/*
 * #%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.search.builder;

import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ComboSearchParamType;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
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.DaoRegistry;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
import ca.uhn.fhir.jpa.dao.IResultIterator;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTagDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.search.ResourceNotFoundInIndexException;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.dao.JpaPidFk;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.BaseTag;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTablePk;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTag;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.search.SearchBuilderLoadIncludesParameters;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.search.SearchConstants;
import ca.uhn.fhir.jpa.search.builder.models.ResolvedSearchQueryExecutor;
import ca.uhn.fhir.jpa.search.builder.models.SearchQueryProperties;
import ca.uhn.fhir.jpa.search.builder.sql.GeneratedSql;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryExecutor;
import ca.uhn.fhir.jpa.search.builder.sql.SqlObjectFactory;
import ca.uhn.fhir.jpa.search.lastn.IElasticsearchSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.util.Dstu3DistanceHelper;
import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
import ca.uhn.fhir.jpa.searchparam.util.LastNParameterHelper;
import ca.uhn.fhir.jpa.util.BaseIterator;
import ca.uhn.fhir.jpa.util.CartesianProductUtil;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.jpa.util.SqlQueryList;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.BaseParamWithPrefix;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.system.HapiSystemProperties;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.StringUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ListMultimap;
import com.google.common.collect.Lists;
import com.google.common.collect.MultimapBuilder;
import com.healthmarketscience.sqlbuilder.Condition;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import jakarta.persistence.EntityManager;
import jakarta.persistence.PersistenceContext;
import jakarta.persistence.PersistenceContextType;
import jakarta.persistence.Query;
import jakarta.persistence.Tuple;
import jakarta.persistence.TypedQuery;
import jakarta.persistence.criteria.CriteriaBuilder;
import org.apache.commons.collections4.ListUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.transaction.support.TransactionSynchronizationManager;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;

import static ca.uhn.fhir.jpa.model.util.JpaConstants.UNDESIRED_RESOURCE_LINKAGES_FOR_EVERYTHING_ON_PATIENT_INSTANCE;
import static ca.uhn.fhir.jpa.search.builder.QueryStack.LOCATION_POSITION;
import static ca.uhn.fhir.jpa.search.builder.QueryStack.SearchForIdsParams.with;
import static ca.uhn.fhir.jpa.util.InClauseNormalizer.normalizeIdListForInClause;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.EQUAL;
import static java.util.Objects.requireNonNull;
import static org.apache.commons.collections4.CollectionUtils.isNotEmpty;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.stripStart;

/**
 * The SearchBuilder is responsible for actually forming the SQL query that handles
 * searches for resources
 */
public class SearchBuilder implements ISearchBuilder<JpaPid> {

        /**
         * See loadResourcesByPid
         * for an explanation of why we use the constant 800
         */
        // NB: keep public
        @Deprecated
        public static final int MAXIMUM_PAGE_SIZE = SearchConstants.MAX_PAGE_SIZE;

        public static final String RESOURCE_ID_ALIAS = "resource_id";
        public static final String PARTITION_ID_ALIAS = "partition_id";
        public static final String RESOURCE_VERSION_ALIAS = "resource_version";
        private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
        private static final JpaPid NO_MORE = JpaPid.fromId(-1L);
        private static final String MY_SOURCE_RESOURCE_PID = "mySourceResourcePid";
        private static final String MY_SOURCE_RESOURCE_PARTITION_ID = "myPartitionIdValue";
        private static final String MY_SOURCE_RESOURCE_TYPE = "mySourceResourceType";
        private static final String MY_TARGET_RESOURCE_PID = "myTargetResourcePid";
        private static final String MY_TARGET_RESOURCE_PARTITION_ID = "myTargetResourcePartitionId";
        private static final String MY_TARGET_RESOURCE_TYPE = "myTargetResourceType";
        private static final String MY_TARGET_RESOURCE_VERSION = "myTargetResourceVersion";
        public static final JpaPid[] EMPTY_JPA_PID_ARRAY = new JpaPid[0];
        public static boolean myUseMaxPageSize50ForTest = false;
        public static Integer myMaxPageSizeForTests = null;
        protected final IInterceptorBroadcaster myInterceptorBroadcaster;
        protected final IResourceTagDao myResourceTagDao;
        private String myResourceName;
        private final Class<? extends IBaseResource> myResourceType;
        private final HapiFhirLocalContainerEntityManagerFactoryBean myEntityManagerFactory;
        private final SqlObjectFactory mySqlBuilderFactory;
        private final HibernatePropertiesProvider myDialectProvider;
        private final ISearchParamRegistry mySearchParamRegistry;
        private final PartitionSettings myPartitionSettings;
        private final DaoRegistry myDaoRegistry;
        private final FhirContext myContext;
        private final IIdHelperService<JpaPid> myIdHelperService;
        private final JpaStorageSettings myStorageSettings;

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

        private CriteriaBuilder myCriteriaBuilder;
        private SearchParameterMap myParams;
        private String mySearchUuid;
        private int myFetchSize;

        private boolean myRequiresTotal;

        /**
         * @see SearchBuilder#setDeduplicateInDatabase(boolean)
         */
        private Set<JpaPid> myPidSet;

        private boolean myHasNextIteratorQuery = false;
        private RequestPartitionId myRequestPartitionId;

        private SearchQueryProperties mySearchProperties;

        @Autowired(required = false)
        private IFulltextSearchSvc myFulltextSearchSvc;

        @Autowired(required = false)
        private IElasticsearchSvc myIElasticsearchSvc;

        @Autowired
        private IJpaStorageResourceParser myJpaStorageResourceParser;

        @Autowired
        private IResourceHistoryTableDao myResourceHistoryTableDao;

        @Autowired
        private IResourceHistoryTagDao myResourceHistoryTagDao;

        @Autowired
        private IRequestPartitionHelperSvc myPartitionHelperSvc;

        /**
         * Constructor
         */
        @SuppressWarnings({"rawtypes", "unchecked"})
        public SearchBuilder(
                        String theResourceName,
                        JpaStorageSettings theStorageSettings,
                        HapiFhirLocalContainerEntityManagerFactoryBean theEntityManagerFactory,
                        SqlObjectFactory theSqlBuilderFactory,
                        HibernatePropertiesProvider theDialectProvider,
                        ISearchParamRegistry theSearchParamRegistry,
                        PartitionSettings thePartitionSettings,
                        IInterceptorBroadcaster theInterceptorBroadcaster,
                        IResourceTagDao theResourceTagDao,
                        DaoRegistry theDaoRegistry,
                        FhirContext theContext,
                        IIdHelperService theIdHelperService,
                        Class<? extends IBaseResource> theResourceType) {
                myResourceName = theResourceName;
                myResourceType = theResourceType;
                myStorageSettings = theStorageSettings;

                myEntityManagerFactory = theEntityManagerFactory;
                mySqlBuilderFactory = theSqlBuilderFactory;
                myDialectProvider = theDialectProvider;
                mySearchParamRegistry = theSearchParamRegistry;
                myPartitionSettings = thePartitionSettings;
                myInterceptorBroadcaster = theInterceptorBroadcaster;
                myResourceTagDao = theResourceTagDao;
                myDaoRegistry = theDaoRegistry;
                myContext = theContext;
                myIdHelperService = theIdHelperService;

                mySearchProperties = new SearchQueryProperties();
        }

        @VisibleForTesting
        void setResourceName(String theName) {
                myResourceName = theName;
        }

