/*
 * #%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.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
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.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.dao.IJpaDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
import ca.uhn.fhir.jpa.dao.index.DaoSearchParamSynchronizer;
import ca.uhn.fhir.jpa.dao.index.SearchParamWithInlineReferencesExtractor;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.esr.ExternallyStoredResourceAddress;
import ca.uhn.fhir.jpa.esr.ExternallyStoredResourceAddressMetadataKey;
import ca.uhn.fhir.jpa.esr.ExternallyStoredResourceServiceRegistry;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
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.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.entity.TagDefinition;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.model.search.ExtendedHSearchIndexData;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
import ca.uhn.fhir.jpa.searchparam.extractor.LogicalReferenceHelper;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryMatchResult;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.AddRemoveCount;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.MetaUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.XmlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import com.google.common.collect.Sets;
import com.google.common.hash.HashCode;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import jakarta.annotation.PostConstruct;
import jakarta.persistence.EntityManager;
import jakarta.persistence.PersistenceContext;
import jakarta.persistence.PersistenceContextType;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseMetaType;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IDomainResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.stereotype.Repository;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.stream.Collectors;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;

import static java.util.Objects.nonNull;
import static org.apache.commons.collections4.CollectionUtils.isEqualCollection;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.trim;

/**
 * TODO: JA - This class has only one subclass now. Historically it was a common
 * ancestor for BaseHapiFhirSystemDao and BaseHapiFhirResourceDao but I've untangled
 * the former from this hierarchy in order to simplify moving common functionality
 * for resource DAOs into the hapi-fhir-storage project. This class should be merged
 * into BaseHapiFhirResourceDao, but that should be done in its own dedicated PR
 * since it'll be a noisy change.
 */
@SuppressWarnings("WeakerAccess")
@Repository
public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStorageResourceDao<T>
                implements IDao, IJpaDao<T>, ApplicationContextAware {

        public static final String NS_JPA_PROFILE = "https://github.com/hapifhir/hapi-fhir/ns/jpa/profile";
        private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiFhirDao.class);
        private static boolean ourValidationDisabledForUnitTest;
        private static boolean ourDisableIncrementOnUpdateForUnitTest = false;

        @PersistenceContext(type = PersistenceContextType.TRANSACTION)
        protected EntityManager myEntityManager;

        @Autowired
        protected IIdHelperService<JpaPid> myIdHelperService;

        @Autowired
        protected ISearchCoordinatorSvc<JpaPid> mySearchCoordinatorSvc;

        @Autowired
        protected ITermReadSvc myTerminologySvc;

        @Autowired
        protected IResourceHistoryTableDao myResourceHistoryTableDao;

        @Autowired
        protected IResourceTableDao myResourceTableDao;

        @Autowired
        protected IResourceLinkDao myResourceLinkDao;

        @Autowired
        protected IResourceTagDao myResourceTagDao;

        @Autowired
        protected DeleteConflictService myDeleteConflictService;

        @Autowired
        protected IInterceptorBroadcaster myInterceptorBroadcaster;

        @Autowired
        protected InMemoryResourceMatcher myInMemoryResourceMatcher;

        @Autowired
        protected IJpaStorageResourceParser myJpaStorageResourceParser;

        @Autowired
        protected PartitionSettings myPartitionSettings;

        @Autowired
        ExpungeService myExpungeService;

        @Autowired
        private ExternallyStoredResourceServiceRegistry myExternallyStoredResourceServiceRegistry;

        @Autowired
        private ISearchParamPresenceSvc mySearchParamPresenceSvc;

        @Autowired
        private SearchParamWithInlineReferencesExtractor mySearchParamWithInlineReferencesExtractor;

        @Autowired
        private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;

        private FhirContext myContext;
        private ApplicationContext myApplicationContext;

        @Autowired
        private IPartitionLookupSvc myPartitionLookupSvc;

        @Autowired(required = false)
        private IFulltextSearchSvc myFulltextSearchSvc;

        @Autowired
        protected ResourceHistoryCalculator myResourceHistoryCalculator;

        @Autowired
        protected CacheTagDefinitionDao cacheTagDefinitionDao;

        protected final CodingSpy myCodingSpy = new CodingSpy();

        @VisibleForTesting
        public void setExternallyStoredResourceServiceRegistryForUnitTest(
                        ExternallyStoredResourceServiceRegistry theExternallyStoredResourceServiceRegistry) {
                myExternallyStoredResourceServiceRegistry = theExternallyStoredResourceServiceRegistry;
        }

        @VisibleForTesting
        public void setSearchParamPresenceSvc(ISearchParamPresenceSvc theSearchParamPresenceSvc) {
                mySearchParamPresenceSvc = theSearchParamPresenceSvc;
        }

        @VisibleForTesting
        public void setResourceHistoryCalculator(ResourceHistoryCalculator theResourceHistoryCalculator) {
                myResourceHistoryCalculator = theResourceHistoryCalculator;
        }

        @Override
        protected IInterceptorBroadcaster getInterceptorBroadcaster() {
                return myInterceptorBroadcaster;
        }

        protected ApplicationContext getApplicationContext() {
                return myApplicationContext;
        }

        @Override
        public void setApplicationContext(@Nonnull ApplicationContext theApplicationContext) throws BeansException {
                /*
                 * We do a null check here because Smile's module system tries to
                 * initialize the application context twice if two modules depend on
                 * the persistence module. The second time sets the dependency's appctx.
                 */
                if (myApplicationContext == null) {
                        myApplicationContext = theApplicationContext;
                }
        }

        private void extractHapiTags(
                        TransactionDetails theTransactionDetails,
                        IResource theResource,
                        ResourceTable theEntity,
                        Set<ResourceTag> allDefs) {
                TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(theResource);
                if (tagList != null) {
                        for (Tag next : tagList) {
                                TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
                                                theTransactionDetails,
                                                TagTypeEnum.TAG,
                                                next.getScheme(),
                                                next.getTerm(),
                                                next.getLabel(),
                                                next.getVersion(),
                                                myCodingSpy.getBooleanObject(next));
                                if (def != null) {
                                        ResourceTag tag = theEntity.addTag(def);
                                        allDefs.add(tag);
                                        theEntity.setHasTags(true);
                                }
                        }
                }

                List<BaseCodingDt> securityLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(theResource);
                if (securityLabels != null) {
                        for (BaseCodingDt next : securityLabels) {
                                TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
                                                theTransactionDetails,
                                                TagTypeEnum.SECURITY_LABEL,
                                                next.getSystemElement().getValue(),
                                                next.getCodeElement().getValue(),
                                                next.getDisplayElement().getValue(),
                                                next.getVersionElement().getValue(),
                                                next.getUserSelectedElement().getValue());
                                if (def != null) {
                                        ResourceTag tag = theEntity.addTag(def);
                                        allDefs.add(tag);
                                        theEntity.setHasTags(true);
                                }
                        }
                }

                List<IdDt> profiles = ResourceMetadataKeyEnum.PROFILES.get(theResource);
                if (profiles != null) {
                        for (IIdType next : profiles) {
                                TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
                                                theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null, null, null);
                                if (def != null) {
                                        ResourceTag tag = theEntity.addTag(def);
                                        allDefs.add(tag);
                                        theEntity.setHasTags(true);
                                }
                        }
                }
        }

        private void extractRiTags(
                        TransactionDetails theTransactionDetails,
                        IAnyResource theResource,
                        ResourceTable theEntity,
                        Set<ResourceTag> theAllTags) {
                List<? extends IBaseCoding> tagList = theResource.getMeta().getTag();
                if (tagList != null) {
                        for (IBaseCoding next : tagList) {
                                TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
                                                theTransactionDetails,
                                                TagTypeEnum.TAG,
                                                next.getSystem(),
                                                next.getCode(),
                                                next.getDisplay(),
                                                next.getVersion(),
                                                myCodingSpy.getBooleanObject(next));
                                if (def != null) {
                                        ResourceTag tag = theEntity.addTag(def);
                                        theAllTags.add(tag);
                                        theEntity.setHasTags(true);
                                }
                        }
                }

