new HookParams()
                                        .add(IBaseResource.class, theResource)
                                        .add(RequestDetails.class, theRequest)
                                        .addIfMatchesType(ServletRequestDetails.class, theRequest)
                                        .add(TransactionDetails.class, theTransactionDetails)
                                        .add(
                                                        InterceptorInvocationTimingEnum.class,
                                                        theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED));
                        doCallHooks(theTransactionDetails, theRequest, Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, hookParams);
                }

                DaoMethodOutcome outcome = toMethodOutcome(theRequest, entity, theResource, theMatchUrl, theOperationType)
                                .setCreated(true);

                if (!thePerformIndexing) {
                        outcome.setId(theResource.getIdElement());
                }

                populateOperationOutcomeForUpdate(w, outcome, theMatchUrl, theOperationType, theTransactionDetails);

                return outcome;
        }

        /**
         * Check for an id on the resource and if so,
         * store it in ResourceTable.
         *
         * The fhirId property is either set here with the resource id
         * OR by hibernate once the PK is generated for a server-assigned id.
         *
         * Used for both client-assigned id and for server-assigned UUIDs.
         *
         * @return true if this is a client-assigned id
         *
         * @see ca.uhn.fhir.jpa.model.entity.ResourceTable.FhirIdGenerator
         */
        private boolean storeNonPidResourceId(T theResource, ResourceTable entity) {
                String resourceIdBeforeStorage = theResource.getIdElement().getIdPart();
                boolean resourceHadIdBeforeStorage = isNotBlank(resourceIdBeforeStorage);
                boolean resourceIdWasServerAssigned =
                                theResource.getUserData(JpaConstants.RESOURCE_ID_SERVER_ASSIGNED) == Boolean.TRUE;

                // We distinguish actual client-assigned ids from UUIDs which the server assigned.
                boolean isClientAssigned = resourceHadIdBeforeStorage && !resourceIdWasServerAssigned;

                // But both need to be set on the entity fhirId field.
                if (resourceHadIdBeforeStorage) {
                        entity.setFhirId(resourceIdBeforeStorage);
                }

                return isClientAssigned;
        }

        void validateResourceIdCreation(T theResource, RequestDetails theRequest) {
                JpaStorageSettings.ClientIdStrategyEnum strategy = getStorageSettings().getResourceClientIdStrategy();

                if (strategy == JpaStorageSettings.ClientIdStrategyEnum.NOT_ALLOWED) {
                        if (!isSystemRequest(theRequest)) {
                                throw new ResourceNotFoundException(Msg.code(959)
                                                + getMessageSanitized(
                                                                "failedToCreateWithClientAssignedIdNotAllowed",
                                                                theResource.getIdElement().getIdPart()));
                        }
                }

                if (strategy == JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC) {
                        if (theResource.getIdElement().isIdPartValidLong()) {
                                throw new InvalidRequestException(Msg.code(960)
                                                + getMessageSanitized(
                                                                "failedToCreateWithClientAssignedNumericId",
                                                                theResource.getIdElement().getIdPart()));
                        }
                }
        }

        protected String getMessageSanitized(String theKey, String theIdPart) {
                return getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, theKey, theIdPart);
        }

        private boolean isSystemRequest(RequestDetails theRequest) {
                return theRequest instanceof SystemRequestDetails;
        }

        private IInstanceValidatorModule getInstanceValidator() {
                return myInstanceValidator;
        }

        /**
         * @deprecated Use {@link #delete(IIdType, RequestDetails)} instead
         */
        @Override
        public DaoMethodOutcome delete(IIdType theId) {
                return delete(theId, null);
        }

        @Override
        public DaoMethodOutcome delete(IIdType theId, RequestDetails theRequestDetails) {
                TransactionDetails transactionDetails = new TransactionDetails();

                validateIdPresentForDelete(theId);
                validateDeleteEnabled();

                return myTransactionService.execute(theRequestDetails, transactionDetails, tx -> {
                        DeleteConflictList deleteConflicts = new DeleteConflictList();
                        if (isNotBlank(theId.getValue())) {
                                deleteConflicts.setResourceIdMarkedForDeletion(theId);
                        }

                        StopWatch w = new StopWatch();

                        DaoMethodOutcome retVal = delete(theId, deleteConflicts, theRequestDetails, transactionDetails);

                        DeleteConflictUtil.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);

                        ourLog.debug("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
                        return retVal;
                });
        }

        @Override
        public DaoMethodOutcome delete(
                        IIdType theId,
                        DeleteConflictList theDeleteConflicts,
                        RequestDetails theRequestDetails,
                        @Nonnull TransactionDetails theTransactionDetails) {
                validateIdPresentForDelete(theId);
                validateDeleteEnabled();

                RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForRead(
                                theRequestDetails, getResourceName(), theId);

                final ResourceTable entity;
                try {
                        entity = readEntityLatestVersion(theRequestDetails, theId, requestPartitionId, theTransactionDetails);
                } catch (ResourceNotFoundException ex) {
                        // we don't want to throw 404s.
                        // if not found, return an outcome anyway.
                        // Because no object actually existed, we'll
                        // just set the id and nothing else
                        return createMethodOutcomeForResourceId(
                                        theId.getValue(),
                                        MESSAGE_KEY_DELETE_RESOURCE_NOT_EXISTING,
                                        StorageResponseCodeEnum.SUCCESSFUL_DELETE_NOT_FOUND);
                }

                if (theId.hasVersionIdPart() && Long.parseLong(theId.getVersionIdPart()) != entity.getVersion()) {
                        throw new ResourceVersionConflictException(
                                        Msg.code(961) + "Trying to delete " + theId + " but this is not the current version");
                }

                JpaPid persistentId = entity.getId();
                theTransactionDetails.addDeletedResourceId(persistentId);

                // Don't delete again if it's already deleted
                if (isDeleted(entity)) {
                        DaoMethodOutcome outcome = createMethodOutcomeForResourceId(
                                        entity.getIdDt().getValue(),
                                        MESSAGE_KEY_DELETE_RESOURCE_ALREADY_DELETED,
                                        StorageResponseCodeEnum.SUCCESSFUL_DELETE_ALREADY_DELETED);

                        // used to exist, so we'll set the persistent id
                        outcome.setPersistentId(persistentId);
                        outcome.setEntity(entity);

                        return outcome;
                }

                StopWatch w = new StopWatch();

                T resourceToDelete = myJpaStorageResourceParser.toResource(myResourceType, entity, null, false);
                theDeleteConflicts.setResourceIdMarkedForDeletion(theId);

                // Notify IServerOperationInterceptors about pre-action call
                HookParams hook = new HookParams()
                                .add(IBaseResource.class, resourceToDelete)
                                .add(RequestDetails.class, theRequestDetails)
                                .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                .add(TransactionDetails.class, theTransactionDetails);
                doCallHooks(theTransactionDetails, theRequestDetails, Pointcut.STORAGE_PRESTORAGE_RESOURCE_DELETED, hook);

                myDeleteConflictService.validateOkToDelete(
                                theDeleteConflicts, entity, false, theRequestDetails, theTransactionDetails);

                preDelete(resourceToDelete, entity, theRequestDetails);

                ResourceTable savedEntity = updateEntityForDelete(theRequestDetails, theTransactionDetails, entity);
                resourceToDelete.setId(entity.getIdDt());

                // Notify JPA interceptors
                HookParams hookParams = new HookParams()
                                .add(IBaseResource.class, resourceToDelete)
                                .add(RequestDetails.class, theRequestDetails)
                                .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                .add(TransactionDetails.class, theTransactionDetails)
                                .add(
                                                InterceptorInvocationTimingEnum.class,
                                                theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED));

                doCallHooks(theTransactionDetails, theRequestDetails, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);

                DaoMethodOutcome outcome = toMethodOutcome(
                                                theRequestDetails, savedEntity, resourceToDelete, null, RestOperationTypeEnum.DELETE)
                                .setCreated(true);

                String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulDeletes", 1);
                msg += " "
                                + getContext()
                                                .getLocalizer()
                                                .getMessageSanitized(BaseStorageDao.class, "successfulTimingSuffix", w.getMillis());
                outcome.setOperationOutcome(createInfoOperationOutcome(msg, StorageResponseCodeEnum.SUCCESSFUL_DELETE));

                myIdHelperService.addResolvedPidToFhirIdAfterCommit(
                                entity.getPersistentId(),
                                requestPartitionId,
                                entity.getResourceType(),
                                entity.getFhirId(),
                                entity.getDeleted());

                return outcome;
        }

        @Override
        public DeleteMethodOutcome deleteByUrl(String theUrl, RequestDetails theRequest) {
                validateDeleteEnabled();

                TransactionDetails transactionDetails = new TransactionDetails();
                ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(theUrl);

                if (resourceSearch.isDeleteExpunge()) {
                        return deleteExpunge(theUrl, theRequest);
                }

                return myTransactionService
                                .withRequest(theRequest)
                                .withTransactionDetails(transactionDetails)
                                .execute(tx -> {
                                        DeleteConflictList deleteConflicts = new DeleteConflictList();
                                        DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequest, transactionDetails);
                                        DeleteConflictUtil.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
                                        return outcome;
                                });
        }

        /**
         * This method gets called by {@link #deleteByUrl(String, RequestDetails)} as well as by
         * transaction processors
         */
        @Override
        public DeleteMethodOutcome deleteByUrl(
                        String theUrl,
                        DeleteConflictList deleteConflicts,
                        RequestDetails theRequestDetails,
                        @Nonnull TransactionDetails theTransactionDetails) {
                validateDeleteEnabled();

                return myTransactionService
                                .withRequest(theRequestDetails)
                                .withTransactionDetails(theTransactionDetails)
                                .execute(tx -> doDeleteByUrl(theUrl, deleteConflicts, theTransactionDetails, theRequestDetails));
        }

        @Nonnull
        private DeleteMethodOutcome doDeleteByUrl(
                        String theUrl,
                        DeleteConflictList deleteConflicts,
                        TransactionDetails theTransactionDetails,
                        RequestDetails theRequestDetails) {
                ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(theUrl);
                SearchParameterMap paramMap = resourceSearch.getSearchParameterMap();
                paramMap.setLoadSynchronous(true);