        @Override
        public void setMaxResultsToFetch(Integer theMaxResultsToFetch) {
                mySearchProperties.setMaxResultsRequested(theMaxResultsToFetch);
        }

        @Override
        public void setDeduplicateInDatabase(boolean theShouldDeduplicateInDB) {
                mySearchProperties.setDeduplicateInDatabase(theShouldDeduplicateInDB);
        }

        @Override
        public void setRequireTotal(boolean theRequireTotal) {
                myRequiresTotal = theRequireTotal;
        }

        @Override
        public boolean requiresTotal() {
                return myRequiresTotal;
        }

        private void searchForIdsWithAndOr(
                        SearchQueryBuilder theSearchSqlBuilder,
                        QueryStack theQueryStack,
                        @Nonnull SearchParameterMap theParams,
                        RequestDetails theRequest) {
                myParams = theParams;
                mySearchProperties.setSortSpec(myParams.getSort());

                // Remove any empty parameters
                theParams.clean();

                // For DSTU3, pull out near-distance first so when it comes time to evaluate near, we already know the distance
                if (myContext.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
                        Dstu3DistanceHelper.setNearDistance(myResourceType, theParams);
                }

                // Attempt to lookup via composite unique key.
                if (isCompositeUniqueSpCandidate()) {
                        attemptComboUniqueSpProcessing(theQueryStack, theParams, theRequest);
                }

                // Handle _id and _tag last, since they can typically be tacked onto a different parameter
                List<String> paramNames = myParams.keySet().stream()
                                .filter(t -> !t.equals(IAnyResource.SP_RES_ID))
                                .filter(t -> !t.equals(Constants.PARAM_TAG))
                                .collect(Collectors.toList());
                if (myParams.containsKey(IAnyResource.SP_RES_ID)) {
                        paramNames.add(IAnyResource.SP_RES_ID);
                }
                if (myParams.containsKey(Constants.PARAM_TAG)) {
                        paramNames.add(Constants.PARAM_TAG);
                }

                // Handle each parameter
                for (String nextParamName : paramNames) {
                        if (myParams.isLastN() && LastNParameterHelper.isLastNParameter(nextParamName, myContext)) {
                                // Skip parameters for Subject, Patient, Code and Category for LastN as these will be filtered by
                                // Elasticsearch
                                continue;
                        }
                        List<List<IQueryParameterType>> andOrParams = myParams.get(nextParamName);
                        Condition predicate = theQueryStack.searchForIdsWithAndOr(with().setResourceName(myResourceName)
                                        .setParamName(nextParamName)
                                        .setAndOrParams(andOrParams)
                                        .setRequest(theRequest)
                                        .setRequestPartitionId(myRequestPartitionId));
                        if (predicate != null) {
                                theSearchSqlBuilder.addPredicate(predicate);
                        }
                }
        }

        /**
         * A search is a candidate for Composite Unique SP if unique indexes are enabled, there is no EverythingMode, and the
         * parameters all have no modifiers.
         */
        private boolean isCompositeUniqueSpCandidate() {
                return myStorageSettings.isUniqueIndexesEnabled() && myParams.getEverythingMode() == null;
        }

        @SuppressWarnings("ConstantConditions")
        @Override
        public Long createCountQuery(
                        SearchParameterMap theParams,
                        String theSearchUuid,
                        RequestDetails theRequest,
                        @Nonnull RequestPartitionId theRequestPartitionId) {

                assert theRequestPartitionId != null;
                assert TransactionSynchronizationManager.isActualTransactionActive();

                init(theParams, theSearchUuid, theRequestPartitionId);

                if (checkUseHibernateSearch()) {
                        return myFulltextSearchSvc.count(myResourceName, theParams.clone());
                }

                SearchQueryProperties properties = mySearchProperties.clone();
                properties.setDoCountOnlyFlag(true);
                properties.setSortSpec(null); // counts don't require sorts
                properties.setMaxResultsRequested(null);
                properties.setOffset(null);
                List<ISearchQueryExecutor> queries = createQuery(theParams.clone(), properties, theRequest, null);
                if (queries.isEmpty()) {
                        return 0L;
                } else {
                        JpaPid jpaPid = queries.get(0).next();
                        return jpaPid.getId();
                }
        }

        /**
         * @param thePidSet May be null
         */
        @Override
        public void setPreviouslyAddedResourcePids(@Nonnull List<JpaPid> thePidSet) {
                myPidSet = new HashSet<>(thePidSet);
        }

        @SuppressWarnings("ConstantConditions")
        @Override
        public IResultIterator<JpaPid> createQuery(
                        SearchParameterMap theParams,
                        SearchRuntimeDetails theSearchRuntimeDetails,
                        RequestDetails theRequest,
                        @Nonnull RequestPartitionId theRequestPartitionId) {
                assert theRequestPartitionId != null;
                assert TransactionSynchronizationManager.isActualTransactionActive();

                init(theParams, theSearchRuntimeDetails.getSearchUuid(), theRequestPartitionId);

                if (myPidSet == null) {
                        myPidSet = new HashSet<>();
                }

                return new QueryIterator(theSearchRuntimeDetails, theRequest);
        }

        private void init(SearchParameterMap theParams, String theSearchUuid, RequestPartitionId theRequestPartitionId) {
                myCriteriaBuilder = myEntityManager.getCriteriaBuilder();
                // we mutate the params.  Make a private copy.
                myParams = theParams.clone();
                mySearchProperties.setSortSpec(myParams.getSort());
                mySearchUuid = theSearchUuid;
                myRequestPartitionId = theRequestPartitionId;
        }

        /**
         * The query created can be either a count query or the
         * actual query.
         * This is why it takes a SearchQueryProperties object
         * (and doesn't use the local version of it).
         * The properties may differ slightly for whichever
         * query this is.
         */
        private List<ISearchQueryExecutor> createQuery(
                        SearchParameterMap theParams,
                        SearchQueryProperties theSearchProperties,
                        RequestDetails theRequest,
                        SearchRuntimeDetails theSearchRuntimeDetails) {
                ArrayList<ISearchQueryExecutor> queries = new ArrayList<>();

                if (checkUseHibernateSearch()) {
                        // we're going to run at least part of the search against the Fulltext service.

                        // Ugh - we have two different return types for now
                        ISearchQueryExecutor fulltextExecutor = null;
                        List<JpaPid> fulltextMatchIds = null;
                        int resultCount = 0;
                        if (myParams.isLastN()) {
                                fulltextMatchIds = executeLastNAgainstIndex(theRequest, theSearchProperties.getMaxResultsRequested());
                                resultCount = fulltextMatchIds.size();
                        } else if (myParams.getEverythingMode() != null) {
                                fulltextMatchIds = queryHibernateSearchForEverythingPids(theRequest);
                                resultCount = fulltextMatchIds.size();
                        } else {
                                // todo performance MB - some queries must intersect with JPA (e.g. they have a chain, or we haven't
                                // enabled SP indexing).
                                // and some queries don't need JPA.  We only need the scroll when we need to intersect with JPA.
                                // It would be faster to have a non-scrolled search in this case, since creating the scroll requires
                                // extra work in Elastic.
                                // if (eligibleToSkipJPAQuery) fulltextExecutor = myFulltextSearchSvc.searchNotScrolled( ...