                List<? extends IBaseCoding> securityLabels = theResource.getMeta().getSecurity();
                if (securityLabels != null) {
                        for (IBaseCoding next : securityLabels) {
                                TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
                                                theTransactionDetails,
                                                TagTypeEnum.SECURITY_LABEL,
                                                next.getSystem(),
                                                next.getCode(),
                                                next.getDisplay(),
                                                next.getVersion(),
                                                myCodingSpy.getBooleanObject(next));
                                if (def != null) {
                                        ResourceTag tag = theEntity.addTag(def);
                                        theAllTags.add(tag);
                                        theEntity.setHasTags(true);
                                }
                        }
                }

                List<? extends IPrimitiveType<String>> profiles = theResource.getMeta().getProfile();
                if (profiles != null) {
                        for (IPrimitiveType<String> next : profiles) {
                                TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
                                                theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null, null, null);
                                if (def != null) {
                                        ResourceTag tag = theEntity.addTag(def);
                                        theAllTags.add(tag);
                                        theEntity.setHasTags(true);
                                }
                        }
                }
        }

        private void extractProfileTags(
                        TransactionDetails theTransactionDetails,
                        IBaseResource theResource,
                        ResourceTable theEntity,
                        Set<ResourceTag> theAllTags) {
                RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
                if (!def.isStandardType()) {
                        String profile = def.getResourceProfile("");
                        if (isNotBlank(profile)) {
                                TagDefinition profileDef = cacheTagDefinitionDao.getTagOrNull(
                                                theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null, null, null);

                                ResourceTag tag = theEntity.addTag(profileDef);
                                theAllTags.add(tag);
                                theEntity.setHasTags(true);
                        }
                }
        }

        private Set<ResourceTag> getAllTagDefinitions(ResourceTable theEntity) {
                HashSet<ResourceTag> retVal = Sets.newHashSet();
                if (theEntity.isHasTags()) {
                        retVal.addAll(theEntity.getTags());
                }
                return retVal;
        }

        @Override
        public JpaStorageSettings getStorageSettings() {
                return myStorageSettings;
        }

        @Override
        public FhirContext getContext() {
                return myContext;
        }

        @Autowired
        public void setContext(FhirContext theContext) {
                super.myFhirContext = theContext;
                myContext = theContext;
        }

        void incrementId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
                if (theResourceId == null || theResourceId.getVersionIdPart() == null) {
                        theSavedEntity.initializeVersion();
                } else {
                        theSavedEntity.markVersionUpdatedInCurrentTransaction();
                }

                assert theResourceId != null;
                String newVersion = Long.toString(theSavedEntity.getVersion());
                IIdType newId = theResourceId.withVersion(newVersion);
                theResource.getIdElement().setValue(newId.getValue());
        }

        public boolean isLogicalReference(IIdType theId) {
                return LogicalReferenceHelper.isLogicalReference(myStorageSettings, theId);
        }

        /**
         * Returns {@literal true} if the resource has changed (either the contents or the tags)
         */
        protected EncodedResource populateResourceIntoEntity(
                        TransactionDetails theTransactionDetails,
                        RequestDetails theRequest,
                        IBaseResource theResource,
                        ResourceTable theEntity,
                        boolean thePerformIndexing) {
                if (theEntity.getResourceType() == null) {
                        theEntity.setResourceType(toResourceName(theResource));
                }

                byte[] resourceBinary;
                String resourceText;
                ResourceEncodingEnum encoding;
                boolean changed = false;

                if (theEntity.getDeleted() == null) {

                        if (thePerformIndexing) {

                                ExternallyStoredResourceAddress address = null;
                                if (myExternallyStoredResourceServiceRegistry.hasProviders()) {
                                        address = ExternallyStoredResourceAddressMetadataKey.INSTANCE.get(theResource);
                                }

                                if (address != null) {

                                        encoding = ResourceEncodingEnum.ESR;
                                        resourceBinary = null;
                                        resourceText = address.getProviderId() + ":" + address.getLocation();
                                        changed = true;

                                } else {

                                        encoding = myStorageSettings.getResourceEncoding();

                                        String resourceType = theEntity.getResourceType();

                                        List<String> excludeElements = new ArrayList<>(8);
                                        IBaseMetaType meta = theResource.getMeta();

                                        IBaseExtension<?, ?> sourceExtension = getExcludedElements(resourceType, excludeElements, meta);

                                        theEntity.setFhirVersion(myContext.getVersion().getVersion());

                                        // TODO:  LD: Once 2024-02 it out the door we should consider further refactoring here to move
                                        // more of this logic within the calculator and eliminate more local variables
                                        final ResourceHistoryState calculate = myResourceHistoryCalculator.calculateResourceHistoryState(
                                                        theResource, encoding, excludeElements);

                                        resourceText = calculate.getResourceText();
                                        resourceBinary = calculate.getResourceBinary();
                                        encoding = calculate.getEncoding(); // This may be a no-op
                                        final HashCode hashCode = calculate.getHashCode();

                                        String hashSha256 = hashCode.toString();
                                        if (!hashSha256.equals(theEntity.getHashSha256())) {
                                                changed = true;
                                        }
                                        theEntity.setHashSha256(hashSha256);

                                        if (sourceExtension != null) {
                                                IBaseExtension<?, ?> newSourceExtension = ((IBaseHasExtensions) meta).addExtension();
                                                newSourceExtension.setUrl(sourceExtension.getUrl());
                                                newSourceExtension.setValue(sourceExtension.getValue());
                                        }
                                }

                        } else {

                                encoding = null;
                                resourceBinary = null;
                                resourceText = null;
                        }

                        boolean skipUpdatingTags = myStorageSettings.isMassIngestionMode() && theEntity.isHasTags();
                        skipUpdatingTags |= myStorageSettings.getTagStorageMode() == JpaStorageSettings.TagStorageModeEnum.INLINE;

                        if (!skipUpdatingTags) {
                                changed |= updateTags(theTransactionDetails, theRequest, theResource, theEntity);
                        }

                } else {

                        if (nonNull(theEntity.getHashSha256())) {
                                theEntity.setHashSha256(null);
                                changed = true;
                        }

                        resourceBinary = null;
                        resourceText = null;
                        encoding = ResourceEncodingEnum.DEL;
                }

                if (thePerformIndexing && !changed) {
                        if (theEntity.getId() == null) {
                                changed = true;
                        } else if (myStorageSettings.isMassIngestionMode()) {

                                // Don't check existing - We'll rely on the SHA256 hash only

                        } else if (theEntity.getVersion() == 1L && theEntity.getCurrentVersionEntity() == null) {

                                // No previous version if this is the first version

                        } else {
                                ResourceHistoryTable currentHistoryVersion = theEntity.getCurrentVersionEntity();
                                if (currentHistoryVersion == null) {
                                        currentHistoryVersion = myResourceHistoryTableDao.findForIdAndVersion(
                                                        theEntity.getId().toFk(), theEntity.getVersion());
                                }
                                if (currentHistoryVersion == null || !currentHistoryVersion.hasResource()) {
                                        changed = true;
                                } else {
                                        // TODO:  LD: Once 2024-02 it out the door we should consider further refactoring here to move
                                        // more of this logic within the calculator and eliminate more local variables
                                        changed = myResourceHistoryCalculator.isResourceHistoryChanged(
                                                        currentHistoryVersion, resourceBinary, resourceText);
                                }
                        }
                }