                Set<JpaPid> resourceIds = myMatchResourceUrlService.search(paramMap, myResourceType, theRequestDetails, null);

                if (resourceIds.size() > 1) {
                        if (!getStorageSettings().isAllowMultipleDelete()) {
                                throw new PreconditionFailedException(Msg.code(962)
                                                + getContext()
                                                                .getLocalizer()
                                                                .getMessageSanitized(
                                                                                BaseStorageDao.class,
                                                                                "transactionOperationWithMultipleMatchFailure",
                                                                                "DELETE",
                                                                                myResourceName,
                                                                                theUrl,
                                                                                resourceIds.size()));
                        }
                        // TODO: LD: There is a still a bug on slow deletes:  https://github.com/hapifhir/hapi-fhir/issues/5675
                        final long threshold = getStorageSettings().getRestDeleteByUrlResourceIdThreshold();
                        if (resourceIds.size() > threshold) {
                                throw new PreconditionFailedException(Msg.code(2496)
                                                + getContext()
                                                                .getLocalizer()
                                                                .getMessageSanitized(
                                                                                BaseStorageDao.class,
                                                                                "deleteByUrlThresholdExceeded",
                                                                                theUrl,
                                                                                resourceIds.size(),
                                                                                threshold));
                        }
                }

                return deletePidList(theUrl, resourceIds, deleteConflicts, theRequestDetails, theTransactionDetails);
        }

        @Override
        public <P extends IResourcePersistentId> void expunge(Collection<P> theResourceIds, RequestDetails theRequest) {
                ExpungeOptions options = new ExpungeOptions();
                options.setExpungeDeletedResources(true);
                for (P pid : theResourceIds) {
                        if (pid instanceof JpaPid) {
                                ResourceTable entity = myEntityManager.find(ResourceTable.class, pid.getId());

                                forceExpungeInExistingTransaction(entity.getIdDt().toVersionless(), options, theRequest);
                        } else {
                                ourLog.warn("Unable to process expunge on resource {}", pid);
                                return;
                        }
                }
        }

        @Nonnull
        @Override
        public <P extends IResourcePersistentId> DeleteMethodOutcome deletePidList(
                        String theUrl,
                        Collection<P> theResourceIds,
                        DeleteConflictList theDeleteConflicts,
                        RequestDetails theRequestDetails,
                        TransactionDetails theTransactionDetails) {
                StopWatch w = new StopWatch();
                TransactionDetails transactionDetails =
                                theTransactionDetails != null ? theTransactionDetails : new TransactionDetails();
                List<ResourceTable> deletedResources = new ArrayList<>();

                List<IResourcePersistentId<?>> resolvedIds =
                                theResourceIds.stream().map(t -> (IResourcePersistentId<?>) t).collect(Collectors.toList());
                mySystemDao.preFetchResources(resolvedIds, false);

                for (P pid : theResourceIds) {
                        JpaPid jpaPid = (JpaPid) pid;

                        // This shouldn't actually need to hit the DB because we pre-fetch above
                        ResourceTable entity = myEntityManager.find(ResourceTable.class, jpaPid);
                        deletedResources.add(entity);

                        T resourceToDelete = myJpaStorageResourceParser.toResource(myResourceType, entity, null, false);

                        transactionDetails.addDeletedResourceId(pid);

                        // Notify IServerOperationInterceptors about pre-action call
                        HookParams hooks = new HookParams()
                                        .add(IBaseResource.class, resourceToDelete)
                                        .add(RequestDetails.class, theRequestDetails)
                                        .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                        .add(TransactionDetails.class, transactionDetails);
                        doCallHooks(transactionDetails, theRequestDetails, Pointcut.STORAGE_PRESTORAGE_RESOURCE_DELETED, hooks);

                        myDeleteConflictService.validateOkToDelete(
                                        theDeleteConflicts, entity, false, theRequestDetails, transactionDetails);

                        // Perform delete

                        preDelete(resourceToDelete, entity, theRequestDetails);

                        updateEntityForDelete(theRequestDetails, transactionDetails, entity);
                        resourceToDelete.setId(entity.getIdDt());

                        // Notify JPA interceptors
                        TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronization() {
                                @Override
                                public void beforeCommit(boolean readOnly) {
                                        HookParams hookParams = new HookParams()
                                                        .add(IBaseResource.class, resourceToDelete)
                                                        .add(RequestDetails.class, theRequestDetails)
                                                        .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                                        .add(TransactionDetails.class, transactionDetails)
                                                        .add(
                                                                        InterceptorInvocationTimingEnum.class,
                                                                        transactionDetails.getInvocationTiming(
                                                                                        Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED));
                                        doCallHooks(
                                                        transactionDetails,
                                                        theRequestDetails,
                                                        Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED,
                                                        hookParams);
                                }
                        });
                }

                IBaseOperationOutcome oo;
                if (deletedResources.isEmpty()) {
                        String msg = getContext()
                                        .getLocalizer()
                                        .getMessageSanitized(BaseStorageDao.class, "unableToDeleteNotFound", theUrl);
                        oo = createOperationOutcome(
                                        OO_SEVERITY_WARN, msg, "not-found", StorageResponseCodeEnum.SUCCESSFUL_DELETE_NOT_FOUND);
                } else {
                        String msg = getContext()
                                        .getLocalizer()
                                        .getMessageSanitized(BaseStorageDao.class, "successfulDeletes", deletedResources.size());
                        msg += " "
                                        + getContext()
                                                        .getLocalizer()
                                                        .getMessageSanitized(BaseStorageDao.class, "successfulTimingSuffix", w.getMillis());
                        oo = createInfoOperationOutcome(msg, StorageResponseCodeEnum.SUCCESSFUL_DELETE);
                }

                ourLog.debug(
                                "Processed delete on {} (matched {} resource(s)) in {}ms",
                                theUrl,
                                deletedResources.size(),
                                w.getMillis());

                DeleteMethodOutcome retVal = new DeleteMethodOutcome();
                retVal.setDeletedEntities(deletedResources);
                retVal.setOperationOutcome(oo);
                return retVal;
        }

        protected ResourceTable updateEntityForDelete(
                        RequestDetails theRequest, TransactionDetails theTransactionDetails, ResourceTable theEntity) {
                myResourceSearchUrlSvc.deleteByResId(theEntity.getPersistentId());
                Date updateTime = new Date();
                return updateEntity(theRequest, null, theEntity, updateTime, true, true, theTransactionDetails, false, true);
        }

        private void validateDeleteEnabled() {
                if (!getStorageSettings().isDeleteEnabled()) {
                        String msg = getContext().getLocalizer().getMessage(BaseStorageDao.class, "deleteBlockedBecauseDisabled");
                        throw new PreconditionFailedException(Msg.code(966) + msg);
                }
        }

        private void validateIdPresentForDelete(IIdType theId) {
                if (theId == null || !theId.hasIdPart()) {
                        throw new InvalidRequestException(Msg.code(967) + "Can not perform delete, no ID provided");
                }
        }

        private <MT extends IBaseMetaType> void doMetaAdd(
                        MT theMetaAdd,
                        BaseHasResource<?> theEntity,
                        RequestDetails theRequestDetails,
                        TransactionDetails theTransactionDetails) {
                IBaseResource oldVersion = myJpaStorageResourceParser.toResource(theEntity, false);

                List<TagDefinition> tags = toTagList(theMetaAdd);
                for (TagDefinition nextDef : tags) {

                        boolean entityHasTag = false;
                        for (BaseTag next : theEntity.getTags()) {
                                if (Objects.equals(next.getTag().getTagType(), nextDef.getTagType())
                                                && Objects.equals(next.getTag().getSystem(), nextDef.getSystem())
                                                && Objects.equals(next.getTag().getCode(), nextDef.getCode())
                                                && Objects.equals(next.getTag().getVersion(), nextDef.getVersion())
                                                && Objects.equals(next.getTag().getUserSelected(), nextDef.getUserSelected())) {
                                        entityHasTag = true;
                                        break;
                                }
                        }

                        if (!entityHasTag) {
                                theEntity.setHasTags(true);

                                TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
                                                theTransactionDetails,
                                                nextDef.getTagType(),
                                                nextDef.getSystem(),
                                                nextDef.getCode(),
                                                nextDef.getDisplay(),
                                                nextDef.getVersion(),
                                                nextDef.getUserSelected());
                                if (def != null) {
                                        BaseTag newEntity = theEntity.addTag(def);
                                        if (newEntity.getTagId() == null) {
                                                myEntityManager.persist(newEntity);
                                        }
                                }
                        }
                }

                validateMetaCount(theEntity.getTags().size());

                myEntityManager.merge(theEntity);

                // Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
                IBaseResource newVersion = myJpaStorageResourceParser.toResource(theEntity, false);
                HookParams preStorageParams = new HookParams()
                                .add(IBaseResource.class, oldVersion)
                                .add(IBaseResource.class, newVersion)
                                .add(RequestDetails.class, theRequestDetails)
                                .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                .add(TransactionDetails.class, theTransactionDetails);
                myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, preStorageParams);

                // Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
                HookParams preCommitParams = new HookParams()
                                .add(IBaseResource.class, oldVersion)
                                .add(IBaseResource.class, newVersion)
                                .add(RequestDetails.class, theRequestDetails)
                                .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                .add(TransactionDetails.class, theTransactionDetails)
                                .add(
                                                InterceptorInvocationTimingEnum.class,
                                                theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED));
                myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, preCommitParams);
        }

        private <MT extends IBaseMetaType> void doMetaDelete(
                        MT theMetaDel,
                        BaseHasResource theEntity,
                        RequestDetails theRequestDetails,
                        TransactionDetails theTransactionDetails) {

                // todo mb update hibernate search index if we are storing resources - it assumes inline tags.
                IBaseResource oldVersion = myJpaStorageResourceParser.toResource(theEntity, false);

                List<TagDefinition> tags = toTagList(theMetaDel);

                for (TagDefinition nextDef : tags) {
                        for (BaseTag next : new ArrayList<BaseTag>(theEntity.getTags())) {
                                if (Objects.equals(next.getTag().getTagType(), nextDef.getTagType())
                                                && Objects.equals(next.getTag().getSystem(), nextDef.getSystem())
                                                && Objects.equals(next.getTag().getCode(), nextDef.getCode())) {
                                        myEntityManager.remove(next);
                                        theEntity.getTags().remove(next);
                                }
                        }
                }

                if (theEntity.getTags().isEmpty()) {
                        theEntity.setHasTags(false);
                }

                theEntity = myEntityManager.merge(theEntity);

                // Interceptor call: STORAGE_PRECOMMIT_RESOURCE_UPDATED
                IBaseResource newVersion = myJpaStorageResourceParser.toResource(theEntity, false);
                HookParams preStorageParams = new HookParams()
                                .add(IBaseResource.class, oldVersion)
                                .add(IBaseResource.class, newVersion)
                                .add(RequestDetails.class, theRequestDetails)
                                .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                .add(TransactionDetails.class, theTransactionDetails);
                myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED, preStorageParams);

                HookParams preCommitParams = new HookParams()
                                .add(IBaseResource.class, oldVersion)
                                .add(IBaseResource.class, newVersion)
                                .add(RequestDetails.class, theRequestDetails)
                                .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                .add(TransactionDetails.class, theTransactionDetails)
                                .add(
                                                InterceptorInvocationTimingEnum.class,
                                                theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED));

                myInterceptorBroadcaster.callHooks(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, preCommitParams);
        }