                                // we might need to intersect with JPA.  So we might need to traverse ALL results from lucene, not just
                                // a page.
                                fulltextExecutor = myFulltextSearchSvc.searchScrolled(myResourceName, myParams, theRequest);
                        }

                        if (fulltextExecutor == null) {
                                fulltextExecutor =
                                                SearchQueryExecutors.from(fulltextMatchIds != null ? fulltextMatchIds : new ArrayList<>());
                        }

                        if (theSearchRuntimeDetails != null) {
                                theSearchRuntimeDetails.setFoundIndexMatchesCount(resultCount);
                                IInterceptorBroadcaster compositeBroadcaster =
                                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest);
                                if (compositeBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INDEXSEARCH_QUERY_COMPLETE)) {
                                        HookParams params = new HookParams()
                                                        .add(RequestDetails.class, theRequest)
                                                        .addIfMatchesType(ServletRequestDetails.class, theRequest)
                                                        .add(SearchRuntimeDetails.class, theSearchRuntimeDetails);
                                        compositeBroadcaster.callHooks(Pointcut.JPA_PERFTRACE_INDEXSEARCH_QUERY_COMPLETE, params);
                                }
                        }

                        // can we skip the database entirely and return the pid list from here?
                        boolean canSkipDatabase =
                                        // if we processed an AND clause, and it returned nothing, then nothing can match.
                                        !fulltextExecutor.hasNext()
                                                        ||
                                                        // Our hibernate search query doesn't respect partitions yet
                                                        (!myPartitionSettings.isPartitioningEnabled()
                                                                        &&
                                                                        // were there AND terms left?  Then we still need the db.
                                                                        theParams.isEmpty()
                                                                        &&
                                                                        // not every param is a param. :-(
                                                                        theParams.getNearDistanceParam() == null
                                                                        &&
                                                                        // todo MB don't we support _lastUpdated and _offset now?
                                                                        theParams.getLastUpdated() == null
                                                                        && theParams.getEverythingMode() == null
                                                                        && theParams.getOffset() == null);

                        if (canSkipDatabase) {
                                ourLog.trace("Query finished after HSearch.  Skip db query phase");
                                if (theSearchProperties.hasMaxResultsRequested()) {
                                        fulltextExecutor = SearchQueryExecutors.limited(
                                                        fulltextExecutor, theSearchProperties.getMaxResultsRequested());
                                }
                                queries.add(fulltextExecutor);
                        } else {
                                ourLog.trace("Query needs db after HSearch.  Chunking.");
                                // Finish the query in the database for the rest of the search parameters, sorting, partitioning, etc.
                                // We break the pids into chunks that fit in the 1k limit for jdbc bind params.
                                new QueryChunker<JpaPid>()
                                                .chunk(
                                                                fulltextExecutor,
                                                                SearchBuilder.getMaximumPageSize(),
                                                                // for each list of (SearchBuilder.getMaximumPageSize())
                                                                // we create a chunked query and add it to 'queries'
                                                                t -> doCreateChunkedQueries(theParams, t, theSearchProperties, theRequest, queries));
                        }
                } else {
                        // do everything in the database.
                        createChunkedQuery(theParams, theSearchProperties, theRequest, null, queries);
                }

                return queries;
        }

        /**
         * Check to see if query should use Hibernate Search, and error if the query can't continue.
         *
         * @return true if the query should first be processed by Hibernate Search
         * @throws InvalidRequestException if fulltext search is not enabled but the query requires it - _content or _text
         */
        private boolean checkUseHibernateSearch() {
                boolean fulltextEnabled = (myFulltextSearchSvc != null) && !myFulltextSearchSvc.isDisabled();

                if (!fulltextEnabled) {
                        failIfUsed(Constants.PARAM_TEXT);
                        failIfUsed(Constants.PARAM_CONTENT);
                } else {
                        for (SortSpec sortSpec : myParams.getAllChainsInOrder()) {
                                final String paramName = sortSpec.getParamName();
                                if (paramName.contains(".")) {
                                        failIfUsedWithChainedSort(Constants.PARAM_TEXT);
                                        failIfUsedWithChainedSort(Constants.PARAM_CONTENT);
                                }
                        }
                }

                // someday we'll want a query planner to figure out if we _should_ or _must_ use the ft index, not just if we
                // can.
                return fulltextEnabled
                                && myParams != null
                                && myParams.getSearchContainedMode() == SearchContainedModeEnum.FALSE
                                && myFulltextSearchSvc.canUseHibernateSearch(myResourceName, myParams)
                                && myFulltextSearchSvc.supportsAllSortTerms(myResourceName, myParams);
        }

        private void failIfUsed(String theParamName) {
                if (myParams.containsKey(theParamName)) {
                        throw new InvalidRequestException(Msg.code(1192)
                                        + "Fulltext search is not enabled on this service, can not process parameter: " + theParamName);
                }
        }

        private void failIfUsedWithChainedSort(String theParamName) {
                if (myParams.containsKey(theParamName)) {
                        throw new InvalidRequestException(Msg.code(2524)
                                        + "Fulltext search combined with chained sorts are not supported, can not process parameter: "
                                        + theParamName);
                }
        }

        private List<JpaPid> executeLastNAgainstIndex(RequestDetails theRequestDetails, Integer theMaximumResults) {
                // Can we use our hibernate search generated index on resource to support lastN?:
                if (myStorageSettings.isAdvancedHSearchIndexing()) {
                        if (myFulltextSearchSvc == null) {
                                throw new InvalidRequestException(Msg.code(2027)
                                                + "LastN operation is not enabled on this service, can not process this request");
                        }
                        return myFulltextSearchSvc.lastN(myParams, theMaximumResults).stream()
                                        .map(t -> (JpaPid) t)
                                        .collect(Collectors.toList());
                } else {
                        throw new InvalidRequestException(
                                        Msg.code(2033) + "LastN operation is not enabled on this service, can not process this request");
                }
        }

        private List<JpaPid> queryHibernateSearchForEverythingPids(RequestDetails theRequestDetails) {
                JpaPid pid = null;
                if (myParams.get(IAnyResource.SP_RES_ID) != null) {
                        String idParamValue;
                        IQueryParameterType idParam =
                                        myParams.get(IAnyResource.SP_RES_ID).get(0).get(0);
                        if (idParam instanceof TokenParam) {
                                TokenParam idParm = (TokenParam) idParam;
                                idParamValue = idParm.getValue();
                        } else {
                                StringParam idParm = (StringParam) idParam;
                                idParamValue = idParm.getValue();
                        }

                        pid = myIdHelperService
                                        .resolveResourceIdentity(
                                                        myRequestPartitionId,
                                                        myResourceName,
                                                        idParamValue,
                                                        ResolveIdentityMode.includeDeleted().cacheOk())
                                        .getPersistentId();
                }
                return myFulltextSearchSvc.everything(myResourceName, myParams, pid, theRequestDetails);
        }

        private void doCreateChunkedQueries(
                        SearchParameterMap theParams,
                        List<JpaPid> thePids,
                        SearchQueryProperties theSearchQueryProperties,
                        RequestDetails theRequest,
                        ArrayList<ISearchQueryExecutor> theQueries) {

                if (thePids.size() < getMaximumPageSize()) {
                        thePids = normalizeIdListForInClause(thePids);
                }
                theSearchQueryProperties.setMaxResultsRequested(thePids.size());
                createChunkedQuery(theParams, theSearchQueryProperties, theRequest, thePids, theQueries);
        }