                EncodedResource retVal = new EncodedResource();
                retVal.setEncoding(encoding);
                retVal.setResourceBinary(resourceBinary);
                retVal.setResourceText(resourceText);
                retVal.setChanged(changed);

                return retVal;
        }

        /**
         * helper to format the meta element for serialization of the resource.
         *
         * @param theResourceType    the resource type of the resource
         * @param theExcludeElements list of extensions in the meta element to exclude from serialization
         * @param theMeta            the meta element of the resource
         * @return source extension if present in the meta element
         */
        private IBaseExtension<?, ?> getExcludedElements(
                        String theResourceType, List<String> theExcludeElements, IBaseMetaType theMeta) {
                boolean hasExtensions = false;
                IBaseExtension<?, ?> sourceExtension = null;
                if (theMeta instanceof IBaseHasExtensions) {
                        List<? extends IBaseExtension<?, ?>> extensions = ((IBaseHasExtensions) theMeta).getExtension();
                        if (!extensions.isEmpty()) {
                                hasExtensions = true;

                                /*
                                 * FHIR DSTU3 did not have the Resource.meta.source field, so we use a
                                 * custom HAPI FHIR extension in Resource.meta to store that field. However,
                                 * we put the value for that field in a separate table, so we don't want to serialize
                                 * it into the stored BLOB. Therefore: remove it from the resource temporarily
                                 * and restore it afterward.
                                 */
                                if (myFhirContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
                                        for (int i = 0; i < extensions.size(); i++) {
                                                if (extensions.get(i).getUrl().equals(HapiExtensions.EXT_META_SOURCE)) {
                                                        sourceExtension = extensions.remove(i);
                                                        i--;
                                                }
                                        }
                                }
                                boolean allExtensionsRemoved = extensions.isEmpty();
                                if (allExtensionsRemoved) {
                                        hasExtensions = false;
                                }
                        }
                }

                theExcludeElements.add("id");
                boolean inlineTagMode =
                                getStorageSettings().getTagStorageMode() == JpaStorageSettings.TagStorageModeEnum.INLINE;
                if (hasExtensions || inlineTagMode) {
                        if (!inlineTagMode) {
                                theExcludeElements.add(theResourceType + ".meta.profile");
                                theExcludeElements.add(theResourceType + ".meta.tag");
                                theExcludeElements.add(theResourceType + ".meta.security");
                        }
                        theExcludeElements.add(theResourceType + ".meta.versionId");
                        theExcludeElements.add(theResourceType + ".meta.lastUpdated");
                        theExcludeElements.add(theResourceType + ".meta.source");
                } else {
                        /*
                         * If there are no extensions in the meta element, we can just exclude the
                         * whole meta element, which avoids adding an empty "meta":{}
                         * from showing up in the serialized JSON.
                         */
                        theExcludeElements.add(theResourceType + ".meta");
                }
                return sourceExtension;
        }

        private boolean updateTags(
                        TransactionDetails theTransactionDetails,
                        RequestDetails theRequest,
                        IBaseResource theResource,
                        ResourceTable theEntity) {
                Set<ResourceTag> allResourceTagsFromTheResource = new HashSet<>();
                Set<ResourceTag> allOriginalResourceTagsFromTheEntity = getAllTagDefinitions(theEntity);

                if (theResource instanceof IResource) {
                        extractHapiTags(theTransactionDetails, (IResource) theResource, theEntity, allResourceTagsFromTheResource);
                } else {
                        extractRiTags(theTransactionDetails, (IAnyResource) theResource, theEntity, allResourceTagsFromTheResource);
                }

                extractProfileTags(theTransactionDetails, theResource, theEntity, allResourceTagsFromTheResource);

                // the extract[Hapi|Ri|Profile]Tags methods above will have populated the allResourceTagsFromTheResource Set
                // AND
                // added all tags from theResource.meta.tags to theEntity.meta.tags.  the next steps are to:
                // 1- remove duplicates;
                // 2- remove tags from theEntity that are not present in theResource if header HEADER_META_SNAPSHOT_MODE
                // is present in the request;
                //
                Set<ResourceTag> allResourceTagsNewAndOldFromTheEntity = getAllTagDefinitions(theEntity);
                Set<TagDefinition> allTagDefinitionsPresent = new HashSet<>();

                allResourceTagsNewAndOldFromTheEntity.forEach(tag -> {

                        // Don't keep duplicate tags or tags with a missing definition
                        TagDefinition tagDefinition = tag.getTag();
                        if (tagDefinition == null || !allTagDefinitionsPresent.add(tagDefinition)) {
                                theEntity.getTags().remove(tag);
                        }

                        // Drop any tags that have been removed
                        if (tagDefinition != null && !allResourceTagsFromTheResource.contains(tag)) {
                                if (shouldDroppedTagBeRemovedOnUpdate(theRequest, tag)) {
                                        theEntity.getTags().remove(tag);
                                } else if (HapiExtensions.EXT_SUBSCRIPTION_MATCHING_STRATEGY.equals(tagDefinition.getSystem())) {
                                        theEntity.getTags().remove(tag);
                                }
                        }
                });

                // at this point, theEntity.meta.tags will be up to date:
                // 1- it was stripped from tags that needed removing;
                // 2- it has new tags from a resource update through theResource;
                // 3- it has tags from the previous version;
                //
                // Since tags are merged on updates, we add tags from theEntity that theResource does not have
                Set<ResourceTag> allUpdatedResourceTagsNewAndOldMinusRemovalsFromTheEntity = getAllTagDefinitions(theEntity);

                allUpdatedResourceTagsNewAndOldMinusRemovalsFromTheEntity.forEach(aResourcetag -> {
                        if (!allResourceTagsFromTheResource.contains(aResourcetag)) {
                                IBaseCoding iBaseCoding = theResource
                                                .getMeta()
                                                .addTag()
                                                .setCode(aResourcetag.getTag().getCode())
                                                .setSystem(aResourcetag.getTag().getSystem())
                                                .setVersion(aResourcetag.getTag().getVersion());

                                allResourceTagsFromTheResource.add(aResourcetag);

                                if (aResourcetag.getTag().getUserSelected() != null) {
                                        iBaseCoding.setUserSelected(aResourcetag.getTag().getUserSelected());
                                }
                        }
                });

                theEntity.setHasTags(!allUpdatedResourceTagsNewAndOldMinusRemovalsFromTheEntity.isEmpty());
                return !isEqualCollection(allOriginalResourceTagsFromTheEntity, allResourceTagsFromTheResource);
        }

        /**
         * Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database
         *
         * @param theEntity The resource
         */
        protected void postDelete(ResourceTable theEntity) {
                // nothing
        }

        /**
         * Subclasses may override to provide behaviour. Called when a resource has been inserted into the database for the first time.
         *
         * @param theEntity         The entity being updated (Do not modify the entity! Undefined behaviour will occur!)
         * @param theResource       The resource being persisted
         * @param theRequestDetails The request details, needed for partition support
         */
        protected void postPersist(ResourceTable theEntity, T theResource, RequestDetails theRequestDetails) {
                // nothing
        }

        /**
         * Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database
         *
         * @param theEntity         The resource
         * @param theResource       The resource being persisted
         * @param theRequestDetails The request details, needed for partition support
         */
        protected void postUpdate(ResourceTable theEntity, T theResource, RequestDetails theRequestDetails) {
                // nothing
        }

        @Override
        @CoverageIgnore
        public BaseHasResource readEntity(IIdType theValueId, RequestDetails theRequest) {
                throw new NotImplementedException(Msg.code(927));
        }

        /**
         * This method is called when an update to an existing resource detects that the resource supplied for update is missing a tag/profile/security label that the currently persisted resource holds.
         * <p>
         * The default implementation removes any profile declarations, but leaves tags and security labels in place. Subclasses may choose to override and change this behaviour.
         * </p>
         * <p>
         * See <a href="http://hl7.org/fhir/resource.html#tag-updates">Updates to Tags, Profiles, and Security Labels</a> for a description of the logic that the default behaviour follows.
         * </p>
         *
         * @param theTag The tag
         * @return Returns <code>true</code> if the tag should be removed
         */
        protected boolean shouldDroppedTagBeRemovedOnUpdate(RequestDetails theRequest, ResourceTag theTag) {
                if (theTag.getTag() == null) {
                        return true;
                }