        @Override
        public ExpungeOutcome expunge(IIdType theId, ExpungeOptions theExpungeOptions, RequestDetails theRequest) {
                HapiTransactionService.noTransactionAllowed();
                validateExpungeEnabled();
                return forceExpungeInExistingTransaction(theId, theExpungeOptions, theRequest);
        }

        @Override
        public ExpungeOutcome expunge(ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
                HapiTransactionService.noTransactionAllowed();
                ourLog.info("Beginning TYPE[{}] expunge operation", getResourceName());
                validateExpungeEnabled();
                return myExpungeService.expunge(getResourceName(), null, theExpungeOptions, theRequestDetails);
        }

        private void validateExpungeEnabled() {
                if (!getStorageSettings().isExpungeEnabled()) {
                        throw new MethodNotAllowedException(Msg.code(968) + "$expunge is not enabled on this server");
                }
        }

        @Override
        public ExpungeOutcome forceExpungeInExistingTransaction(
                        IIdType theId, ExpungeOptions theExpungeOptions, RequestDetails theRequest) {
                TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);

                BaseHasResource<?> entity = txTemplate.execute(t -> readEntity(theId, theRequest));
                Validate.notNull(entity, "Resource with ID %s not found in database", theId);

                if (theId.hasVersionIdPart()) {
                        BaseHasResource<?> currentVersion;
                        currentVersion = txTemplate.execute(t -> readEntity(theId.toVersionless(), theRequest));
                        Validate.notNull(
                                        currentVersion,
                                        "Current version of resource with ID %s not found in database",
                                        theId.toVersionless());

                        if (entity.getVersion() == currentVersion.getVersion()) {
                                throw new PreconditionFailedException(
                                                Msg.code(969) + "Can not perform version-specific expunge of resource "
                                                                + theId.toUnqualified().getValue() + " as this is the current version");
                        }

                        return myExpungeService.expunge(getResourceName(), entity.getResourceId(), theExpungeOptions, theRequest);
                }

                // Downstream code expects the version to be null in the JpaPid if we're not
                // doing a version specific expunge
                JpaPid resourceId = entity.getResourceId();
                resourceId = JpaPid.fromId(resourceId.getId(), resourceId.getPartitionId());

                return myExpungeService.expunge(getResourceName(), resourceId, theExpungeOptions, theRequest);
        }

        @Override
        @Nonnull
        public String getResourceName() {
                return myResourceName;
        }

        @Override
        public Class<T> getResourceType() {
                return myResourceType;
        }

        @SuppressWarnings("unchecked")
        public void setResourceType(Class<? extends IBaseResource> theTableType) {
                myResourceType = (Class<T>) theTableType;
        }

        @Override
        public IBundleProvider history(Date theSince, Date theUntil, Integer theOffset, RequestDetails theRequestDetails) {
                StopWatch w = new StopWatch();
                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForHistory(
                                                theRequestDetails, myResourceName, null);
                IBundleProvider retVal = myTransactionService
                                .withRequest(theRequestDetails)
                                .withRequestPartitionId(requestPartitionId)
                                .execute(() -> myPersistedJpaBundleProviderFactory.history(
                                                theRequestDetails, myResourceName, null, theSince, theUntil, theOffset, requestPartitionId));

                ourLog.debug("Processed history on {} in {}ms", myResourceName, w.getMillisAndRestart());
                return retVal;
        }

        /**
         * @deprecated Use {@link #history(IIdType, HistorySearchDateRangeParam, RequestDetails)} instead
         */
        @Override
        public IBundleProvider history(
                        final IIdType theId, final Date theSince, Date theUntil, Integer theOffset, RequestDetails theRequest) {
                StopWatch w = new StopWatch();

                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForHistory(
                                                theRequest, myResourceName, theId);
                IBundleProvider retVal = myTransactionService
                                .withRequest(theRequest)
                                .withRequestPartitionId(requestPartitionId)
                                .execute(() -> {
                                        IIdType id = theId.withResourceType(myResourceName).toUnqualifiedVersionless();
                                        BaseHasResource entity = readEntity(id, true, theRequest, requestPartitionId);

                                        return myPersistedJpaBundleProviderFactory.history(
                                                        theRequest,
                                                        myResourceName,
                                                        entity.getResourceId(),
                                                        theSince,
                                                        theUntil,
                                                        theOffset,
                                                        requestPartitionId);
                                });

                ourLog.debug("Processed history on {} in {}ms", theId, w.getMillisAndRestart());
                return retVal;
        }

        @Override
        public IBundleProvider history(
                        final IIdType theId,
                        final HistorySearchDateRangeParam theHistorySearchDateRangeParam,
                        RequestDetails theRequest) {
                StopWatch w = new StopWatch();
                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForHistory(
                                                theRequest, myResourceName, theId);
                IBundleProvider retVal = myTransactionService
                                .withRequest(theRequest)
                                .withRequestPartitionId(requestPartitionId)
                                .execute(() -> {
                                        IIdType id = theId.withResourceType(myResourceName).toUnqualifiedVersionless();
                                        BaseHasResource entity = readEntity(id, true, theRequest, requestPartitionId);

                                        return myPersistedJpaBundleProviderFactory.history(
                                                        theRequest,
                                                        myResourceName,
                                                        entity.getResourceId(),
                                                        theHistorySearchDateRangeParam.getLowerBoundAsInstant(),
                                                        theHistorySearchDateRangeParam.getUpperBoundAsInstant(),
                                                        theHistorySearchDateRangeParam.getOffset(),
                                                        theHistorySearchDateRangeParam.getHistorySearchType(),
                                                        requestPartitionId);
                                });

                ourLog.debug("Processed history on {} in {}ms", theId, w.getMillisAndRestart());
                return retVal;
        }

        protected boolean isPagingProviderDatabaseBacked(RequestDetails theRequestDetails) {
                if (theRequestDetails == null || theRequestDetails.getServer() == null) {
                        return false;
                }
                IRestfulServerDefaults server = theRequestDetails.getServer();
                IPagingProvider pagingProvider = server.getPagingProvider();
                return pagingProvider != null;
        }

        protected void requestReindexForRelatedResources(
                        Boolean theCurrentlyReindexing, List<String> theBase, RequestDetails theRequestDetails) {
                // Avoid endless loops
                if (Boolean.TRUE.equals(theCurrentlyReindexing) || shouldSkipReindex(theRequestDetails)) {
                        return;
                }

                if (getStorageSettings().isMarkResourcesForReindexingUponSearchParameterChange()) {

                        ReindexJobParameters params = new ReindexJobParameters();

                        List<String> urls = List.of();
                        if (!isCommonSearchParam(theBase)) {
                                urls = theBase.stream().map(t -> t + "?").collect(Collectors.toList());
                        }

                        myJobPartitionProvider.getPartitionedUrls(theRequestDetails, urls).forEach(params::addPartitionedUrl);

                        JobInstanceStartRequest request = new JobInstanceStartRequest();
                        request.setJobDefinitionId(JOB_REINDEX);
                        request.setParameters(params);
                        myJobCoordinator.startInstance(theRequestDetails, request);

                        ourLog.debug("Started reindex job with parameters {}", params);
                }

                mySearchParamRegistry.requestRefresh();
        }

        protected final boolean shouldSkipReindex(RequestDetails theRequestDetails) {
                if (theRequestDetails == null) {
                        return false;
                }
                Object shouldSkip = theRequestDetails.getUserData().getOrDefault(JpaConstants.SKIP_REINDEX_ON_UPDATE, false);
                return Boolean.parseBoolean(shouldSkip.toString());
        }

        private boolean isCommonSearchParam(List<String> theBase) {
                // If the base contains the special resource "Resource", this is a common SP that applies to all resources
                return theBase.stream().map(String::toLowerCase).anyMatch(BASE_RESOURCE_NAME::equals);
        }

        @Override
        @Transactional
        public <MT extends IBaseMetaType> MT metaAddOperation(
                        IIdType theResourceId, MT theMetaAdd, RequestDetails theRequest) {

                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForServerOperation(
                                                theRequest, JpaConstants.OPERATION_META_ADD);

                myTransactionService
                                .withRequest(theRequest)
                                .withRequestPartitionId(requestPartitionId)
                                .execute(() -> doMetaAddOperation(theResourceId, theMetaAdd, theRequest, requestPartitionId));

                @SuppressWarnings("unchecked")
                MT retVal = (MT) metaGetOperation(theMetaAdd.getClass(), theResourceId, theRequest);
                return retVal;
        }

        protected <MT extends IBaseMetaType> void doMetaAddOperation(
                        IIdType theResourceId, MT theMetaAdd, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
                TransactionDetails transactionDetails = new TransactionDetails();

                StopWatch w = new StopWatch();
                BaseHasResource entity = readEntity(theResourceId, true, theRequest, theRequestPartitionId);

                if (isNull(entity)) {
                        throw new ResourceNotFoundException(Msg.code(1993) + theResourceId);
                }

                ResourceTable latestVersion =
                                readEntityLatestVersion(theRequest, theResourceId, theRequestPartitionId, transactionDetails);
                if (latestVersion.getVersion() != entity.getVersion()) {
                        doMetaAdd(theMetaAdd, entity, theRequest, transactionDetails);
                } else {
                        doMetaAdd(theMetaAdd, latestVersion, theRequest, transactionDetails);

                        // Also update history entry
                        ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(
                                        entity.getResourceId().toFk(), entity.getVersion());
                        doMetaAdd(theMetaAdd, history, theRequest, transactionDetails);
                }

                ourLog.debug("Processed metaAddOperation on {} in {}ms", theResourceId, w.getMillisAndRestart());
        }

        @Override
        @Transactional
        public <MT extends IBaseMetaType> MT metaDeleteOperation(
                        IIdType theResourceId, MT theMetaDel, RequestDetails theRequest) {

                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForServerOperation(
                                                theRequest, JpaConstants.OPERATION_META_DELETE);

                myTransactionService
                                .withRequest(theRequest)
                                .withRequestPartitionId(requestPartitionId)
                                .execute(() -> doMetaDeleteOperation(theResourceId, theMetaDel, theRequest, requestPartitionId));

                @SuppressWarnings("unchecked")
                MT retVal = (MT) metaGetOperation(theMetaDel.getClass(), theResourceId, theRequest);
                return retVal;
        }

        @Transactional
        public <MT extends IBaseMetaType> void doMetaDeleteOperation(
                        IIdType theResourceId, MT theMetaDel, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
                TransactionDetails transactionDetails = new TransactionDetails();
                StopWatch w = new StopWatch();