        /**
         * Combs through the params for any _id parameters and extracts the PIDs for them
         */
        private void extractTargetPidsFromIdParams(Set<JpaPid> theTargetPids) {
                // get all the IQueryParameterType objects
                // for _id -> these should all be StringParam values
                HashSet<IIdType> ids = new HashSet<>();
                List<List<IQueryParameterType>> params = myParams.get(IAnyResource.SP_RES_ID);
                for (List<IQueryParameterType> paramList : params) {
                        for (IQueryParameterType param : paramList) {
                                String id;
                                if (param instanceof StringParam) {
                                        // we expect all _id values to be StringParams
                                        id = ((StringParam) param).getValue();
                                } else if (param instanceof TokenParam) {
                                        id = ((TokenParam) param).getValue();
                                } else {
                                        // we do not expect the _id parameter to be a non-string value
                                        throw new IllegalArgumentException(
                                                        Msg.code(1193) + "_id parameter must be a StringParam or TokenParam");
                                }

                                IIdType idType = myContext.getVersion().newIdType();
                                if (id.contains("/")) {
                                        idType.setValue(id);
                                } else {
                                        idType.setValue(myResourceName + "/" + id);
                                }
                                ids.add(idType);
                        }
                }

                // fetch our target Pids
                // this will throw if an id is not found
                Map<IIdType, IResourceLookup<JpaPid>> idToIdentity = myIdHelperService.resolveResourceIdentities(
                                myRequestPartitionId,
                                new ArrayList<>(ids),
                                ResolveIdentityMode.failOnDeleted().noCacheUnlessDeletesDisabled());

                // add the pids to targetPids
                for (IResourceLookup<JpaPid> pid : idToIdentity.values()) {
                        theTargetPids.add(pid.getPersistentId());
                }
        }

        private void createChunkedQuery(
                        SearchParameterMap theParams,
                        SearchQueryProperties theSearchProperties,
                        RequestDetails theRequest,
                        List<JpaPid> thePidList,
                        List<ISearchQueryExecutor> theSearchQueryExecutors) {
                if (myParams.getEverythingMode() != null) {
                        createChunkedQueryForEverythingSearch(
                                        theRequest, theParams, theSearchProperties, thePidList, theSearchQueryExecutors);
                } else {
                        createChunkedQueryNormalSearch(
                                        theParams, theSearchProperties, theRequest, thePidList, theSearchQueryExecutors);
                }
        }

        private void createChunkedQueryNormalSearch(
                        SearchParameterMap theParams,
                        SearchQueryProperties theSearchProperties,
                        RequestDetails theRequest,
                        List<JpaPid> thePidList,
                        List<ISearchQueryExecutor> theSearchQueryExecutors) {
                SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(
                                myContext,
                                myStorageSettings,
                                myPartitionSettings,
                                myRequestPartitionId,
                                myResourceName,
                                mySqlBuilderFactory,
                                myDialectProvider,
                                theSearchProperties.isDoCountOnlyFlag());
                QueryStack queryStack3 = new QueryStack(
                                theRequest,
                                theParams,
                                myStorageSettings,
                                myContext,
                                sqlBuilder,
                                mySearchParamRegistry,
                                myPartitionSettings);

                if (theParams.keySet().size() > 1
                                || theParams.getSort() != null
                                || theParams.keySet().contains(Constants.PARAM_HAS)
                                || isPotentiallyContainedReferenceParameterExistsAtRoot(theParams)) {
                        List<RuntimeSearchParam> activeComboParams = mySearchParamRegistry.getActiveComboSearchParams(
                                        myResourceName, theParams.keySet(), ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                        if (activeComboParams.isEmpty()) {
                                sqlBuilder.setNeedResourceTableRoot(true);
                        }
                }

                /*
                 * If we're doing a filter, always use the resource table as the root - This avoids the possibility of
                 * specific filters with ORs as their root from working around the natural resource type / deletion
                 * status / partition IDs built into queries.
                 */
                if (theParams.containsKey(Constants.PARAM_FILTER)) {
                        Condition partitionIdPredicate = sqlBuilder
                                        .getOrCreateResourceTablePredicateBuilder()
                                        .createPartitionIdPredicate(myRequestPartitionId);
                        if (partitionIdPredicate != null) {
                                sqlBuilder.addPredicate(partitionIdPredicate);
                        }
                }

                // Normal search
                searchForIdsWithAndOr(sqlBuilder, queryStack3, myParams, theRequest);

                // If we haven't added any predicates yet, we're doing a search for all resources. Make sure we add the
                // partition ID predicate in that case.
                if (!sqlBuilder.haveAtLeastOnePredicate()) {
                        Condition partitionIdPredicate = sqlBuilder
                                        .getOrCreateResourceTablePredicateBuilder()
                                        .createPartitionIdPredicate(myRequestPartitionId);
                        if (partitionIdPredicate != null) {
                                sqlBuilder.addPredicate(partitionIdPredicate);
                        }
                }

                // Add PID list predicate for full text search and/or lastn operation
                addPidListPredicate(thePidList, sqlBuilder);

                // Last updated
                addLastUpdatePredicate(sqlBuilder);

                /*
                 * Exclude the pids already in the previous iterator. This is an optimization, as opposed
                 * to something needed to guarantee correct results.
                 *
                 * Why do we need it? Suppose for example, a query like:
                 *    Observation?category=foo,bar,baz
                 * And suppose you have many resources that have all 3 of these category codes. In this case
                 * the SQL query will probably return the same PIDs multiple times, and if this happens enough
                 * we may exhaust the query results without getting enough distinct results back. When that
                 * happens we re-run the query with a larger limit. Excluding results we already know about
                 * tries to ensure that we get new unique results.
                 *
                 * The challenge with that though is that lots of DBs have an issue with too many
                 * parameters in one query. So we only do this optimization if there aren't too
                 * many results.
                 */
                if (myHasNextIteratorQuery) {
                        if (myPidSet.size() + sqlBuilder.countBindVariables() < 900) {
                                sqlBuilder.excludeResourceIdsPredicate(myPidSet);
                        }
                }

                /*
                 * If offset is present, we want to deduplicate the results by using GROUP BY;
                 * OR
                 * if the MaxResultsToFetch is null, we are requesting "everything",
                 * so we'll let the db do the deduplication (instead of in-memory)
                 */
                if (theSearchProperties.isDeduplicateInDatabase()) {
                        queryStack3.addGrouping();
                        queryStack3.setUseAggregate(true);
                }

                /*
                 * Sort
                 *
                 * If we have a sort, we wrap the criteria search (the search that actually
                 * finds the appropriate resources) in an outer search which is then sorted
                 */
                if (theSearchProperties.hasSort()) {
                        assert !theSearchProperties.isDoCountOnlyFlag();

                        createSort(queryStack3, theSearchProperties.getSortSpec(), theParams);
                }