                Set<TagTypeEnum> metaSnapshotModeTokens = null;

                if (theRequest != null) {
                        List<String> metaSnapshotMode = theRequest.getHeaders(JpaConstants.HEADER_META_SNAPSHOT_MODE);
                        if (metaSnapshotMode != null && !metaSnapshotMode.isEmpty()) {
                                metaSnapshotModeTokens = new HashSet<>();
                                for (String nextHeaderValue : metaSnapshotMode) {
                                        StringTokenizer tok = new StringTokenizer(nextHeaderValue, ",");
                                        while (tok.hasMoreTokens()) {
                                                switch (trim(tok.nextToken())) {
                                                        case "TAG":
                                                                metaSnapshotModeTokens.add(TagTypeEnum.TAG);
                                                                break;
                                                        case "PROFILE":
                                                                metaSnapshotModeTokens.add(TagTypeEnum.PROFILE);
                                                                break;
                                                        case "SECURITY_LABEL":
                                                                metaSnapshotModeTokens.add(TagTypeEnum.SECURITY_LABEL);
                                                                break;
                                                }
                                        }
                                }
                        }
                }

                if (metaSnapshotModeTokens == null) {
                        metaSnapshotModeTokens = Collections.singleton(TagTypeEnum.PROFILE);
                }

                return metaSnapshotModeTokens.contains(theTag.getTag().getTagType());
        }

        String toResourceName(IBaseResource theResource) {
                return myContext.getResourceType(theResource);
        }

        @VisibleForTesting
        public void setEntityManager(EntityManager theEntityManager) {
                myEntityManager = theEntityManager;
        }

        @VisibleForTesting
        public void setSearchParamWithInlineReferencesExtractor(
                        SearchParamWithInlineReferencesExtractor theSearchParamWithInlineReferencesExtractor) {
                mySearchParamWithInlineReferencesExtractor = theSearchParamWithInlineReferencesExtractor;
        }

        @VisibleForTesting
        public void setResourceHistoryTableDao(IResourceHistoryTableDao theResourceHistoryTableDao) {
                myResourceHistoryTableDao = theResourceHistoryTableDao;
        }

        @VisibleForTesting
        public void setDaoSearchParamSynchronizer(DaoSearchParamSynchronizer theDaoSearchParamSynchronizer) {
                myDaoSearchParamSynchronizer = theDaoSearchParamSynchronizer;
        }

        private void verifyMatchUrlForConditionalCreateOrUpdate(
                        CreateOrUpdateByMatch theCreateOrUpdate,
                        IBaseResource theResource,
                        String theIfNoneExist,
                        ResourceIndexedSearchParams theParams,
                        RequestDetails theRequestDetails) {
                // Make sure that the match URL was actually appropriate for the supplied resource
                InMemoryMatchResult outcome =
                                myInMemoryResourceMatcher.match(theIfNoneExist, theResource, theParams, theRequestDetails);

                if (outcome.supported() && !outcome.matched()) {
                        String errorMsg = getConditionalCreateOrUpdateErrorMsg(theCreateOrUpdate);
                        throw new InvalidRequestException(Msg.code(929) + errorMsg);
                }
        }

        private String getConditionalCreateOrUpdateErrorMsg(CreateOrUpdateByMatch theCreateOrUpdate) {
                return String.format(
                                "Failed to process conditional %s. " + "The supplied resource did not satisfy the conditional URL.",
                                theCreateOrUpdate.name().toLowerCase());
        }

        @SuppressWarnings("unchecked")
        @Override
        public ResourceTable updateEntity(
                        RequestDetails theRequest,
                        final IBaseResource theResource,
                        IBasePersistedResource theEntity,
                        Date theDeletedTimestampOrNull,
                        boolean thePerformIndexing,
                        boolean theUpdateVersion,
                        TransactionDetails theTransactionDetails,
                        boolean theForceUpdate,
                        boolean theCreateNewHistoryEntry) {
                Validate.notNull(theEntity);
                Validate.isTrue(
                                theDeletedTimestampOrNull != null || theResource != null,
                                "Must have either a resource[%s] or a deleted timestamp[%s] for resource PID[%s]",
                                theDeletedTimestampOrNull != null,
                                theResource != null,
                                theEntity.getPersistentId());

                ourLog.debug("Starting entity update");

                ResourceTable entity = (ResourceTable) theEntity;

                /*
                 * This should be the very first thing..
                 */
                if (theResource != null) {
                        if (thePerformIndexing && theDeletedTimestampOrNull == null) {
                                if (!ourValidationDisabledForUnitTest) {
                                        validateResourceForStorage((T) theResource, entity);
                                }
                        }
                        if (!StringUtils.isBlank(entity.getResourceType())) {
                                String resourceType = myContext.getResourceType(theResource);
                                // This is just a sanity check and should never actually fail.
                                // We resolve the ID using IdLookupService, and there should be
                                // no way to get it to give you a mismatched type for an ID.
                                Validate.isTrue(resourceType.equals(entity.getResourceType()));
                        }
                }

                if (entity.getPublished() == null) {
                        ourLog.debug("Entity has published time: {}", theTransactionDetails.getTransactionDate());
                        entity.setPublished(theTransactionDetails.getTransactionDate());
                }

                ResourceIndexedSearchParams existingParams = null;

                ResourceIndexedSearchParams newParams = null;

                EncodedResource changed;
                if (theDeletedTimestampOrNull != null) {
                        // DELETE

                        entity.setDeleted(theDeletedTimestampOrNull);
                        entity.setUpdated(theDeletedTimestampOrNull);
                        entity.setNarrativeText(null);
                        entity.setContentText(null);
                        entity.setIndexStatus(getEntityIndexedStatusEnum());
                        changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);

                } else {

                        // CREATE or UPDATE

                        IdentityHashMap<ResourceTable, ResourceIndexedSearchParams> existingSearchParams =
                                        getSearchParamsMapFromTransaction(theTransactionDetails);
                        existingParams = existingSearchParams.get(entity);
                        if (existingParams == null) {
                                existingParams = ResourceIndexedSearchParams.withLists(entity);
                                /*
                                 * If we have lots of resource links, this proactively fetches the targets so
                                 * that we don't look them up one-by-one when comparing the new set to the
                                 * old set later on
                                 */
                                if (existingParams.getResourceLinks().size() >= 10) {
                                        List<Long> allPids = existingParams.getResourceLinks().stream()
                                                        .map(ResourceLink::getId)
                                                        .collect(Collectors.toList());
                                        new QueryChunker<Long>().chunk(allPids, chunkPids -> {
                                                List<ResourceLink> targets = myResourceLinkDao.findByPidAndFetchTargetDetails(chunkPids);
                                                ourLog.trace("Prefetched targets: {}", targets);
                                        });
                                }
                                existingSearchParams.put(entity, existingParams);
                        }
                        entity.setDeleted(null);

                        // TODO: is this IF statement always true? Try removing it
                        if (thePerformIndexing || theEntity.getVersion() == 1) {

                                newParams = ResourceIndexedSearchParams.withSets();

                                RequestPartitionId requestPartitionId;
                                if (!myPartitionSettings.isPartitioningEnabled()) {
                                        requestPartitionId = RequestPartitionId.allPartitions();
                                } else if (entity.getPartitionId() != null) {
                                        requestPartitionId = entity.getPartitionId().toPartitionId();
                                } else {
                                        requestPartitionId = RequestPartitionId.defaultPartition();
                                }

                                // Extract search params for resource
                                mySearchParamWithInlineReferencesExtractor.populateFromResource(
                                                requestPartitionId,
                                                newParams,
                                                theTransactionDetails,
                                                entity,
                                                theResource,
                                                existingParams,
                                                theRequest,
                                                thePerformIndexing);

                                // Actually persist the ResourceTable and ResourceHistoryTable entities
                                changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);

                                if (theForceUpdate) {
                                        changed.setChanged(true);
                                }