                BaseHasResource entity = readEntity(theResourceId, true, theRequest, theRequestPartitionId);

                if (isNull(entity)) {
                        throw new ResourceNotFoundException(Msg.code(1994) + theResourceId);
                }

                ResourceTable latestVersion =
                                readEntityLatestVersion(theRequest, theResourceId, theRequestPartitionId, transactionDetails);
                boolean nonVersionedTags =
                                myStorageSettings.getTagStorageMode() != JpaStorageSettings.TagStorageModeEnum.VERSIONED;

                if (latestVersion.getVersion() != entity.getVersion() || nonVersionedTags) {
                        doMetaDelete(theMetaDel, entity, theRequest, transactionDetails);
                } else {
                        doMetaDelete(theMetaDel, latestVersion, theRequest, transactionDetails);
                        // Also update history entry
                        ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(
                                        entity.getResourceId().toFk(), entity.getVersion());
                        doMetaDelete(theMetaDel, history, theRequest, transactionDetails);
                }

                ourLog.debug("Processed metaDeleteOperation on {} in {}ms", theResourceId.getValue(), w.getMillisAndRestart());
        }

        @Override
        public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequest) {
                return myTransactionService.withRequest(theRequest).execute(() -> {
                        Set<TagDefinition> tagDefs = new HashSet<>();
                        BaseHasResource<?> entity = readEntity(theId, theRequest);
                        for (BaseTag next : entity.getTags()) {
                                tagDefs.add(next.getTag());
                        }
                        MT retVal = toMetaDt(theType, tagDefs);

                        retVal.setLastUpdated(entity.getUpdatedDate());
                        retVal.setVersionId(Long.toString(entity.getVersion()));

                        return retVal;
                });
        }

        @Override
        @Transactional
        public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, RequestDetails theRequestDetails) {
                String sql =
                                "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t WHERE t.myResourceType = :res_type)";
                TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
                q.setParameter("res_type", myResourceName);
                List<TagDefinition> tagDefinitions = q.getResultList();

                return toMetaDt(theType, tagDefinitions);
        }

        private boolean isDeleted(BaseHasResource entityToUpdate) {
                return entityToUpdate.getDeleted() != null;
        }

        @PostConstruct
        @Override
        public void start() {
                assert getStorageSettings() != null;

                RuntimeResourceDefinition def = getContext().getResourceDefinition(myResourceType);
                myResourceName = def.getName();

                if (mySearchDao != null && mySearchDao.isDisabled()) {
                        mySearchDao = null;
                }

                ourLog.debug("Starting resource DAO for type: {}", getResourceName());
                myInstanceValidator = getApplicationContext().getBean(IInstanceValidatorModule.class);
                myTxTemplate = new TransactionTemplate(myPlatformTransactionManager);
                super.start();
        }

        /**
         * Subclasses may override to provide behaviour. Invoked within a delete
         * transaction with the resource that is about to be deleted.
         */
        protected void preDelete(T theResourceToDelete, ResourceTable theEntityToDelete, RequestDetails theRequestDetails) {
                // nothing by default
        }

        @Override
        @Transactional
        public T readByPid(IResourcePersistentId thePid) {
                return readByPid(thePid, false);
        }

        @Override
        @Transactional
        public T readByPid(IResourcePersistentId thePid, boolean theDeletedOk) {
                StopWatch w = new StopWatch();
                JpaPid jpaPid = (JpaPid) thePid;

                Optional<ResourceTable> entity = myResourceTableDao.findById(jpaPid);
                if (entity.isEmpty()) {
                        throw new ResourceNotFoundException(Msg.code(975) + "No resource found with PID " + jpaPid);
                }
                if (isDeleted(entity.get()) && !theDeletedOk) {
                        throw createResourceGoneException(entity.get());
                }

                T retVal = myJpaStorageResourceParser.toResource(myResourceType, entity.get(), null, false);

                ourLog.debug("Processed read on {} in {}ms", jpaPid, w.getMillis());
                return retVal;
        }

        /**
         * @deprecated Use {@link #read(IIdType, RequestDetails)} instead
         */
        @Override
        public T read(IIdType theId) {
                return read(theId, null);
        }

        @Override
        public T read(IIdType theId, RequestDetails theRequestDetails) {
                return read(theId, theRequestDetails, false);
        }

        @Override
        public T read(IIdType theId, RequestDetails theRequest, boolean theDeletedOk) {
                validateResourceTypeAndThrowInvalidRequestException(theId);
                TransactionDetails transactionDetails = new TransactionDetails();

                RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForRead(
                                theRequest, myResourceName, theId);

                return myTransactionService
                                .withRequest(theRequest)
                                .withTransactionDetails(transactionDetails)
                                .withRequestPartitionId(requestPartitionId)
                                .read(() -> doReadInTransaction(theId, theRequest, theDeletedOk, requestPartitionId));
        }

        private T doReadInTransaction(
                        IIdType theId, RequestDetails theRequest, boolean theDeletedOk, RequestPartitionId theRequestPartitionId) {
                assert TransactionSynchronizationManager.isActualTransactionActive();

                StopWatch w = new StopWatch();
                BaseHasResource<?> entity = readEntity(theId, true, theRequest, theRequestPartitionId);
                validateResourceType(entity);

                T retVal = myJpaStorageResourceParser.toResource(
                                myResourceType, (IBaseResourceEntity<JpaPid>) entity, null, false);

                if (!theDeletedOk) {
                        if (isDeleted(entity)) {
                                throw createResourceGoneException(entity);
                        }
                }
                // If the resolved fhir model is null, we don't need to run pre-access over or pre-show over it.
                if (retVal != null) {
                        invokeStoragePreAccessResources(theId, theRequest, retVal);
                        retVal = invokeStoragePreShowResources(theRequest, retVal);
                }

                ourLog.debug("Processed read on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
                return retVal;
        }

        @Nullable
        private T invokeStoragePreShowResources(RequestDetails theRequest, T retVal) {
                retVal = invokeStoragePreShowResources(myInterceptorBroadcaster, theRequest, retVal);
                return retVal;
        }

        private void invokeStoragePreAccessResources(IIdType theId, RequestDetails theRequest, T theResource) {
                invokeStoragePreAccessResources(myInterceptorBroadcaster, theRequest, theId, theResource);
        }

        private Optional<T> invokeStoragePreAccessResources(RequestDetails theRequest, T theResource) {
                IInterceptorBroadcaster compositeBroadcaster =
                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest);
                if (compositeBroadcaster.hasHooks(Pointcut.STORAGE_PREACCESS_RESOURCES)) {
                        SimplePreResourceAccessDetails accessDetails = new SimplePreResourceAccessDetails(theResource);
                        HookParams params = new HookParams()
                                        .add(IPreResourceAccessDetails.class, accessDetails)
                                        .add(RequestDetails.class, theRequest)
                                        .addIfMatchesType(ServletRequestDetails.class, theRequest);
                        compositeBroadcaster.callHooks(Pointcut.STORAGE_PREACCESS_RESOURCES, params);
                        if (accessDetails.isDontReturnResourceAtIndex(0)) {
                                return Optional.empty();
                        }
                }
                return Optional.of(theResource);
        }

        @Override
        public BaseHasResource readEntity(IIdType theId, RequestDetails theRequest) {
                RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForRead(
                                theRequest, myResourceName, theId);
                return myTransactionService
                                .withRequest(theRequest)
                                .withRequestPartitionId(requestPartitionId)
                                .execute(() -> readEntity(theId, true, theRequest, requestPartitionId));
        }

        @Override
        public ReindexOutcome reindex(
                        IResourcePersistentId thePid,
                        ReindexParameters theReindexParameters,
                        RequestDetails theRequest,
                        TransactionDetails theTransactionDetails) {
                ReindexOutcome retVal = new ReindexOutcome();

                JpaPid jpaPid = (JpaPid) thePid;

                // Careful!  Reindex only reads ResourceTable, but we tell Hibernate to check version
                // to ensure Hibernate will catch concurrent updates (PUT/DELETE) elsewhere.
                // Otherwise, we may index stale data.  See #4584
                // We use the main entity as the lock object since all the index rows hang off it.
                ResourceTable entity;
                if (theReindexParameters.isOptimisticLock()) {
                        entity = myEntityManager.find(ResourceTable.class, jpaPid, LockModeType.OPTIMISTIC);
                } else {
                        entity = myEntityManager.find(ResourceTable.class, jpaPid);
                }

                if (entity == null) {
                        retVal.addWarning("Unable to find entity with PID: " + jpaPid.getId());
                        return retVal;
                }

                if (theReindexParameters.getReindexSearchParameters() == ReindexParameters.ReindexSearchParametersEnum.ALL) {
                        reindexSearchParameters(entity, retVal, theTransactionDetails);
                }
                if (theReindexParameters.getOptimizeStorage() != ReindexParameters.OptimizeStorageModeEnum.NONE) {
                        reindexOptimizeStorage(entity, theReindexParameters.getOptimizeStorage());
                }

                return retVal;
        }

        @SuppressWarnings("unchecked")
        private void reindexSearchParameters(
                        ResourceTable entity, ReindexOutcome theReindexOutcome, TransactionDetails theTransactionDetails) {
                try {
                        T resource = (T) myJpaStorageResourceParser.toResource(entity, false);
                        reindexSearchParameters(resource, entity, theTransactionDetails);
                } catch (Exception e) {
                        ourLog.warn("Failure during reindex: {}", e.toString());
                        theReindexOutcome.addWarning("Failed to reindex resource " + entity.getIdDt() + ": " + e);
                        myResourceTableDao.updateIndexStatus(entity.getId(), EntityIndexStatusEnum.INDEXING_FAILED);
                }
        }

        /**
         * @deprecated Use {@link #reindex(IResourcePersistentId, ReindexParameters, RequestDetails, TransactionDetails)}
         */
        @Deprecated
        @Override
        public void reindex(T theResource, IBasePersistedResource theEntity) {
                assert TransactionSynchronizationManager.isActualTransactionActive();
                ResourceTable entity = (ResourceTable) theEntity;
                TransactionDetails transactionDetails = new TransactionDetails(entity.getUpdatedDate());

                reindexSearchParameters(theResource, theEntity, transactionDetails);
        }

        private void reindexSearchParameters(
                        T theResource, IBasePersistedResource theEntity, TransactionDetails transactionDetails) {
                ourLog.debug("Indexing resource {} - PID {}", theEntity.getIdDt().getValue(), theEntity.getPersistentId());
                if (theResource != null) {
                        CURRENTLY_REINDEXING.put(theResource, Boolean.TRUE);
                }