                /*
                 * Now perform the search
                 */
                executeSearch(theSearchProperties, theSearchQueryExecutors, sqlBuilder);
        }

        private void executeSearch(
                        SearchQueryProperties theProperties,
                        List<ISearchQueryExecutor> theSearchQueryExecutors,
                        SearchQueryBuilder sqlBuilder) {
                GeneratedSql generatedSql =
                                sqlBuilder.generate(theProperties.getOffset(), theProperties.getMaxResultsRequested());
                if (!generatedSql.isMatchNothing()) {
                        SearchQueryExecutor executor =
                                        mySqlBuilderFactory.newSearchQueryExecutor(generatedSql, theProperties.getMaxResultsRequested());
                        theSearchQueryExecutors.add(executor);
                }
        }

        private void createChunkedQueryForEverythingSearch(
                        RequestDetails theRequest,
                        SearchParameterMap theParams,
                        SearchQueryProperties theSearchQueryProperties,
                        List<JpaPid> thePidList,
                        List<ISearchQueryExecutor> theSearchQueryExecutors) {

                SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(
                                myContext,
                                myStorageSettings,
                                myPartitionSettings,
                                myRequestPartitionId,
                                null,
                                mySqlBuilderFactory,
                                myDialectProvider,
                                theSearchQueryProperties.isDoCountOnlyFlag());

                QueryStack queryStack3 = new QueryStack(
                                theRequest,
                                theParams,
                                myStorageSettings,
                                myContext,
                                sqlBuilder,
                                mySearchParamRegistry,
                                myPartitionSettings);

                JdbcTemplate jdbcTemplate = initializeJdbcTemplate(theSearchQueryProperties.getMaxResultsRequested());

                Set<JpaPid> targetPids = new HashSet<>();
                if (myParams.get(IAnyResource.SP_RES_ID) != null) {

                        extractTargetPidsFromIdParams(targetPids);

                        // add the target pids to our executors as the first
                        // results iterator to go through
                        theSearchQueryExecutors.add(new ResolvedSearchQueryExecutor(new ArrayList<>(targetPids)));
                } else {
                        // For Everything queries, we make the query root by the ResourceLink table, since this query
                        // is basically a reverse-include search. For type/Everything (as opposed to instance/Everything)
                        // the one problem with this approach is that it doesn't catch Patients that have absolutely
                        // nothing linked to them. So we do one additional query to make sure we catch those too.
                        SearchQueryBuilder fetchPidsSqlBuilder = new SearchQueryBuilder(
                                        myContext,
                                        myStorageSettings,
                                        myPartitionSettings,
                                        myRequestPartitionId,
                                        myResourceName,
                                        mySqlBuilderFactory,
                                        myDialectProvider,
                                        theSearchQueryProperties.isDoCountOnlyFlag());
                        GeneratedSql allTargetsSql = fetchPidsSqlBuilder.generate(
                                        theSearchQueryProperties.getOffset(), mySearchProperties.getMaxResultsRequested());
                        String sql = allTargetsSql.getSql();
                        Object[] args = allTargetsSql.getBindVariables().toArray(new Object[0]);

                        List<JpaPid> output =
                                        jdbcTemplate.query(sql, args, new JpaPidRowMapper(myPartitionSettings.isPartitioningEnabled()));

                        // we add a search executor to fetch unlinked patients first
                        theSearchQueryExecutors.add(new ResolvedSearchQueryExecutor(output));
                }

                List<String> typeSourceResources = new ArrayList<>();
                if (myParams.get(Constants.PARAM_TYPE) != null) {
                        typeSourceResources.addAll(extractTypeSourceResourcesFromParams());
                }

                queryStack3.addPredicateEverythingOperation(
                                myResourceName, typeSourceResources, targetPids.toArray(EMPTY_JPA_PID_ARRAY));

                // Add PID list predicate for full text search and/or lastn operation
                addPidListPredicate(thePidList, sqlBuilder);

                /*
                 * If offset is present, we want deduplicate the results by using GROUP BY
                 * ORDER BY is required to make sure we return unique results for each page
                 */
                if (theSearchQueryProperties.hasOffset()) {
                        queryStack3.addGrouping();
                        queryStack3.addOrdering();
                        queryStack3.setUseAggregate(true);
                }

                /*
                 * Now perform the search
                 */
                executeSearch(theSearchQueryProperties, theSearchQueryExecutors, sqlBuilder);
        }

        private void addPidListPredicate(List<JpaPid> thePidList, SearchQueryBuilder theSqlBuilder) {
                if (thePidList != null && !thePidList.isEmpty()) {
                        theSqlBuilder.addResourceIdsPredicate(thePidList);
                }
        }

        private void addLastUpdatePredicate(SearchQueryBuilder theSqlBuilder) {
                DateRangeParam lu = myParams.getLastUpdated();
                if (lu != null && !lu.isEmpty()) {
                        Condition lastUpdatedPredicates = theSqlBuilder.addPredicateLastUpdated(lu);
                        theSqlBuilder.addPredicate(lastUpdatedPredicates);
                }
        }

        private JdbcTemplate initializeJdbcTemplate(Integer theMaximumResults) {
                JdbcTemplate jdbcTemplate = new JdbcTemplate(myEntityManagerFactory.getDataSource());
                jdbcTemplate.setFetchSize(myFetchSize);
                if (theMaximumResults != null) {
                        jdbcTemplate.setMaxRows(theMaximumResults);
                }
                return jdbcTemplate;
        }

        private Collection<String> extractTypeSourceResourcesFromParams() {

                List<List<IQueryParameterType>> listOfList = myParams.get(Constants.PARAM_TYPE);

                // first off, let's flatten the list of list
                List<IQueryParameterType> iQueryParameterTypesList =
                                listOfList.stream().flatMap(List::stream).collect(Collectors.toList());

                // then, extract all elements of each CSV into one big list
                List<String> resourceTypes = iQueryParameterTypesList.stream()
                                .map(param -> ((StringParam) param).getValue())
                                .map(csvString -> List.of(csvString.split(",")))
                                .flatMap(List::stream)
                                .collect(Collectors.toList());

                Set<String> knownResourceTypes = myContext.getResourceTypes();

                // remove leading/trailing whitespaces if any and remove duplicates
                Set<String> retVal = new HashSet<>();

                for (String type : resourceTypes) {
                        String trimmed = type.trim();
                        if (!knownResourceTypes.contains(trimmed)) {
                                throw new ResourceNotFoundException(
                                                Msg.code(2197) + "Unknown resource type '" + trimmed + "' in _type parameter.");
                        }
                        retVal.add(trimmed);
                }

                return retVal;
        }

        private boolean isPotentiallyContainedReferenceParameterExistsAtRoot(SearchParameterMap theParams) {
                return myStorageSettings.isIndexOnContainedResources()
                                && theParams.values().stream()
                                                .flatMap(Collection::stream)
                                                .flatMap(Collection::stream)
                                                .anyMatch(ReferenceParam.class::isInstance);
        }

        private void createSort(QueryStack theQueryStack, SortSpec theSort, SearchParameterMap theParams) {
                if (theSort == null || isBlank(theSort.getParamName())) {
                        return;
                }

                boolean ascending = (theSort.getOrder() == null) || (theSort.getOrder() == SortOrderEnum.ASC);

                if (IAnyResource.SP_RES_ID.equals(theSort.getParamName())) {

                        theQueryStack.addSortOnResourceId(ascending);

                } else if (Constants.PARAM_PID.equals(theSort.getParamName())) {

                        theQueryStack.addSortOnResourcePID(ascending);