                                if (changed.isChanged()) {
                                        checkConditionalMatch(
                                                        entity, theUpdateVersion, theResource, thePerformIndexing, newParams, theRequest);

                                        if (CURRENTLY_REINDEXING.get(theResource) != Boolean.TRUE) {
                                                entity.setUpdated(theTransactionDetails.getTransactionDate());
                                        }
                                        newParams.populateResourceTableSearchParamsPresentFlags(entity);
                                        entity.setIndexStatus(getEntityIndexedStatusEnum());
                                }

                                if (myFulltextSearchSvc != null && !myFulltextSearchSvc.isDisabled()) {
                                        populateFullTextFields(myContext, theResource, entity, newParams);
                                }

                        } else {

                                entity.setUpdated(theTransactionDetails.getTransactionDate());
                                entity.setIndexStatus(null);

                                changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, false);
                        }
                }

                if (thePerformIndexing
                                && changed != null
                                && !changed.isChanged()
                                && !theForceUpdate
                                && myStorageSettings.isSuppressUpdatesWithNoChange()
                                && (entity.getVersion() > 1 || theUpdateVersion)) {
                        ourLog.debug(
                                        "Resource {} has not changed",
                                        entity.getIdDt().toUnqualified().getValue());
                        if (theResource != null) {
                                myJpaStorageResourceParser.updateResourceMetadata(entity, theResource);
                        }
                        entity.setUnchangedInCurrentOperation(true);
                        return entity;
                }

                if (entity.getId().getId() != null && theUpdateVersion) {
                        entity.markVersionUpdatedInCurrentTransaction();
                }

                /*
                 * Save the resource itself
                 */
                if (entity.getId().getId() == null) {
                        myEntityManager.persist(entity);

                        if (entity.getFhirId() == null) {
                                entity.setFhirId(Long.toString(entity.getId().getId()));
                        }

                        postPersist(entity, (T) theResource, theRequest);

                } else if (entity.getDeleted() != null) {
                        entity = myEntityManager.merge(entity);

                        postDelete(entity);

                } else {
                        entity = myEntityManager.merge(entity);

                        postUpdate(entity, (T) theResource, theRequest);
                }

                if (theCreateNewHistoryEntry) {
                        createHistoryEntry(theRequest, theResource, entity, changed);
                }

                /*
                 * Update the "search param present" table which is used for the
                 * ?foo:missing=true queries
                 *
                 * Note that we're only populating this for reference params
                 * because the index tables for all other types have a MISSING column
                 * right on them for handling the :missing queries. We can't use the
                 * index table for resource links (reference indexes) because we index
                 * those by path and not by parameter name.
                 */
                if (thePerformIndexing && newParams != null) {
                        AddRemoveCount presenceCount =
                                        mySearchParamPresenceSvc.updatePresence(entity, newParams.mySearchParamPresentEntities);

                        // Interceptor broadcast: JPA_PERFTRACE_INFO
                        if (!presenceCount.isEmpty()) {
                                IInterceptorBroadcaster compositeBroadcaster =
                                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest);
                                if (compositeBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO)) {
                                        StorageProcessingMessage message = new StorageProcessingMessage();
                                        message.setMessage(
                                                        "For " + entity.getIdDt().toUnqualifiedVersionless().getValue() + " added "
                                                                        + presenceCount.getAddCount() + " and removed " + presenceCount.getRemoveCount()
                                                                        + " resource search parameter presence entries");
                                        HookParams params = new HookParams()
                                                        .add(RequestDetails.class, theRequest)
                                                        .addIfMatchesType(ServletRequestDetails.class, theRequest)
                                                        .add(StorageProcessingMessage.class, message);
                                        compositeBroadcaster.callHooks(Pointcut.JPA_PERFTRACE_INFO, params);
                                }
                        }
                }

                /*
                 * Indexing
                 */
                if (thePerformIndexing) {
                        if (newParams == null) {
                                myExpungeService.deleteAllSearchParams(entity.getPersistentId());
                                entity.clearAllParamsPopulated();
                        } else {

                                // Synchronize search param indexes
                                AddRemoveCount searchParamAddRemoveCount =
                                                myDaoSearchParamSynchronizer.synchronizeSearchParamsToDatabase(
                                                                newParams, entity, existingParams);

                                newParams.populateResourceTableParamCollections(entity);

                                // Interceptor broadcast: JPA_PERFTRACE_INFO
                                if (!searchParamAddRemoveCount.isEmpty()) {
                                        IInterceptorBroadcaster compositeBroadcaster =
                                                        CompositeInterceptorBroadcaster.newCompositeBroadcaster(
                                                                        myInterceptorBroadcaster, theRequest);
                                        if (compositeBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO)) {
                                                StorageProcessingMessage message = new StorageProcessingMessage();
                                                message.setMessage("For "
                                                                + entity.getIdDt().toUnqualifiedVersionless().getValue() + " added "
                                                                + searchParamAddRemoveCount.getAddCount() + " and removed "
                                                                + searchParamAddRemoveCount.getRemoveCount()
                                                                + " resource search parameter index entries");
                                                HookParams params = new HookParams()
                                                                .add(RequestDetails.class, theRequest)
                                                                .addIfMatchesType(ServletRequestDetails.class, theRequest)
                                                                .add(StorageProcessingMessage.class, message);
                                                compositeBroadcaster.callHooks(Pointcut.JPA_PERFTRACE_INFO, params);
                                        }
                                }

                                // Put the final set of search params into the transaction
                                getSearchParamsMapFromTransaction(theTransactionDetails).put(entity, newParams);
                        }
                }

                if (theResource != null) {
                        myJpaStorageResourceParser.updateResourceMetadata(entity, theResource);
                }

                return entity;
        }

        private static IdentityHashMap<ResourceTable, ResourceIndexedSearchParams> getSearchParamsMapFromTransaction(
                        TransactionDetails theTransactionDetails) {
                return theTransactionDetails.getOrCreateUserData(
                                HapiTransactionService.XACT_USERDATA_KEY_EXISTING_SEARCH_PARAMS, IdentityHashMap::new);
        }

        /**
         * This methor returns the {@link EntityIndexStatusEnum} value that should be
         * used for a successfully fully indexed resource. This method will return
         * {@link EntityIndexStatusEnum#INDEXED_ALL} or {@link EntityIndexStatusEnum#INDEXED_RDBMS_ONLY}
         * depending on configuration.
         */
        @Nonnull
        private EntityIndexStatusEnum getEntityIndexedStatusEnum() {
                if (myStorageSettings.isHibernateSearchIndexFullText()
                                || myStorageSettings.isHibernateSearchIndexSearchParams()) {
                        return EntityIndexStatusEnum.INDEXED_ALL;
                } else {
                        return EntityIndexStatusEnum.INDEXED_RDBMS_ONLY;
                }
        }

        /**
         * Make sure that the match URL was actually appropriate for the supplied
         * resource, if so configured, or do it only for first version, since technically it
         * is possible (and legal) for someone to be using a conditional update
         * to match a resource and then update it in a way that it no longer
         * matches.
         */
        private void checkConditionalMatch(
                        ResourceTable theEntity,
                        boolean theUpdateVersion,
                        IBaseResource theResource,
                        boolean thePerformIndexing,
                        ResourceIndexedSearchParams theNewParams,
                        RequestDetails theRequest) {

                if (!thePerformIndexing) {
                        return;
                }

                if (theEntity.getCreatedByMatchUrl() == null && theEntity.getUpdatedByMatchUrl() == null) {
                        return;
                }

                // version is not updated at this point, but could be pending for update, which we consider here
                long pendingVersion = theEntity.getVersion();
                if (theUpdateVersion && !theEntity.isVersionUpdatedInCurrentTransaction()) {
                        pendingVersion++;
                }

                if (myStorageSettings.isPreventInvalidatingConditionalMatchCriteria() || pendingVersion <= 1L) {
                        String createOrUpdateUrl;
                        CreateOrUpdateByMatch createOrUpdate;