                SystemRequestDetails request = new SystemRequestDetails();
                request.getUserData().put(JpaConstants.SKIP_REINDEX_ON_UPDATE, Boolean.TRUE);

                updateEntity(
                                request, theResource, theEntity, theEntity.getDeleted(), true, false, transactionDetails, true, false);
                if (theResource != null) {
                        CURRENTLY_REINDEXING.put(theResource, null);
                }
        }

        private void reindexOptimizeStorage(
                        ResourceTable entity, ReindexParameters.OptimizeStorageModeEnum theOptimizeStorageMode) {
                ResourceHistoryTable historyEntity = entity.getCurrentVersionEntity();
                if (historyEntity != null) {
                        reindexOptimizeStorageHistoryEntity(entity, historyEntity);
                        if (theOptimizeStorageMode == ReindexParameters.OptimizeStorageModeEnum.ALL_VERSIONS) {
                                int pageSize = 100;
                                for (int page = 0; ((long) page * pageSize) < entity.getVersion(); page++) {

                                        // We need to sort the pages, because we are updating the same data we are paging through.
                                        // If not sorted explicitly, a database like Postgres returns the same data multiple times on
                                        // different pages as the underlying data gets updated.
                                        PageRequest pageRequest = PageRequest.of(page, pageSize, Sort.by("myId"));
                                        Slice<ResourceHistoryTable> historyEntities =
                                                        myResourceHistoryTableDao.findAllVersionsExceptSpecificForResourcePid(
                                                                        pageRequest, entity.getId().toFk(), historyEntity.getVersion());

                                        for (ResourceHistoryTable next : historyEntities) {
                                                reindexOptimizeStorageHistoryEntity(entity, next);
                                        }
                                }
                        }
                }
        }

        /**
         * Note that the entity will be detached after being saved if it has changed
         * in order to avoid growing the number of resources in memory to be too big
         */
        private void reindexOptimizeStorageHistoryEntity(ResourceTable entity, ResourceHistoryTable historyEntity) {
                if (historyEntity.getEncoding() == ResourceEncodingEnum.JSONC
                                || historyEntity.getEncoding() == ResourceEncodingEnum.JSON) {
                        byte[] resourceBytes = historyEntity.getResource();
                        if (resourceBytes != null) {
                                String resourceText = decodeResource(resourceBytes, historyEntity.getEncoding());
                                myResourceHistoryCalculator.conditionallyAlterHistoryEntity(entity, historyEntity, resourceText);
                        }
                }
                if (myStorageSettings.isAccessMetaSourceInformationFromProvenanceTable()) {
                        if (isBlank(historyEntity.getSourceUri()) && isBlank(historyEntity.getRequestId())) {
                                IdAndPartitionId id = historyEntity.getId().asIdAndPartitionId();
                                Optional<ResourceHistoryProvenanceEntity> provenanceEntityOpt =
                                                myResourceHistoryProvenanceDao.findById(id);
                                if (provenanceEntityOpt.isPresent()) {
                                        ResourceHistoryProvenanceEntity provenanceEntity = provenanceEntityOpt.get();
                                        historyEntity.setSourceUri(provenanceEntity.getSourceUri());
                                        historyEntity.setRequestId(provenanceEntity.getRequestId());
                                        myResourceHistoryProvenanceDao.delete(provenanceEntity);
                                }
                        }
                }
        }

        private BaseHasResource<?> readEntity(
                        IIdType theId,
                        boolean theCheckForForcedId,
                        RequestDetails theRequest,
                        RequestPartitionId requestPartitionId) {
                validateResourceTypeAndThrowInvalidRequestException(theId);

                BaseHasResource entity;
                JpaPid pid = myIdHelperService
                                .resolveResourceIdentity(
                                                requestPartitionId,
                                                getResourceName(),
                                                theId.getIdPart(),
                                                ResolveIdentityMode.includeDeleted().cacheOk())
                                .getPersistentId();
                Set<Integer> readPartitions = null;
                if (requestPartitionId.isAllPartitions()) {
                        entity = myEntityManager.find(ResourceTable.class, pid);
                } else {
                        readPartitions = myRequestPartitionHelperService.toReadPartitions(requestPartitionId);
                        if (readPartitions.size() == 1) {
                                if (readPartitions.contains(null)) {
                                        entity = myResourceTableDao
                                                        .readByPartitionIdNull(pid.getId())
                                                        .orElse(null);
                                } else {
                                        entity = myResourceTableDao
                                                        .readByPartitionId(readPartitions.iterator().next(), pid.getId())
                                                        .orElse(null);
                                }
                        } else {
                                if (readPartitions.contains(null)) {
                                        List<Integer> readPartitionsWithoutNull =
                                                        readPartitions.stream().filter(Objects::nonNull).collect(Collectors.toList());
                                        entity = myResourceTableDao
                                                        .readByPartitionIdsOrNull(readPartitionsWithoutNull, pid.getId())
                                                        .orElse(null);
                                } else {
                                        entity = myResourceTableDao
                                                        .readByPartitionIds(readPartitions, pid.getId())
                                                        .orElse(null);
                                }
                        }
                }

                // Verify that the resource is for the correct partition
                if (entity != null && readPartitions != null && entity.getPartitionId() != null) {
                        if (!readPartitions.contains(entity.getPartitionId().getPartitionId())) {
                                ourLog.debug(
                                                "Performing a read for PartitionId={} but entity has partition: {}",
                                                requestPartitionId,
                                                entity.getPartitionId());
                                entity = null;
                        }
                }

                if (theId.hasVersionIdPart()) {
                        if (!theId.isVersionIdPartValidLong()) {
                                throw new ResourceNotFoundException(Msg.code(978)
                                                + getContext()
                                                                .getLocalizer()
                                                                .getMessageSanitized(
                                                                                BaseStorageDao.class,
                                                                                "invalidVersion",
                                                                                theId.getVersionIdPart(),
                                                                                theId.toUnqualifiedVersionless()));
                        }
                        if (entity.getVersion() != theId.getVersionIdPartAsLong()) {
                                entity = null;
                        }
                }

                if (entity == null) {
                        if (theId.hasVersionIdPart()) {
                                TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(
                                                "SELECT t from ResourceHistoryTable t WHERE t.myResourceId = :RID AND t.myResourceType = :RTYP AND t.myResourceVersion = :RVER",
                                                ResourceHistoryTable.class);
                                q.setParameter("RID", pid.getId());
                                q.setParameter("RTYP", myResourceName);
                                q.setParameter("RVER", theId.getVersionIdPartAsLong());
                                try {
                                        entity = q.getSingleResult();
                                } catch (NoResultException e) {
                                        throw new ResourceNotFoundException(Msg.code(979)
                                                        + getContext()
                                                                        .getLocalizer()
                                                                        .getMessageSanitized(
                                                                                        BaseStorageDao.class,
                                                                                        "invalidVersion",
                                                                                        theId.getVersionIdPart(),
                                                                                        theId.toUnqualifiedVersionless()));
                                }
                        }
                }

                if (entity == null) {
                        throw new ResourceNotFoundException(Msg.code(1996) + "Resource " + theId + " is not known");
                }

                validateResourceType(entity);

                if (theCheckForForcedId) {
                        validateGivenIdIsAppropriateToRetrieveResource(theId, entity);
                }
                return entity;
        }

        @Override
        protected IBasePersistedResource readEntityLatestVersion(
                        IResourcePersistentId thePersistentId,
                        RequestDetails theRequestDetails,
                        TransactionDetails theTransactionDetails) {
                JpaPid jpaPid = (JpaPid) thePersistentId;
                return myEntityManager.find(ResourceTable.class, jpaPid);
        }

        @Override
        @Nonnull
        protected ResourceTable readEntityLatestVersion(
                        IIdType theId, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
                RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForRead(
                                theRequestDetails, getResourceName(), theId);

                return myTransactionService
                                .withRequest(theRequestDetails)
                                .withRequestPartitionId(requestPartitionId)
                                .execute(() ->
                                                readEntityLatestVersion(theRequestDetails, theId, requestPartitionId, theTransactionDetails));
        }

        @Nonnull
        private ResourceTable readEntityLatestVersion(
                        RequestDetails theRequestDetails,
                        IIdType theId,
                        @Nonnull RequestPartitionId theRequestPartitionId,
                        TransactionDetails theTransactionDetails) {
                HapiTransactionService.requireTransaction();

                IIdType id = theId;
                validateResourceTypeAndThrowInvalidRequestException(id);
                if (!id.hasResourceType()) {
                        id = id.withResourceType(getResourceName());
                }

                JpaPid persistentId = null;
                if (theTransactionDetails != null) {
                        if (theTransactionDetails.isResolvedResourceIdEmpty(id.toUnqualifiedVersionless())) {
                                throw new ResourceNotFoundException(Msg.code(1997) + id);
                        }
                        if (theTransactionDetails.hasResolvedResourceIds()) {
                                persistentId = (JpaPid) theTransactionDetails.getResolvedResourceId(id);
                        }
                }

                if (persistentId == null) {
                        persistentId = myIdHelperService.resolveResourceIdentityPid(
                                        theRequestPartitionId,
                                        id.getResourceType(),
                                        id.getIdPart(),
                                        ResolveIdentityMode.includeDeleted().cacheOk());
                }

                ResourceTable entity = myEntityManager.find(ResourceTable.class, persistentId);
                if (entity == null) {
                        throw new ResourceNotFoundException(Msg.code(1998) + id);
                }
                validateGivenIdIsAppropriateToRetrieveResource(id, entity);
                return entity;
        }

        @Transactional
        @Override
        public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm) {
                removeTag(theId, theTagType, theScheme, theTerm, null);
        }

        @Transactional
        @Override
        public void removeTag(
                        IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, RequestDetails theRequest) {
                StopWatch w = new StopWatch();
                BaseHasResource<?> entity = readEntity(theId, theRequest);
                if (entity == null) {
                        throw new ResourceNotFoundException(Msg.code(1999) + theId);
                }

                for (BaseTag next : new ArrayList<>(entity.getTags())) {
                        if (Objects.equals(next.getTag().getTagType(), theTagType)
                                        && Objects.equals(next.getTag().getSystem(), theScheme)
                                        && Objects.equals(next.getTag().getCode(), theTerm)) {
                                myEntityManager.remove(next);
                                entity.getTags().remove(next);
                        }
                }

                if (entity.getTags().isEmpty()) {
                        entity.setHasTags(false);
                }

                myEntityManager.merge(entity);

                ourLog.debug(
                                "Processed remove tag {}/{} on {} in {}ms",
                                theScheme,
                                theTerm,
                                theId.getValue(),
                                w.getMillisAndRestart());
        }

        /**
         * @deprecated Use {@link #search(SearchParameterMap, RequestDetails)} instead
         */
        @Transactional(propagation = Propagation.SUPPORTS)
        @Override
        public IBundleProvider search(final SearchParameterMap theParams) {
                return search(theParams, null);
        }