                } else if (Constants.PARAM_LASTUPDATED.equals(theSort.getParamName())) {

                        theQueryStack.addSortOnLastUpdated(ascending);

                } else {
                        RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
                                        myResourceName, theSort.getParamName(), ISearchParamRegistry.SearchParamLookupContextEnum.SORT);

                        /*
                         * If we have a sort like _sort=subject.name and we  have an
                         * uplifted refchain for that combination we can do it more efficiently
                         * by using the index associated with the uplifted refchain. In this case,
                         * we need to find the actual target search parameter (corresponding
                         * to "name" in this example) so that we know what datatype it is.
                         */
                        String paramName = theSort.getParamName();
                        if (param == null && myStorageSettings.isIndexOnUpliftedRefchains()) {
                                String[] chains = StringUtils.split(paramName, '.');
                                if (chains.length == 2) {

                                        // Given: Encounter?_sort=Patient:subject.name
                                        String referenceParam = chains[0]; // subject
                                        String referenceParamTargetType = null; // Patient
                                        String targetParam = chains[1]; // name

                                        int colonIdx = referenceParam.indexOf(':');
                                        if (colonIdx > -1) {
                                                referenceParamTargetType = referenceParam.substring(0, colonIdx);
                                                referenceParam = referenceParam.substring(colonIdx + 1);
                                        }
                                        RuntimeSearchParam outerParam = mySearchParamRegistry.getActiveSearchParam(
                                                        myResourceName, referenceParam, ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
                                        if (outerParam == null) {
                                                throwInvalidRequestExceptionForUnknownSortParameter(myResourceName, referenceParam);
                                        } else if (outerParam.hasUpliftRefchain(targetParam)) {
                                                for (String nextTargetType : outerParam.getTargets()) {
                                                        if (referenceParamTargetType != null && !referenceParamTargetType.equals(nextTargetType)) {
                                                                continue;
                                                        }
                                                        RuntimeSearchParam innerParam = mySearchParamRegistry.getActiveSearchParam(
                                                                        nextTargetType,
                                                                        targetParam,
                                                                        ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
                                                        if (innerParam != null) {
                                                                param = innerParam;
                                                                break;
                                                        }
                                                }
                                        }
                                }
                        }

                        int colonIdx = paramName.indexOf(':');
                        String referenceTargetType = null;
                        if (colonIdx > -1) {
                                referenceTargetType = paramName.substring(0, colonIdx);
                                paramName = paramName.substring(colonIdx + 1);
                        }

                        int dotIdx = paramName.indexOf('.');
                        String chainName = null;
                        if (param == null && dotIdx > -1) {
                                chainName = paramName.substring(dotIdx + 1);
                                paramName = paramName.substring(0, dotIdx);
                                if (chainName.contains(".")) {
                                        String msg = myContext
                                                        .getLocalizer()
                                                        .getMessageSanitized(
                                                                        BaseStorageDao.class,
                                                                        "invalidSortParameterTooManyChains",
                                                                        paramName + "." + chainName);
                                        throw new InvalidRequestException(Msg.code(2286) + msg);
                                }
                        }

                        if (param == null) {
                                param = mySearchParamRegistry.getActiveSearchParam(
                                                myResourceName, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
                        }

                        if (param == null) {
                                throwInvalidRequestExceptionForUnknownSortParameter(getResourceName(), paramName);
                        }

                        // param will never be null here (the above line throws if it does)
                        // this is just to prevent the warning
                        assert param != null;
                        if (isNotBlank(chainName) && param.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
                                throw new InvalidRequestException(
                                                Msg.code(2285) + "Invalid chain, " + paramName + " is not a reference SearchParameter");
                        }

                        switch (param.getParamType()) {
                                case STRING:
                                        theQueryStack.addSortOnString(myResourceName, paramName, ascending);
                                        break;
                                case DATE:
                                        theQueryStack.addSortOnDate(myResourceName, paramName, ascending);
                                        break;
                                case REFERENCE:
                                        theQueryStack.addSortOnResourceLink(
                                                        myResourceName, referenceTargetType, paramName, chainName, ascending, theParams);
                                        break;
                                case TOKEN:
                                        theQueryStack.addSortOnToken(myResourceName, paramName, ascending);
                                        break;
                                case NUMBER:
                                        theQueryStack.addSortOnNumber(myResourceName, paramName, ascending);
                                        break;
                                case URI:
                                        theQueryStack.addSortOnUri(myResourceName, paramName, ascending);
                                        break;
                                case QUANTITY:
                                        theQueryStack.addSortOnQuantity(myResourceName, paramName, ascending);
                                        break;
                                case COMPOSITE:
                                        List<RuntimeSearchParam> compositeList =
                                                        JpaParamUtil.resolveComponentParameters(mySearchParamRegistry, param);
                                        if (compositeList == null) {
                                                throw new InvalidRequestException(Msg.code(1195) + "The composite _sort parameter " + paramName
                                                                + " is not defined by the resource " + myResourceName);
                                        }
                                        if (compositeList.size() != 2) {
                                                throw new InvalidRequestException(Msg.code(1196) + "The composite _sort parameter " + paramName
                                                                + " must have 2 composite types declared in parameter annotation, found "
                                                                + compositeList.size());
                                        }
                                        RuntimeSearchParam left = compositeList.get(0);
                                        RuntimeSearchParam right = compositeList.get(1);

                                        createCompositeSort(theQueryStack, left.getParamType(), left.getName(), ascending);
                                        createCompositeSort(theQueryStack, right.getParamType(), right.getName(), ascending);

                                        break;
                                case SPECIAL:
                                        if (LOCATION_POSITION.equals(param.getPath())) {
                                                theQueryStack.addSortOnCoordsNear(paramName, ascending, theParams);
                                                break;
                                        }
                                        throw new InvalidRequestException(
                                                        Msg.code(2306) + "This server does not support _sort specifications of type "
                                                                        + param.getParamType() + " - Can't serve _sort=" + paramName);

                                case HAS:
                                default:
                                        throw new InvalidRequestException(
                                                        Msg.code(1197) + "This server does not support _sort specifications of type "
                                                                        + param.getParamType() + " - Can't serve _sort=" + paramName);
                        }
                }

                // Recurse
                createSort(theQueryStack, theSort.getChain(), theParams);
        }

        private void throwInvalidRequestExceptionForUnknownSortParameter(String theResourceName, String theParamName) {
                Collection<String> validSearchParameterNames = mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(
                                theResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
                String msg = myContext
                                .getLocalizer()
                                .getMessageSanitized(
                                                BaseStorageDao.class,
                                                "invalidSortParameter",
                                                theParamName,
                                                theResourceName,
                                                validSearchParameterNames);
                throw new InvalidRequestException(Msg.code(1194) + msg);
        }

        private void createCompositeSort(
                        QueryStack theQueryStack,
                        RestSearchParameterTypeEnum theParamType,
                        String theParamName,
                        boolean theAscending) {

                switch (theParamType) {
                        case STRING:
                                theQueryStack.addSortOnString(myResourceName, theParamName, theAscending);
                                break;
                        case DATE:
                                theQueryStack.addSortOnDate(myResourceName, theParamName, theAscending);
                                break;
                        case TOKEN:
                                theQueryStack.addSortOnToken(myResourceName, theParamName, theAscending);
                                break;
                        case QUANTITY:
                                theQueryStack.addSortOnQuantity(myResourceName, theParamName, theAscending);
                                break;
                        case NUMBER:
                        case REFERENCE:
                        case COMPOSITE:
                        case URI:
                        case HAS:
                        case SPECIAL:
                        default:
                                throw new InvalidRequestException(
                                                Msg.code(1198) + "Don't know how to handle composite parameter with type of " + theParamType
                                                                + " on _sort=" + theParamName);
                }
        }

        private void doLoadPids(
                        Collection<JpaPid> thePids,
                        Collection<JpaPid> theIncludedPids,
                        List<IBaseResource> theResourceListToPopulate,
                        boolean theForHistoryOperation,
                        Map<Long, Integer> thePosition) {