                        if (theEntity.getCreatedByMatchUrl() != null) {
                                createOrUpdateUrl = theEntity.getCreatedByMatchUrl();
                                createOrUpdate = CreateOrUpdateByMatch.CREATE;
                        } else {
                                createOrUpdateUrl = theEntity.getUpdatedByMatchUrl();
                                createOrUpdate = CreateOrUpdateByMatch.UPDATE;
                        }

                        verifyMatchUrlForConditionalCreateOrUpdate(
                                        createOrUpdate, theResource, createOrUpdateUrl, theNewParams, theRequest);
                }
        }

        public IBasePersistedResource<?> updateHistoryEntity(
                        RequestDetails theRequest,
                        T theResource,
                        IBasePersistedResource<?> theEntity,
                        IBasePersistedResource<?> theHistoryEntity,
                        IIdType theResourceId,
                        TransactionDetails theTransactionDetails,
                        boolean isUpdatingCurrent) {
                Validate.notNull(theEntity);
                Validate.isTrue(
                                theResource != null,
                                "Must have either a resource[%s] for resource PID[%s]",
                                theResource != null,
                                theEntity.getPersistentId());

                ourLog.debug("Starting history entity update");
                EncodedResource encodedResource = new EncodedResource();
                ResourceHistoryTable historyEntity;

                if (isUpdatingCurrent) {
                        ResourceTable entity = (ResourceTable) theEntity;

                        IBaseResource oldResource;
                        if (getStorageSettings().isMassIngestionMode()) {
                                oldResource = null;
                        } else {
                                oldResource = myJpaStorageResourceParser.toResource(entity, false);
                        }

                        notifyInterceptors(theRequest, theResource, oldResource, theTransactionDetails, true);

                        ResourceTable savedEntity = updateEntity(
                                        theRequest, theResource, entity, null, true, false, theTransactionDetails, false, false);
                        // Have to call populate again for the encodedResource, since using createHistoryEntry() will cause version
                        // constraint failure, ie updating the same resource at the same time
                        encodedResource = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
                        // For some reason the current version entity is not attached until after using updateEntity
                        historyEntity = ((ResourceTable) readEntity(theResourceId, theRequest)).getCurrentVersionEntity();

                        // Update version/lastUpdated so that interceptors see the correct version
                        myJpaStorageResourceParser.updateResourceMetadata(savedEntity, theResource);
                        // Populate the PID in the resource, so it is available to hooks
                        addPidToResource(savedEntity, theResource);

                        if (!savedEntity.isUnchangedInCurrentOperation()) {
                                notifyInterceptors(theRequest, theResource, oldResource, theTransactionDetails, false);
                        }
                } else {
                        historyEntity = (ResourceHistoryTable) theHistoryEntity;
                        if (!StringUtils.isBlank(historyEntity.getResourceType())) {
                                String resourceType = myContext.getResourceType(theResource);
                                if (!resourceType.equals(historyEntity.getResourceType())) {
                                        throw new UnprocessableEntityException(Msg.code(930) + "Existing resource ID["
                                                        + historyEntity.getIdDt().toUnqualifiedVersionless() + "] is of type["
                                                        + historyEntity.getResourceType()
                                                        + "] - Cannot update with [" + resourceType + "]");
                                }
                        }

                        historyEntity.setDeleted(null);

                        // Check if resource is the same
                        ResourceEncodingEnum encoding = myStorageSettings.getResourceEncoding();
                        List<String> excludeElements = new ArrayList<>(8);
                        getExcludedElements(historyEntity.getResourceType(), excludeElements, theResource.getMeta());
                        String encodedResourceString =
                                        myResourceHistoryCalculator.encodeResource(theResource, encoding, excludeElements);
                        byte[] resourceBinary = ResourceHistoryCalculator.getResourceBinary(encoding, encodedResourceString);
                        final boolean changed = myResourceHistoryCalculator.isResourceHistoryChanged(
                                        historyEntity, resourceBinary, encodedResourceString);

                        historyEntity.setUpdated(theTransactionDetails.getTransactionDate());

                        if (!changed && myStorageSettings.isSuppressUpdatesWithNoChange() && (historyEntity.getVersion() > 1)) {
                                ourLog.debug(
                                                "Resource {} has not changed",
                                                historyEntity.getIdDt().toUnqualified().getValue());
                                myJpaStorageResourceParser.updateResourceMetadata(historyEntity, theResource);
                                return historyEntity;
                        }

                        myResourceHistoryCalculator.populateEncodedResource(
                                        encodedResource, encodedResourceString, resourceBinary, encoding);
                }
                /*
                 * Save the resource itself to the resourceHistoryTable
                 */
                historyEntity = myEntityManager.merge(historyEntity);
                historyEntity.setEncoding(encodedResource.getEncoding());
                historyEntity.setResource(encodedResource.getResourceBinary());
                historyEntity.setResourceTextVc(encodedResource.getResourceText());
                myResourceHistoryTableDao.save(historyEntity);

                myJpaStorageResourceParser.updateResourceMetadata(historyEntity, theResource);

                return historyEntity;
        }

        private void populateEncodedResource(
                        EncodedResource encodedResource,
                        String encodedResourceString,
                        byte[] theResourceBinary,
                        ResourceEncodingEnum theEncoding) {
                encodedResource.setResourceText(encodedResourceString);
                encodedResource.setResourceBinary(theResourceBinary);
                encodedResource.setEncoding(theEncoding);
        }

        private void createHistoryEntry(
                        RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, EncodedResource theChanged) {
                boolean versionedTags =
                                getStorageSettings().getTagStorageMode() == JpaStorageSettings.TagStorageModeEnum.VERSIONED;

                ResourceHistoryTable historyEntry = null;
                long resourceVersion = theEntity.getVersion();
                if (!myStorageSettings.isResourceDbHistoryEnabled() && resourceVersion > 1L) {
                        /*
                         * If we're not storing history, then just pull the current history
                         * table row and update it. Note that there is always a chance that
                         * this could return null if the current resourceVersion has been expunged
                         * in which case we'll still create a new one
                         */
                        historyEntry = myResourceHistoryTableDao.findForIdAndVersion(
                                        theEntity.getResourceId().toFk(), resourceVersion - 1);
                        if (historyEntry != null) {
                                theEntity.populateHistoryEntityVersionAndDates(historyEntry);
                                if (versionedTags && theEntity.isHasTags()) {
                                        for (ResourceTag next : theEntity.getTags()) {
                                                historyEntry.addTag(next.getTag());
                                        }
                                }
                        }
                }

                /*
                 * This should basically always be null unless resource history
                 * is disabled on this server. In that case, we'll just be reusing
                 * the previous version entity.
                 */
                if (historyEntry == null) {
                        historyEntry = theEntity.toHistory(versionedTags && theEntity.getDeleted() == null);
                }

                historyEntry.setEncoding(theChanged.getEncoding());
                historyEntry.setResource(theChanged.getResourceBinary());
                historyEntry.setResourceTextVc(theChanged.getResourceText());

                ourLog.debug("Saving history entry ID[{}] for RES_ID[{}]", historyEntry.getId(), historyEntry.getResourceId());
                myEntityManager.persist(historyEntry);
                theEntity.setCurrentVersionEntity(historyEntry);

                // Save resource source
                String source = null;

                if (theResource != null) {
                        if (myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
                                IBaseMetaType meta = theResource.getMeta();
                                source = MetaUtil.getSource(myContext, meta);
                        }
                        if (myContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
                                source = ((IBaseHasExtensions) theResource.getMeta())
                                                .getExtension().stream()
                                                                .filter(t -> HapiExtensions.EXT_META_SOURCE.equals(t.getUrl()))
                                                                .filter(t -> t.getValue() instanceof IPrimitiveType)
                                                                .map(t -> ((IPrimitiveType<?>) t.getValue()).getValueAsString())
                                                                .findFirst()
                                                                .orElse(null);
                        }
                }