        @Transactional(propagation = Propagation.SUPPORTS)
        @Override
        public IBundleProvider search(final SearchParameterMap theParams, RequestDetails theRequest) {
                return search(theParams, theRequest, null);
        }

        @Transactional(propagation = Propagation.SUPPORTS)
        @Override
        public IBundleProvider search(
                        final SearchParameterMap theParams, RequestDetails theRequest, HttpServletResponse theServletResponse) {

                if (theParams.getSearchContainedMode() == SearchContainedModeEnum.BOTH) {
                        throw new MethodNotAllowedException(Msg.code(983) + "Contained mode 'both' is not currently supported");
                }
                if (theParams.getSearchContainedMode() != SearchContainedModeEnum.FALSE
                                && !myStorageSettings.isIndexOnContainedResources()) {
                        throw new MethodNotAllowedException(
                                        Msg.code(984) + "Searching with _contained mode enabled is not enabled on this server");
                }

                translateListSearchParams(theParams);

                setOffsetAndCount(theParams, theRequest);

                CacheControlDirective cacheControlDirective = new CacheControlDirective();
                if (theRequest != null) {
                        cacheControlDirective.parse(theRequest.getHeaders(Constants.HEADER_CACHE_CONTROL));
                }

                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(
                                                theRequest, getResourceName(), theParams);
                IBundleProvider retVal = mySearchCoordinatorSvc.registerSearch(
                                this, theParams, getResourceName(), cacheControlDirective, theRequest, requestPartitionId);

                if (retVal instanceof PersistedJpaBundleProvider) {
                        PersistedJpaBundleProvider provider = (PersistedJpaBundleProvider) retVal;
                        provider.setRequestPartitionId(requestPartitionId);
                        if (provider.getCacheStatus() == SearchCacheStatusEnum.HIT) {
                                if (theServletResponse != null && theRequest != null) {
                                        String value = "HIT from " + theRequest.getFhirServerBase();
                                        theServletResponse.addHeader(Constants.HEADER_X_CACHE, value);
                                }
                        }
                }

                return retVal;
        }

        private void translateListSearchParams(SearchParameterMap theParams) {

                Set<Map.Entry<String, List<List<IQueryParameterType>>>> entryHashSet = new HashSet<>(theParams.entrySet());

                // Translate _list=42 to _has=List:item:_id=42
                for (Map.Entry<String, List<List<IQueryParameterType>>> stringListEntry : entryHashSet) {
                        String key = stringListEntry.getKey();
                        if (Constants.PARAM_LIST.equals((key))) {
                                List<List<IQueryParameterType>> andOrValues = theParams.get(key);
                                theParams.remove(key);
                                List<List<IQueryParameterType>> hasParamValues = new ArrayList<>();
                                for (List<IQueryParameterType> orValues : andOrValues) {
                                        List<IQueryParameterType> orList = new ArrayList<>();
                                        for (IQueryParameterType value : orValues) {
                                                orList.add(new HasParam(
                                                                "List",
                                                                ListResource.SP_ITEM,
                                                                BaseResource.SP_RES_ID,
                                                                value.getValueAsQueryToken(null)));
                                        }
                                        hasParamValues.add(orList);
                                }
                                theParams.put(Constants.PARAM_HAS, hasParamValues);
                        }
                }
        }

        protected void setOffsetAndCount(SearchParameterMap theParams, RequestDetails theRequest) {
                if (theRequest != null) {

                        if (theRequest.isSubRequest()) {
                                Integer max = getStorageSettings().getMaximumSearchResultCountInTransaction();
                                if (max != null) {
                                        Validate.inclusiveBetween(
                                                        1,
                                                        Integer.MAX_VALUE,
                                                        max,
                                                        "Maximum search result count in transaction must be a positive integer");
                                        theParams.setLoadSynchronousUpTo(getStorageSettings().getMaximumSearchResultCountInTransaction());
                                }
                        }

                        final Integer offset = RestfulServerUtils.extractOffsetParameter(theRequest);
                        if (offset != null || !isPagingProviderDatabaseBacked(theRequest)) {
                                theParams.setLoadSynchronous(true);
                                if (offset != null) {
                                        Validate.inclusiveBetween(0, Integer.MAX_VALUE, offset, "Offset must be a positive integer");
                                }
                                theParams.setOffset(offset);
                        }

                        Integer count = RestfulServerUtils.extractCountParameter(theRequest);
                        if (count != null) {
                                Integer maxPageSize = theRequest.getServer().getMaximumPageSize();
                                if (maxPageSize != null && count > maxPageSize) {
                                        ourLog.info(
                                                        "Reducing {} from {} to {} which is the maximum allowable page size.",
                                                        Constants.PARAM_COUNT,
                                                        count,
                                                        maxPageSize);
                                        count = maxPageSize;
                                }
                                theParams.setCount(count);
                        } else if (theRequest.getServer().getDefaultPageSize() != null) {
                                theParams.setCount(theRequest.getServer().getDefaultPageSize());
                        }
                }
        }

        @Override
        public List<JpaPid> searchForIds(
                        SearchParameterMap theParams,
                        RequestDetails theRequest,
                        @Nullable IBaseResource theConditionalOperationTargetOrNull) {
                TransactionDetails transactionDetails = new TransactionDetails();
                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(
                                                theRequest, myResourceName, theParams, theConditionalOperationTargetOrNull);

                return myTransactionService
                                .withRequest(theRequest)
                                .withTransactionDetails(transactionDetails)
                                .withRequestPartitionId(requestPartitionId)
                                .searchList(() -> {
                                        if (isNull(theParams.getLoadSynchronousUpTo())) {
                                                theParams.setLoadSynchronousUpTo(myStorageSettings.getInternalSynchronousSearchSize());
                                        }

                                        ISearchBuilder<JpaPid> builder =
                                                        mySearchBuilderFactory.newSearchBuilder(getResourceName(), getResourceType());

                                        List<JpaPid> ids = new ArrayList<>();

                                        String uuid = UUID.randomUUID().toString();

                                        SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequest, uuid);
                                        try (IResultIterator<JpaPid> iter =
                                                        builder.createQuery(theParams, searchRuntimeDetails, theRequest, requestPartitionId)) {
                                                while (iter.hasNext()) {
                                                        ids.add(iter.next());
                                                }
                                        } catch (IOException e) {
                                                ourLog.error("IO failure during database access", e);
                                        }

                                        return ids;
                                });
        }

        @Override
        public <PID extends IResourcePersistentId<?>> Stream<PID> searchForIdStream(
                        SearchParameterMap theParams,
                        RequestDetails theRequest,
                        @Nullable IBaseResource theConditionalOperationTargetOrNull) {

                // the Stream is useless outside the bound connection time, so require our caller to have a session.
                HapiTransactionService.requireTransaction();

                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(
                                                theRequest, myResourceName, theParams, theConditionalOperationTargetOrNull);

                ISearchBuilder<JpaPid> builder = mySearchBuilderFactory.newSearchBuilder(getResourceName(), getResourceType());

                String uuid = UUID.randomUUID().toString();

                SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequest, uuid);
                //noinspection unchecked
                return (Stream<PID>) myTransactionService
                                .withRequest(theRequest)
                                .search(() ->
                                                builder.createQueryStream(theParams, searchRuntimeDetails, theRequest, requestPartitionId));
        }

        @Override
        public List<T> searchForResources(SearchParameterMap theParams, RequestDetails theRequest) {
                return searchForTransformedIds(theParams, theRequest, this::pidsToResource);
        }

        @Override
        public List<IIdType> searchForResourceIds(SearchParameterMap theParams, RequestDetails theRequest) {
                return searchForTransformedIds(theParams, theRequest, this::pidsToIds);
        }

        private <V> List<V> searchForTransformedIds(
                        SearchParameterMap theParams,
                        RequestDetails theRequest,
                        TriFunction<RequestDetails, Stream<JpaPid>, RequestPartitionId, Stream<V>> transform) {
                RequestPartitionId requestPartitionId =
                                myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(
                                                theRequest, myResourceName, theParams);

                String uuid = UUID.randomUUID().toString();

                SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequest, uuid);
                return myTransactionService
                                .withRequest(theRequest)
                                .withPropagation(Propagation.REQUIRED)
                                .searchList(() -> {
                                        ISearchBuilder<JpaPid> builder =
                                                        mySearchBuilderFactory.newSearchBuilder(getResourceName(), getResourceType());
                                        Stream<JpaPid> pidStream =
                                                        builder.createQueryStream(theParams, searchRuntimeDetails, theRequest, requestPartitionId);

                                        Stream<V> transformedStream = transform.apply(theRequest, pidStream, requestPartitionId);

                                        return transformedStream.collect(Collectors.toList());
                                });
        }

        /**
         * Fetch the resources in chunks and apply PreAccess/PreShow interceptors.
         */
        @Nonnull
        private Stream<T> pidsToResource(
                        RequestDetails theRequest, Stream<JpaPid> thePidStream, RequestPartitionId theRequestPartitionId) {
                ISearchBuilder<JpaPid> searchBuilder =
                                mySearchBuilderFactory.newSearchBuilder(getResourceName(), getResourceType());
                @SuppressWarnings("unchecked")
                Stream<T> resourceStream = (Stream<T>) new QueryChunker<>()
                                .chunk(thePidStream, SearchBuilder.getMaximumPageSize())
                                .flatMap(pidChunk -> searchBuilder.loadResourcesByPid(pidChunk, theRequest).stream());
                // apply interceptors
                return resourceStream
                                .flatMap(resource -> resource == null
                                                ? Stream.empty()
                                                : invokeStoragePreAccessResources(theRequest, resource).stream())
                                .flatMap(resource -> Optional.ofNullable(invokeStoragePreShowResources(theRequest, resource)).stream());
        }

        /**
         * get the Ids from the ResourceTable entities in chunks.
         */
        @Nonnull
        private Stream<IIdType> pidsToIds(
                        RequestDetails theRequestDetails, Stream<JpaPid> thePidStream, RequestPartitionId theRequestPartitionId) {