                Map<JpaPid, Long> resourcePidToVersion = null;
                for (JpaPid next : thePids) {
                        if (next.getVersion() != null && myStorageSettings.isRespectVersionsForSearchIncludes()) {
                                if (resourcePidToVersion == null) {
                                        resourcePidToVersion = new HashMap<>();
                                }
                                resourcePidToVersion.put(next, next.getVersion());
                        }
                }

                List<JpaPid> versionlessPids = new ArrayList<>(thePids);
                if (versionlessPids.size() < getMaximumPageSize()) {
                        versionlessPids = normalizeIdListForInClause(versionlessPids);
                }

                // Load the resource bodies
                List<ResourceHistoryTable> resourceSearchViewList =
                                myResourceHistoryTableDao.findCurrentVersionsByResourcePidsAndFetchResourceTable(
                                                JpaPidFk.fromPids(versionlessPids));

                /*
                 * If we have specific versions to load, replace the history entries with the
                 * correct ones
                 *
                 * TODO: this could definitely be made more efficient, probably by not loading the wrong
                 * version entity first, and by batching the fetches. But this is a fairly infrequently
                 * used feature, and loading history entities by PK is a very efficient query so it's
                 * not the end of the world
                 */
                if (resourcePidToVersion != null) {
                        for (int i = 0; i < resourceSearchViewList.size(); i++) {
                                ResourceHistoryTable next = resourceSearchViewList.get(i);
                                JpaPid resourceId = next.getPersistentId();
                                Long version = resourcePidToVersion.get(resourceId);
                                resourceId.setVersion(version);
                                if (version != null && !version.equals(next.getVersion())) {
                                        ResourceHistoryTable replacement = myResourceHistoryTableDao.findForIdAndVersion(
                                                        next.getResourceId().toFk(), version);
                                        resourceSearchViewList.set(i, replacement);
                                }
                        }
                }

                // -- preload all tags with tag definition if any
                Map<JpaPid, Collection<BaseTag>> tagMap = getResourceTagMap(resourceSearchViewList);

                for (ResourceHistoryTable next : resourceSearchViewList) {
                        if (next.getDeleted() != null) {
                                continue;
                        }

                        Class<? extends IBaseResource> resourceType =
                                        myContext.getResourceDefinition(next.getResourceType()).getImplementingClass();

                        JpaPid resourceId = next.getPersistentId();

                        if (resourcePidToVersion != null) {
                                Long version = resourcePidToVersion.get(resourceId);
                                resourceId.setVersion(version);
                        }

                        IBaseResource resource = null;
                        if (next != null) {
                                resource = myJpaStorageResourceParser.toResource(
                                                resourceType, next, tagMap.get(next.getResourceId()), theForHistoryOperation);
                        }
                        if (resource == null) {
                                if (next != null) {
                                        ourLog.warn(
                                                        "Unable to find resource {}/{}/_history/{} in database",
                                                        next.getResourceType(),
                                                        next.getIdDt().getIdPart(),
                                                        next.getVersion());
                                } else {
                                        ourLog.warn("Unable to find resource in database.");
                                }
                                continue;
                        }

                        Integer index = thePosition.get(resourceId.getId());
                        if (index == null) {
                                ourLog.warn("Got back unexpected resource PID {}", resourceId);
                                continue;
                        }

                        if (theIncludedPids.contains(resourceId)) {
                                ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(resource, BundleEntrySearchModeEnum.INCLUDE);
                        } else {
                                ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(resource, BundleEntrySearchModeEnum.MATCH);
                        }

                        theResourceListToPopulate.set(index, resource);
                }
        }

        private Map<JpaPid, Collection<BaseTag>> getResourceTagMap(Collection<ResourceHistoryTable> theHistoryTables) {

                switch (myStorageSettings.getTagStorageMode()) {
                        case VERSIONED:
                                return getPidToTagMapVersioned(theHistoryTables);
                        case NON_VERSIONED:
                                return getPidToTagMapUnversioned(theHistoryTables);
                        case INLINE:
                        default:
                                return Map.of();
                }
        }

        @Nonnull
        private Map<JpaPid, Collection<BaseTag>> getPidToTagMapVersioned(
                        Collection<ResourceHistoryTable> theHistoryTables) {
                List<ResourceHistoryTablePk> idList = new ArrayList<>(theHistoryTables.size());

                // -- find all resource has tags
                for (ResourceHistoryTable resource : theHistoryTables) {
                        if (resource.isHasTags()) {
                                idList.add(resource.getId());
                        }
                }

                Map<JpaPid, Collection<BaseTag>> tagMap = new HashMap<>();

                // -- no tags
                if (idList.isEmpty()) {
                        return tagMap;
                }

                // -- get all tags for the idList
                Collection<ResourceHistoryTag> tagList = myResourceHistoryTagDao.findByVersionIds(idList);

                // -- build the map, key = resourceId, value = list of ResourceTag
                JpaPid resourceId;
                Collection<BaseTag> tagCol;
                for (ResourceHistoryTag tag : tagList) {

                        resourceId = tag.getResourcePid();
                        tagCol = tagMap.get(resourceId);
                        if (tagCol == null) {
                                tagCol = new ArrayList<>();
                                tagCol.add(tag);
                                tagMap.put(resourceId, tagCol);
                        } else {
                                tagCol.add(tag);
                        }
                }

                return tagMap;
        }

        @Nonnull
        private Map<JpaPid, Collection<BaseTag>> getPidToTagMapUnversioned(
                        Collection<ResourceHistoryTable> theHistoryTables) {
                List<JpaPid> idList = new ArrayList<>(theHistoryTables.size());

                // -- find all resource has tags
                for (ResourceHistoryTable resource : theHistoryTables) {
                        if (resource.isHasTags()) {
                                idList.add(resource.getResourceId());
                        }
                }

                Map<JpaPid, Collection<BaseTag>> tagMap = new HashMap<>();

                // -- no tags
                if (idList.isEmpty()) {
                        return tagMap;
                }

                // -- get all tags for the idList
                Collection<ResourceTag> tagList = myResourceTagDao.findByResourceIds(idList);

                // -- build the map, key = resourceId, value = list of ResourceTag
                JpaPid resourceId;
                Collection<BaseTag> tagCol;
                for (ResourceTag tag : tagList) {