                String requestId = getRequestId(theRequest, source);
                source = MetaUtil.cleanProvenanceSourceUriOrEmpty(source);

                boolean shouldStoreSource =
                                myStorageSettings.getStoreMetaSourceInformation().isStoreSourceUri();
                boolean shouldStoreRequestId =
                                myStorageSettings.getStoreMetaSourceInformation().isStoreRequestId();
                boolean haveSource = isNotBlank(source) && shouldStoreSource;
                boolean haveRequestId = isNotBlank(requestId) && shouldStoreRequestId;
                if (haveSource || haveRequestId) {
                        if (haveRequestId) {
                                String persistedRequestId = left(requestId, Constants.REQUEST_ID_LENGTH);
                                historyEntry.setRequestId(persistedRequestId);
                        }
                        if (haveSource) {
                                String persistedSource = left(source, ResourceHistoryTable.SOURCE_URI_LENGTH);
                                historyEntry.setSourceUri(persistedSource);
                        }
                        if (theResource != null) {
                                MetaUtil.populateResourceSource(
                                                myFhirContext,
                                                shouldStoreSource ? source : null,
                                                shouldStoreRequestId ? requestId : null,
                                                theResource);
                        }
                }
        }

        private String getRequestId(RequestDetails theRequest, String theSource) {
                if (myStorageSettings.isPreserveRequestIdInResourceBody()) {
                        return StringUtils.substringAfter(theSource, "#");
                }
                return theRequest != null ? theRequest.getRequestId() : null;
        }

        @Override
        public DaoMethodOutcome updateInternal(
                        RequestDetails theRequestDetails,
                        T theResource,
                        String theMatchUrl,
                        boolean thePerformIndexing,
                        boolean theForceUpdateVersion,
                        IBasePersistedResource theEntity,
                        IIdType theResourceId,
                        @Nullable IBaseResource theOldResource,
                        RestOperationTypeEnum theOperationType,
                        TransactionDetails theTransactionDetails) {

                ResourceTable entity = (ResourceTable) theEntity;

                // We'll update the resource ID with the correct version later but for
                // now at least set it to something useful for the interceptors
                theResource.setId(entity.getIdDt());

                // Notify IServerOperationInterceptors about pre-action call
                notifyInterceptors(theRequestDetails, theResource, theOldResource, theTransactionDetails, true);

                entity.setUpdatedByMatchUrl(theMatchUrl);

                // Perform update
                ResourceTable savedEntity = updateEntity(
                                theRequestDetails,
                                theResource,
                                entity,
                                null,
                                thePerformIndexing,
                                thePerformIndexing,
                                theTransactionDetails,
                                theForceUpdateVersion,
                                thePerformIndexing);

                /*
                 * If we aren't indexing (meaning we're probably executing a sub-operation within a transaction),
                 * we'll manually increase the version. This is important because we want the updated version number
                 * to be reflected in the resource shared with interceptors
                 */
                if (!thePerformIndexing
                                && !savedEntity.isUnchangedInCurrentOperation()
                                && !ourDisableIncrementOnUpdateForUnitTest) {
                        if (!theResourceId.hasVersionIdPart()) {
                                theResourceId = theResourceId.withVersion(Long.toString(savedEntity.getVersion()));
                        }
                        incrementId(theResource, savedEntity, theResourceId);
                }

                // Update version/lastUpdated so that interceptors see the correct version
                myJpaStorageResourceParser.updateResourceMetadata(savedEntity, theResource);

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

                // Notify interceptors
                if (!savedEntity.isUnchangedInCurrentOperation()) {
                        notifyInterceptors(theRequestDetails, theResource, theOldResource, theTransactionDetails, false);
                }

                Collection<? extends BaseTag> tagList = Collections.emptyList();
                if (entity.isHasTags()) {
                        tagList = entity.getTags();
                }
                long version = entity.getVersion();
                myJpaStorageResourceParser.populateResourceMetadata(entity, false, tagList, version, theResource);

                boolean wasDeleted = false;
                if (theOldResource != null) {
                        wasDeleted = theOldResource.isDeleted();
                }

                if (wasDeleted && !myStorageSettings.isDeleteEnabled()) {
                        String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "cantUndeleteWithDeletesDisabled");
                        throw new InvalidRequestException(Msg.code(2573) + msg);
                }

                DaoMethodOutcome outcome = toMethodOutcome(
                                                theRequestDetails, savedEntity, theResource, theMatchUrl, theOperationType)
                                .setCreated(wasDeleted);

                if (!thePerformIndexing) {
                        IIdType id = getContext().getVersion().newIdType();
                        id.setValue(entity.getIdDt().getValue());
                        outcome.setId(id);
                }

                // Only include a task timer if we're not in a sub-request (i.e. a transaction)
                // since individual item times don't actually make much sense in the context
                // of a transaction
                StopWatch w = null;
                if (theRequestDetails != null && !theRequestDetails.isSubRequest()) {
                        if (theTransactionDetails != null && !theTransactionDetails.isFhirTransaction()) {
                                w = new StopWatch(theTransactionDetails.getTransactionDate());
                        }
                }

                populateOperationOutcomeForUpdate(w, outcome, theMatchUrl, outcome.getOperationType(), theTransactionDetails);

                return outcome;
        }

        private void notifyInterceptors(
                        RequestDetails theRequestDetails,
                        T theResource,
                        IBaseResource theOldResource,
                        TransactionDetails theTransactionDetails,
                        boolean isUnchanged) {
                Pointcut interceptorPointcut = Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED;

                HookParams hookParams = new HookParams()
                                .add(IBaseResource.class, theOldResource)
                                .add(IBaseResource.class, theResource)
                                .add(RequestDetails.class, theRequestDetails)
                                .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
                                .add(TransactionDetails.class, theTransactionDetails);

                if (!isUnchanged) {
                        hookParams.add(
                                        InterceptorInvocationTimingEnum.class,
                                        theTransactionDetails.getInvocationTiming(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED));
                        interceptorPointcut = Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED;
                }

                doCallHooks(theTransactionDetails, theRequestDetails, interceptorPointcut, hookParams);
        }

        protected void addPidToResource(IResourceLookup<JpaPid> theEntity, IBaseResource theResource) {
                if (theResource instanceof IAnyResource) {
                        IDao.RESOURCE_PID.put(theResource, theEntity.getPersistentId());
                } else if (theResource instanceof IResource) {
                        IDao.RESOURCE_PID.put(theResource, theEntity.getPersistentId());
                }
        }

        private void validateChildReferenceTargetTypes(IBase theElement, String thePath) {
                if (theElement == null) {
                        return;
                }
                BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theElement.getClass());
                if (!(def instanceof BaseRuntimeElementCompositeDefinition)) {
                        return;
                }

                BaseRuntimeElementCompositeDefinition<?> cdef = (BaseRuntimeElementCompositeDefinition<?>) def;
                for (BaseRuntimeChildDefinition nextChildDef : cdef.getChildren()) {

                        List<IBase> values = nextChildDef.getAccessor().getValues(theElement);
                        if (values == null || values.isEmpty()) {
                                continue;
                        }

                        String newPath = thePath + "." + nextChildDef.getElementName();

                        for (IBase nextChild : values) {
                                validateChildReferenceTargetTypes(nextChild, newPath);
                        }

                        if (nextChildDef instanceof RuntimeChildResourceDefinition) {
                                RuntimeChildResourceDefinition nextChildDefRes = (RuntimeChildResourceDefinition) nextChildDef;
                                Set<String> validTypes = new HashSet<>();
                                boolean allowAny = false;
                                for (Class<? extends IBaseResource> nextValidType : nextChildDefRes.getResourceTypes()) {
                                        if (nextValidType.isInterface()) {
                                                allowAny = true;
                                                break;
                                        }
                                        validTypes.add(getContext().getResourceType(nextValidType));
                                }

                                if (allowAny) {
                                        continue;
                                }