                Stream<JpaPid> pidStream = thePidStream;

                if (!theRequestPartitionId.isAllPartitions()
                                && theRequestPartitionId.getPartitionIds().size() == 1) {
                        pidStream = pidStream.map(t -> t.setPartitionIdIfNotAlreadySet(
                                        theRequestPartitionId.getPartitionIds().get(0)));
                }

                return new QueryChunker<>()
                                .chunk(pidStream, SearchBuilder.getMaximumPageSize())
                                .flatMap(ids -> myResourceTableDao.findAllById(ids).stream())
                                .map(ResourceTable::getIdDt);
        }

        protected <MT extends IBaseMetaType> MT toMetaDt(Class<MT> theType, Collection<TagDefinition> tagDefinitions) {
                MT retVal = ReflectionUtil.newInstance(theType);
                for (TagDefinition next : tagDefinitions) {
                        switch (next.getTagType()) {
                                case PROFILE:
                                        retVal.addProfile(next.getCode());
                                        break;
                                case SECURITY_LABEL:
                                        retVal.addSecurity()
                                                        .setSystem(next.getSystem())
                                                        .setCode(next.getCode())
                                                        .setDisplay(next.getDisplay());
                                        break;
                                case TAG:
                                        retVal.addTag()
                                                        .setSystem(next.getSystem())
                                                        .setCode(next.getCode())
                                                        .setDisplay(next.getDisplay());
                                        break;
                        }
                }
                myMetaTagSorter.sort(retVal);
                return retVal;
        }

        private ArrayList<TagDefinition> toTagList(IBaseMetaType theMeta) {
                ArrayList<TagDefinition> retVal = new ArrayList<>();

                for (IBaseCoding next : theMeta.getTag()) {
                        retVal.add(new TagDefinition(TagTypeEnum.TAG, next.getSystem(), next.getCode(), next.getDisplay()));
                }
                for (IBaseCoding next : theMeta.getSecurity()) {
                        retVal.add(
                                        new TagDefinition(TagTypeEnum.SECURITY_LABEL, next.getSystem(), next.getCode(), next.getDisplay()));
                }
                for (IPrimitiveType<String> next : theMeta.getProfile()) {
                        retVal.add(new TagDefinition(TagTypeEnum.PROFILE, BaseHapiFhirDao.NS_JPA_PROFILE, next.getValue(), null));
                }

                return retVal;
        }

        /**
         * @deprecated Use {@link #update(T, RequestDetails)} instead
         */
        @Override
        public DaoMethodOutcome update(T theResource) {
                return update(theResource, null, null);
        }

        @Override
        public DaoMethodOutcome update(T theResource, RequestDetails theRequestDetails) {
                return update(theResource, null, theRequestDetails);
        }

        /**
         * @deprecated Use {@link #update(T, String, RequestDetails)} instead
         */
        @Override
        public DaoMethodOutcome update(T theResource, String theMatchUrl) {
                return update(theResource, theMatchUrl, null);
        }

        @Override
        public DaoMethodOutcome update(T theResource, String theMatchUrl, RequestDetails theRequestDetails) {
                return update(theResource, theMatchUrl, true, theRequestDetails);
        }

        @Override
        public DaoMethodOutcome update(
                        T theResource, String theMatchUrl, boolean thePerformIndexing, RequestDetails theRequestDetails) {
                return update(theResource, theMatchUrl, thePerformIndexing, false, theRequestDetails, new TransactionDetails());
        }

        @Override
        public DaoMethodOutcome update(
                        T theResource,
                        String theMatchUrl,
                        boolean thePerformIndexing,
                        boolean theForceUpdateVersion,
                        RequestDetails theRequest,
                        @Nonnull TransactionDetails theTransactionDetails) {
                if (theResource == null) {
                        String msg = getContext().getLocalizer().getMessage(BaseStorageDao.class, "missingBody");
                        throw new InvalidRequestException(Msg.code(986) + msg);
                }
                if (!theResource.getIdElement().hasIdPart() && isBlank(theMatchUrl)) {
                        String type = myFhirContext.getResourceType(theResource);
                        String msg = myFhirContext.getLocalizer().getMessage(BaseStorageDao.class, "updateWithNoId", type);
                        throw new InvalidRequestException(Msg.code(987) + msg);
                }

                /*
                 * Resource updates will modify/update the version of the resource with the new version. This is generally helpful,
                 * but leads to issues if the transaction is rolled back and retried. So if we do a rollback, we reset the resource
                 * version to what it was.
                 */
                String id = theResource.getIdElement().getValue();
                Runnable onRollback = () -> theResource.getIdElement().setValue(id);

                RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineCreatePartitionForRequest(
                                theRequest, theResource, getResourceName());

                Callable<DaoMethodOutcome> updateCallback;
                if (myStorageSettings.isUpdateWithHistoryRewriteEnabled()
                                && theRequest != null
                                && theRequest.isRewriteHistory()) {
                        updateCallback = () ->
                                        doUpdateWithHistoryRewrite(theResource, theRequest, theTransactionDetails, requestPartitionId);
                } else {
                        updateCallback = () -> doUpdate(
                                        theResource,
                                        theMatchUrl,
                                        thePerformIndexing,
                                        theForceUpdateVersion,
                                        theRequest,
                                        theTransactionDetails,
                                        requestPartitionId);
                }

                // Execute the update in a retryable transaction
                return myTransactionService
                                .withRequest(theRequest)
                                .withTransactionDetails(theTransactionDetails)
                                .withRequestPartitionId(requestPartitionId)
                                .onRollback(onRollback)
                                .execute(updateCallback);
        }

        private DaoMethodOutcome doUpdate(
                        T theResource,
                        String theMatchUrl,
                        boolean thePerformIndexing,
                        boolean theForceUpdateVersion,
                        RequestDetails theRequest,
                        TransactionDetails theTransactionDetails,
                        RequestPartitionId theRequestPartitionId) {
                DaoMethodOutcome outcome = null;
                preProcessResourceForStorage(theResource);
                preProcessResourceForStorage(theResource, theRequest, theTransactionDetails, thePerformIndexing);

                ResourceTable entity = null;

                IIdType resourceId = null;
                RestOperationTypeEnum update = RestOperationTypeEnum.UPDATE;
                if (isNotBlank(theMatchUrl)) {
                        // Validate that the supplied resource matches the conditional.
                        Set<JpaPid> match = myMatchResourceUrlService.processMatchUrl(
                                        theMatchUrl, myResourceType, theTransactionDetails, theRequest, theResource);
                        if (match.size() > 1) {
                                String msg = getContext()
                                                .getLocalizer()
                                                .getMessageSanitized(
                                                                BaseStorageDao.class,
                                                                "transactionOperationWithMultipleMatchFailure",
                                                                "UPDATE",
                                                                myResourceName,
                                                                theMatchUrl,
                                                                match.size());
                                throw new PreconditionFailedException(Msg.code(988) + msg);
                        } else if (match.size() == 1) {
                                JpaPid pid = match.iterator().next();
                                entity = myEntityManager.find(ResourceTable.class, pid);
                                resourceId = entity.getIdDt();
                                if (myFhirContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)
                                                && theResource.getIdElement().getIdPart() != null) {
                                        if (!Objects.equals(theResource.getIdElement().getIdPart(), resourceId.getIdPart())) {
                                                String msg = getContext()
                                                                .getLocalizer()
                                                                .getMessageSanitized(
                                                                                BaseStorageDao.class,
                                                                                "transactionOperationWithIdNotMatchFailure",
                                                                                "UPDATE",
                                                                                theMatchUrl);
                                                throw new InvalidRequestException(Msg.code(2279) + msg);
                                        }
                                }
                        } else {
                                // assign UUID if no id provided in the request (numeric id mode is handled in doCreateForPostOrPut)
                                if (!theResource.getIdElement().hasIdPart()
                                                && getStorageSettings().getResourceServerIdStrategy()
                                                                == JpaStorageSettings.IdStrategyEnum.UUID) {
                                        theResource.setId(UUID.randomUUID().toString());
                                        theResource.setUserData(JpaConstants.RESOURCE_ID_SERVER_ASSIGNED, Boolean.TRUE);
                                }
                                outcome = doCreateForPostOrPut(
                                                theRequest,
                                                theResource,
                                                theMatchUrl,
                                                false,
                                                thePerformIndexing,
                                                theRequestPartitionId,
                                                update,
                                                theTransactionDetails);

                                // Pre-cache the match URL
                                if (outcome.getPersistentId() != null) {
                                        myMatchResourceUrlService.matchUrlResolved(
                                                        theTransactionDetails, getResourceName(), theMatchUrl, (JpaPid) outcome.getPersistentId());
                                }
                        }
                } else {
                        /*
                         * Note: resourceId will not be null or empty here, because we
                         * check it and reject requests in
                         * BaseOutcomeReturningMethodBindingWithResourceParam
                         */
                        resourceId = theResource.getIdElement();
                        assert resourceId != null;
                        assert resourceId.hasIdPart();

                        if (!resourceId.hasResourceType()) {
                                resourceId = resourceId.withResourceType(getResourceName());
                        }

                        boolean create = false;

                        if (theRequest != null) {
                                String existenceCheck = theRequest.getHeader(JpaConstants.HEADER_UPSERT_EXISTENCE_CHECK);
                                if (JpaConstants.HEADER_UPSERT_EXISTENCE_CHECK_DISABLED.equals(existenceCheck)) {
                                        create = true;
                                }
                        }

                        if (!create) {
                                if (theTransactionDetails != null && theTransactionDetails.hasNullResolvedResourceId(resourceId)) {
                                        create = true;
                                } else {
                                        try {
                                                entity = readEntityLatestVersion(
                                                                theRequest, resourceId, theRequestPartitionId, theTransactionDetails);
                                        } catch (ResourceNotFoundException e) {
                                                create = true;
                                        }
                                }
                        }

                        if (create) {
                                outcome = doCreateForPostOrPut(
                                                theRequest,
                                                theResource,
                                                null,
                                                false,
                                                thePerformIndexing,
                                                theRequestPartitionId,
                                                update,
                                                theTransactionDetails);
                        }
                }

                // Start
                if (outcome == null) {
                        UpdateParameters updateParameters = new UpdateParameters<>()
                                        .setRequestDetails(theRequest)
                                        .setResourceIdToUpdate(resourceId)
                                        .setMatchUrl(theMatchUrl)
                                        .setShouldPerformIndexing(thePerformIndexing)
                                        .setShouldForceUpdateVersion(theForceUpdateVersion)
                                        .setResource(theResource)
                                        .setEntity(entity)
                                        .setOperationType(update)
                                        .setTransactionDetails(theTransactionDetails)
                                        .setShouldForcePopulateOldResourceForProcessing(false);

                        outcome = doUpdateForUpdateOrPatch(updateParameters);
                }

                postUpdateTransaction(theTransactionDetails);

                return outcome;
        }

        @SuppressWarnings("rawtypes")
        protected void postUpdateTransaction(TransactionDetails theTransactionDetails) {
                // Transactions will delete these at the end of the entire transaction
                if (!theTransactionDetails.isFhirTransaction()) {
                        Set<IResourcePersistentId> resourceIds = theTransactionDetails.getUpdatedResourceIds();
                        if (resourceIds != null && !resourceIds.isEmpty()) {
                                @Nonnull
                                List<JpaPid> ids = resourceIds.stream().map(r -> (JpaPid) r).collect(Collectors.toList());
                                myResourceSearchUrlSvc.deleteByResIds(ids);
                        }
                }
        }

        @Override
        protected DaoMethodOutcome doUpdateForUpdateOrPatch(UpdateParameters<T> theUpdateParameters) {