                                if (getStorageSettings().isEnforceReferenceTargetTypes()) {
                                        for (IBase nextChild : values) {
                                                IBaseReference nextRef = (IBaseReference) nextChild;
                                                IIdType referencedId = nextRef.getReferenceElement();
                                                if (!isBlank(referencedId.getResourceType())) {
                                                        if (!isLogicalReference(referencedId)) {
                                                                if (!referencedId.getValue().contains("?")) {
                                                                        if (!validTypes.contains(referencedId.getResourceType())) {
                                                                                throw new UnprocessableEntityException(Msg.code(931)
                                                                                                + "Invalid reference found at path '" + newPath + "'. Resource type '"
                                                                                                + referencedId.getResourceType() + "' is not valid for this path");
                                                                        }
                                                                }
                                                        }
                                                }
                                        }
                                }
                        }
                }
        }

        protected void validateMetaCount(int theMetaCount) {
                if (myStorageSettings.getResourceMetaCountHardLimit() != null) {
                        if (theMetaCount > myStorageSettings.getResourceMetaCountHardLimit()) {
                                throw new UnprocessableEntityException(Msg.code(932) + "Resource contains " + theMetaCount
                                                + " meta entries (tag/profile/security label), maximum is "
                                                + myStorageSettings.getResourceMetaCountHardLimit());
                        }
                }
        }

        /**
         * This method is invoked immediately before storing a new resource, or an update to an existing resource to allow the DAO to ensure that it is valid for persistence. By default, checks for the
         * "subsetted" tag and rejects resources which have it. Subclasses should call the superclass implementation to preserve this check.
         *
         * @param theResource     The resource that is about to be persisted
         * @param theEntityToSave TODO
         */
        protected void validateResourceForStorage(T theResource, ResourceTable theEntityToSave) {
                Object tag = null;

                int totalMetaCount = 0;

                if (theResource instanceof IResource) {
                        IResource res = (IResource) theResource;
                        TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(res);
                        if (tagList != null) {
                                tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM_DSTU3, Constants.TAG_SUBSETTED_CODE);
                                totalMetaCount += tagList.size();
                        }
                        List<IdDt> profileList = ResourceMetadataKeyEnum.PROFILES.get(res);
                        if (profileList != null) {
                                totalMetaCount += profileList.size();
                        }
                } else {
                        IAnyResource res = (IAnyResource) theResource;
                        tag = res.getMeta().getTag(Constants.TAG_SUBSETTED_SYSTEM_DSTU3, Constants.TAG_SUBSETTED_CODE);
                        totalMetaCount += res.getMeta().getTag().size();
                        totalMetaCount += res.getMeta().getProfile().size();
                        totalMetaCount += res.getMeta().getSecurity().size();
                }

                if (tag != null) {
                        throw new UnprocessableEntityException(
                                        Msg.code(933)
                                                        + "Resource contains the 'subsetted' tag, and must not be stored as it may contain a subset of available data");
                }

                if (getStorageSettings().isEnforceReferenceTargetTypes()) {
                        String resName = getContext().getResourceType(theResource);
                        validateChildReferenceTargetTypes(theResource, resName);
                }

                validateMetaCount(totalMetaCount);
        }

        @PostConstruct
        public void start() {}

        @VisibleForTesting
        public void setStorageSettingsForUnitTest(JpaStorageSettings theStorageSettings) {
                myStorageSettings = theStorageSettings;
        }

        public void populateFullTextFields(
                        final FhirContext theContext,
                        final IBaseResource theResource,
                        ResourceTable theEntity,
                        ResourceIndexedSearchParams theNewParams) {
                if (theEntity.getDeleted() != null) {
                        theEntity.setNarrativeText(null);
                        theEntity.setContentText(null);
                } else {
                        if (myStorageSettings.isHibernateSearchIndexFullText()) {
                                theEntity.setNarrativeText(parseNarrativeTextIntoWords(theResource));
                                theEntity.setContentText(parseContentTextIntoWords(theContext, theResource));
                        }
                        if (myStorageSettings.isHibernateSearchIndexSearchParams()) {
                                ExtendedHSearchIndexData hSearchIndexData =
                                                myFulltextSearchSvc.extractLuceneIndexData(theResource, theEntity, theNewParams);
                                theEntity.setLuceneIndexData(hSearchIndexData);
                        }
                }
        }

        @VisibleForTesting
        public void setPartitionSettingsForUnitTest(PartitionSettings thePartitionSettings) {
                myPartitionSettings = thePartitionSettings;
        }

        /**
         * Do not call this method outside of unit tests
         */
        @VisibleForTesting
        public void setJpaStorageResourceParserForUnitTest(IJpaStorageResourceParser theJpaStorageResourceParser) {
                myJpaStorageResourceParser = theJpaStorageResourceParser;
        }

        @SuppressWarnings("unchecked")
        public static String parseContentTextIntoWords(FhirContext theContext, IBaseResource theResource) {

                Class<IPrimitiveType<String>> stringType = (Class<IPrimitiveType<String>>)
                                theContext.getElementDefinition("string").getImplementingClass();

                StringBuilder retVal = new StringBuilder();
                List<IPrimitiveType<String>> childElements =
                                theContext.newTerser().getAllPopulatedChildElementsOfType(theResource, stringType);
                for (IPrimitiveType<String> nextType : childElements) {
                        if (stringType.equals(nextType.getClass())) {
                                String nextValue = nextType.getValueAsString();
                                if (isNotBlank(nextValue)) {
                                        retVal.append(nextValue.replace("\n", " ").replace("\r", " "));
                                        retVal.append("\n");
                                }
                        }
                }
                return retVal.toString();
        }

        public static String decodeResource(byte[] theResourceBytes, ResourceEncodingEnum theResourceEncoding) {
                String resourceText = null;
                switch (theResourceEncoding) {
                        case JSON:
                                resourceText = new String(theResourceBytes, Charsets.UTF_8);
                                break;
                        case JSONC:
                                resourceText = GZipUtil.decompress(theResourceBytes);
                                break;
                        case DEL:
                        case ESR:
                                break;
                }
                return resourceText;
        }

        private static String parseNarrativeTextIntoWords(IBaseResource theResource) {

                StringBuilder b = new StringBuilder();
                if (theResource instanceof IResource) {
                        IResource resource = (IResource) theResource;
                        List<XMLEvent> xmlEvents = XmlUtil.parse(resource.getText().getDiv().getValue());
                        if (xmlEvents != null) {
                                for (XMLEvent next : xmlEvents) {
                                        if (next.isCharacters()) {
                                                Characters characters = next.asCharacters();
                                                b.append(characters.getData()).append(" ");
                                        }
                                }
                        }
                } else if (theResource instanceof IDomainResource) {
                        IDomainResource resource = (IDomainResource) theResource;
                        try {
                                String divAsString = resource.getText().getDivAsString();
                                List<XMLEvent> xmlEvents = XmlUtil.parse(divAsString);
                                if (xmlEvents != null) {
                                        for (XMLEvent next : xmlEvents) {
                                                if (next.isCharacters()) {
                                                        Characters characters = next.asCharacters();
                                                        b.append(characters.getData()).append(" ");
                                                }
                                        }
                                }
                        } catch (Exception e) {
                                throw new DataFormatException(Msg.code(934) + "Unable to convert DIV to string", e);
                        }
                }
                return b.toString();
        }

        @VisibleForTesting
        public static void setDisableIncrementOnUpdateForUnitTest(boolean theDisableIncrementOnUpdateForUnitTest) {
                ourDisableIncrementOnUpdateForUnitTest = theDisableIncrementOnUpdateForUnitTest;
        }

        /**
         * Do not call this method outside of unit tests
         */
        @VisibleForTesting
        public static void setValidationDisabledForUnitTest(boolean theValidationDisabledForUnitTest) {
                ourValidationDisabledForUnitTest = theValidationDisabledForUnitTest;
        }

        private enum CreateOrUpdateByMatch {
                CREATE,
                UPDATE
        }
}