                /*
                 * We stored a resource searchUrl at creation time to prevent resource duplication.
                 * We'll clear any currently existing urls from the db, otherwise we could hit
                 * duplicate index violations if we try to add another (after this create/update)
                 */
                ResourceTable entity = (ResourceTable) theUpdateParameters.getEntity();

                /*
                 * If we read back the entity from hibernate, and it's already saying
                 * it's been updated in this transaction, then someone is probably
                 * doing multiple modifications of the same resource within the same
                 * database transaction. The only way for this to work cleanly is for
                 * us to flush hibernate now. That way we can increment the version
                 * a second time, create multiple history entries, etc.
                 */
                if (entity != null && entity.isVersionUpdatedInCurrentTransaction()) {
                        myEntityManager.flush();
                }

                if (entity.isSearchUrlPresent()) {
                        JpaPid persistentId = entity.getResourceId();
                        theUpdateParameters.getTransactionDetails().addUpdatedResourceId(persistentId);

                        entity.setSearchUrlPresent(false); // it will be removed at the end
                }

                if (entity.isDeleted()) {
                        // We're un-deleting this entity so let's inform the memory cache service
                        myIdHelperService.addResolvedPidToFhirIdAfterCommit(
                                        entity.getPersistentId(),
                                        entity.getPartitionId() == null
                                                        ? RequestPartitionId.defaultPartition()
                                                        : entity.getPartitionId().toPartitionId(),
                                        entity.getResourceType(),
                                        entity.getFhirId(),
                                        null);
                }

                boolean shouldForcePopulateOldResourceForProcessing = myInterceptorBroadcaster instanceof InterceptorService
                                && ((InterceptorService) myInterceptorBroadcaster)
                                                .hasRegisteredInterceptor(PatientCompartmentEnforcingInterceptor.class);
                theUpdateParameters.setShouldForcePopulateOldResourceForProcessing(shouldForcePopulateOldResourceForProcessing);
                return super.doUpdateForUpdateOrPatch(theUpdateParameters);
        }

        /**
         * Method for updating the historical version of the resource when a history version id is included in the request.
         *
         * @param theResource           to be saved
         * @param theRequest            details of the request
         * @param theTransactionDetails details of the transaction
         * @return the outcome of the operation
         */
        private DaoMethodOutcome doUpdateWithHistoryRewrite(
                        T theResource,
                        RequestDetails theRequest,
                        TransactionDetails theTransactionDetails,
                        RequestPartitionId theRequestPartitionId) {
                StopWatch w = new StopWatch();

                // No need for indexing as this will update a non-current version of the resource which will not be searchable
                preProcessResourceForStorage(theResource, theRequest, theTransactionDetails, false);

                BaseHasResource entity;
                BaseHasResource currentEntity;

                IIdType resourceId;

                resourceId = theResource.getIdElement();
                assert resourceId != null;
                assert resourceId.hasIdPart();

                try {
                        currentEntity = readEntityLatestVersion(
                                        theRequest, resourceId.toVersionless(), theRequestPartitionId, theTransactionDetails);

                        if (!resourceId.hasVersionIdPart()) {
                                throw new InvalidRequestException(
                                                Msg.code(2093) + "Invalid resource ID, ID must contain a history version");
                        }
                        entity = readEntity(resourceId, theRequest);
                        validateResourceType(entity);
                } catch (ResourceNotFoundException e) {
                        throw new ResourceNotFoundException(
                                        Msg.code(2087) + "Resource not found [" + resourceId + "] - Doesn't exist");
                }

                if (resourceId.hasResourceType() && !resourceId.getResourceType().equals(getResourceName())) {
                        throw new UnprocessableEntityException(
                                        Msg.code(2088) + "Invalid resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] of type["
                                                        + entity.getResourceType() + "] - Does not match expected [" + getResourceName() + "]");
                }
                assert resourceId.hasVersionIdPart();

                boolean wasDeleted = isDeleted(entity);
                entity.setDeleted(null);
                boolean isUpdatingCurrent = resourceId.hasVersionIdPart()
                                && Long.parseLong(resourceId.getVersionIdPart()) == currentEntity.getVersion();
                IBasePersistedResource<?> savedEntity = updateHistoryEntity(
                                theRequest, theResource, currentEntity, entity, resourceId, theTransactionDetails, isUpdatingCurrent);
                DaoMethodOutcome outcome = toMethodOutcome(
                                                theRequest, savedEntity, theResource, null, RestOperationTypeEnum.UPDATE)
                                .setCreated(wasDeleted);

                populateOperationOutcomeForUpdate(w, outcome, null, RestOperationTypeEnum.UPDATE, theTransactionDetails);

                return outcome;
        }

        @Override
        public MethodOutcome validate(
                        T theResource,
                        IIdType theId,
                        String theRawResource,
                        EncodingEnum theEncoding,
                        ValidationModeEnum theMode,
                        String theProfile,
                        RequestDetails theRequest) {
                TransactionDetails transactionDetails = new TransactionDetails();

                if (theMode == ValidationModeEnum.DELETE) {
                        if (theId == null || !theId.hasIdPart()) {
                                throw new InvalidRequestException(
                                                Msg.code(991) + "No ID supplied. ID is required when validating with mode=DELETE");
                        }

                        RequestPartitionId requestPartitionId =
                                        myRequestPartitionHelperService.determineReadPartitionForRequestForRead(
                                                        theRequest, getResourceName(), theId);

                        return myTransactionService
                                        .withRequest(theRequest)
                                        .withRequestPartitionId(requestPartitionId)
                                        .execute(() -> {
                                                final ResourceTable entity =
                                                                readEntityLatestVersion(theRequest, theId, requestPartitionId, transactionDetails);

                                                // Validate that there are no resources pointing to the candidate that
                                                // would prevent deletion
                                                DeleteConflictList deleteConflicts = new DeleteConflictList();
                                                if (getStorageSettings().isEnforceReferentialIntegrityOnDelete()) {
                                                        myDeleteConflictService.validateOkToDelete(
                                                                        deleteConflicts, entity, true, theRequest, new TransactionDetails());
                                                }
                                                DeleteConflictUtil.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);

                                                IBaseOperationOutcome oo = createInfoOperationOutcome("Ok to delete");
                                                return new MethodOutcome(new IdDt(theId.getValue()), oo);
                                        });
                }

                FhirValidator validator = getContext().newValidator();
                validator.setInterceptorBroadcaster(
                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest));
                validator.registerValidatorModule(getInstanceValidator());
                validator.registerValidatorModule(new IdChecker(theMode));

                IBaseResource resourceToValidateById = null;
                if (theId != null && theId.hasResourceType() && theId.hasIdPart()) {
                        Class<? extends IBaseResource> type =
                                        getContext().getResourceDefinition(theId.getResourceType()).getImplementingClass();
                        IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDaoOrNull(type);
                        resourceToValidateById = dao.read(theId, theRequest);
                }

                ValidationResult result;
                ValidationOptions options = new ValidationOptions().addProfileIfNotBlank(theProfile);

                if (theResource == null) {
                        if (resourceToValidateById != null) {
                                result = validator.validateWithResult(resourceToValidateById, options);
                        } else {
                                String msg = getContext().getLocalizer().getMessage(BaseStorageDao.class, "cantValidateWithNoResource");
                                throw new InvalidRequestException(Msg.code(992) + msg);
                        }
                } else if (isNotBlank(theRawResource)) {
                        result = validator.validateWithResult(theRawResource, options);
                } else {
                        result = validator.validateWithResult(theResource, options);
                }

                MethodOutcome retVal = new MethodOutcome();
                retVal.setOperationOutcome(result.toOperationOutcome());
                // Note an earlier version of this code returned PreconditionFailedException when the validation
                // failed, but we since realized the spec requires we return 200 regardless of the validation result.
                return retVal;
        }

        /**
         * Get the resource definition from the criteria which specifies the resource type
         */
        @Override
        public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(String criteria) {
                String resourceName;
                if (criteria == null || criteria.trim().isEmpty()) {
                        throw new IllegalArgumentException(Msg.code(994) + "Criteria cannot be empty");
                }
                if (criteria.contains("?")) {
                        resourceName = criteria.substring(0, criteria.indexOf("?"));
                } else {
                        resourceName = criteria;
                }

                return getContext().getResourceDefinition(resourceName);
        }

        private void validateGivenIdIsAppropriateToRetrieveResource(IIdType theId, BaseHasResource entity) {
                if (!entity.getIdDt().getIdPart().equals(theId.getIdPart())) {
                        // This means that the resource with the given numeric ID exists, but it has a "forced ID", meaning
                        // that
                        // as far as the outside world is concerned, the given ID doesn't exist (it's just an internal
                        // pointer
                        // to the
                        // forced ID)
                        throw new ResourceNotFoundException(Msg.code(2000) + theId);
                }
        }

        private void validateResourceType(IBasePersistedResource<?> entity) {
                validateResourceType(entity, myResourceName);
        }

        private void validateResourceTypeAndThrowInvalidRequestException(IIdType theId) {
                if (theId.hasResourceType() && !theId.getResourceType().equals(myResourceName)) {
                        // Note- Throw a HAPI FHIR exception here so that hibernate doesn't try to translate it into a database
                        // exception
                        throw new InvalidRequestException(Msg.code(996) + "Incorrect resource type (" + theId.getResourceType()
                                        + ") for this DAO, wanted: " + myResourceName);
                }
        }

        @VisibleForTesting
        public void setIdHelperSvcForUnitTest(IIdHelperService theIdHelperService) {
                myIdHelperService = theIdHelperService;
        }

        private static class IdChecker implements IValidatorModule {

                private final ValidationModeEnum myMode;

                IdChecker(ValidationModeEnum theMode) {
                        myMode = theMode;
                }

                @Override
                public void validateResource(IValidationContext<IBaseResource> theCtx) {
                        IBaseResource resource = theCtx.getResource();
                        if (resource instanceof Parameters) {
                                List<ParametersParameterComponent> params = ((Parameters) resource).getParameter();
                                params = params.stream()
                                                .filter(param -> param.getName().contains("resource"))
                                                .collect(Collectors.toList());
                                resource = params.get(0).getResource();
                        }
                        boolean hasId = resource.getIdElement().hasIdPart();
                        if (myMode == ValidationModeEnum.CREATE) {
                                if (hasId) {
                                        throw new UnprocessableEntityException(
                                                        Msg.code(997) + "Resource has an ID - ID must not be populated for a FHIR create");
                                }
                        } else if (myMode == ValidationModeEnum.UPDATE) {
                                if (!hasId) {
                                        throw new UnprocessableEntityException(
                                                        Msg.code(998) + "Resource has no ID - ID must be populated for a FHIR update");
                                }
                        }
                }
        }
}