                        resourceId = tag.getResourceId();
                        tagCol = tagMap.get(resourceId);
                        if (tagCol == null) {
                                tagCol = new ArrayList<>();
                                tagCol.add(tag);
                                tagMap.put(resourceId, tagCol);
                        } else {
                                tagCol.add(tag);
                        }
                }

                return tagMap;
        }

        @Override
        public void loadResourcesByPid(
                        Collection<JpaPid> thePids,
                        Collection<JpaPid> theIncludedPids,
                        List<IBaseResource> theResourceListToPopulate,
                        boolean theForHistoryOperation,
                        RequestDetails theDetails) {
                if (thePids.isEmpty()) {
                        ourLog.debug("The include pids are empty");
                }

                // Dupes will cause a crash later anyhow, but this is expensive so only do it
                // when running asserts
                assert new HashSet<>(thePids).size() == thePids.size() : "PID list contains duplicates: " + thePids;

                Map<Long, Integer> position = new HashMap<>();
                for (JpaPid next : thePids) {
                        position.put(next.getId(), theResourceListToPopulate.size());
                        theResourceListToPopulate.add(null);
                }

                // Can we fast track this loading by checking elastic search?
                if (isLoadingFromElasticSearchSupported(thePids)) {
                        try {
                                theResourceListToPopulate.addAll(loadResourcesFromElasticSearch(thePids));
                                return;

                        } catch (ResourceNotFoundInIndexException theE) {
                                // some resources were not found in index, so we will inform this and resort to JPA search
                                ourLog.warn(
                                                "Some resources were not found in index. Make sure all resources were indexed. Resorting to database search.");
                        }
                }

                // We only chunk because some jdbc drivers can't handle long param lists.
                QueryChunker.chunk(
                                thePids,
                                t -> doLoadPids(t, theIncludedPids, theResourceListToPopulate, theForHistoryOperation, position));
        }

        /**
         * Check if we can load the resources from Hibernate Search instead of the database.
         * We assume this is faster.
         * <p>
         * Hibernate Search only stores the current version, and only if enabled.
         *
         * @param thePids the pids to check for versioned references
         * @return can we fetch from Hibernate Search?
         */
        private boolean isLoadingFromElasticSearchSupported(Collection<JpaPid> thePids) {
                // is storage enabled?
                return myStorageSettings.isStoreResourceInHSearchIndex()
                                && myStorageSettings.isAdvancedHSearchIndexing()
                                &&
                                // we don't support history
                                thePids.stream().noneMatch(p -> p.getVersion() != null)
                                &&
                                // skip the complexity for metadata in dstu2
                                myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3);
        }

        private List<IBaseResource> loadResourcesFromElasticSearch(Collection<JpaPid> thePids) {
                // Do we use the fulltextsvc via hibernate-search to load resources or be backwards compatible with older ES
                // only impl
                // to handle lastN?
                if (myStorageSettings.isAdvancedHSearchIndexing() && myStorageSettings.isStoreResourceInHSearchIndex()) {
                        List<Long> pidList = thePids.stream().map(JpaPid::getId).collect(Collectors.toList());

                        return myFulltextSearchSvc.getResources(pidList);
                } else if (!Objects.isNull(myParams) && myParams.isLastN()) {
                        // legacy LastN implementation
                        return myIElasticsearchSvc.getObservationResources(thePids);
                } else {
                        return Collections.emptyList();
                }
        }

        /**
         * THIS SHOULD RETURN HASHSET and not just Set because we add to it later
         * so it can't be Collections.emptySet() or some such thing.
         * The JpaPid returned will have resource type populated.
         */
        @Override
        public Set<JpaPid> loadIncludes(
                        FhirContext theContext,
                        EntityManager theEntityManager,
                        Collection<JpaPid> theMatches,
                        Collection<Include> theIncludes,
                        boolean theReverseMode,
                        DateRangeParam theLastUpdated,
                        String theSearchIdOrDescription,
                        RequestDetails theRequest,
                        Integer theMaxCount) {
                SearchBuilderLoadIncludesParameters<JpaPid> parameters = new SearchBuilderLoadIncludesParameters<>();
                parameters.setFhirContext(theContext);
                parameters.setEntityManager(theEntityManager);
                parameters.setMatches(theMatches);
                parameters.setIncludeFilters(theIncludes);
                parameters.setReverseMode(theReverseMode);
                parameters.setLastUpdated(theLastUpdated);
                parameters.setSearchIdOrDescription(theSearchIdOrDescription);
                parameters.setRequestDetails(theRequest);
                parameters.setMaxCount(theMaxCount);
                return loadIncludes(parameters);
        }

        @Override
        public Set<JpaPid> loadIncludes(SearchBuilderLoadIncludesParameters<JpaPid> theParameters) {
                Collection<JpaPid> matches = theParameters.getMatches();
                Collection<Include> currentIncludes = theParameters.getIncludeFilters();
                boolean reverseMode = theParameters.isReverseMode();
                EntityManager entityManager = theParameters.getEntityManager();
                Integer maxCount = theParameters.getMaxCount();
                FhirContext fhirContext = theParameters.getFhirContext();
                RequestDetails request = theParameters.getRequestDetails();
                String searchIdOrDescription = theParameters.getSearchIdOrDescription();
                List<String> desiredResourceTypes = theParameters.getDesiredResourceTypes();
                boolean hasDesiredResourceTypes = desiredResourceTypes != null && !desiredResourceTypes.isEmpty();
                IInterceptorBroadcaster compositeBroadcaster =
                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, request);

                if (compositeBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_RAW_SQL)) {
                        CurrentThreadCaptureQueriesListener.startCapturing();
                }
                if (matches.isEmpty()) {
                        return new HashSet<>();
                }
                if (currentIncludes == null || currentIncludes.isEmpty()) {
                        return new HashSet<>();
                }
                String searchPidFieldName = reverseMode ? MY_TARGET_RESOURCE_PID : MY_SOURCE_RESOURCE_PID;
                String searchPartitionIdFieldName =
                                reverseMode ? MY_TARGET_RESOURCE_PARTITION_ID : MY_SOURCE_RESOURCE_PARTITION_ID;
                String findPidFieldName = reverseMode ? MY_SOURCE_RESOURCE_PID : MY_TARGET_RESOURCE_PID;
                String findPartitionIdFieldName =
                                reverseMode ? MY_SOURCE_RESOURCE_PARTITION_ID : MY_TARGET_RESOURCE_PARTITION_ID;
                String findResourceTypeFieldName = reverseMode ? MY_SOURCE_RESOURCE_TYPE : MY_TARGET_RESOURCE_TYPE;
                String findVersionFieldName = null;
                if (!reverseMode && myStorageSettings.isRespectVersionsForSearchIncludes()) {
                        findVersionFieldName = MY_TARGET_RESOURCE_VERSION;
                }

                List<JpaPid> nextRoundMatches = new ArrayList<>(matches);
                HashSet<JpaPid> allAdded = new HashSet<>();
                HashSet<JpaPid> original = new HashSet<>(matches);
                ArrayList<Include> includes = new ArrayList<>(currentIncludes);

                int roundCounts = 0;
                StopWatch w = new StopWatch();

                boolean addedSomeThisRound;
                do {
                        roundCounts++;

                        HashSet<JpaPid> pidsToInclude = new HashSet<>();

                        for (Iterator<Include> iter = includes.iterator(); iter.hasNext(); ) {
                                Include nextInclude = iter.next();
                                if (!nextInclude.isRecurse()) {
                                        iter.remove();
                                }

                                // Account for _include=*
                                boolean matchAll = "*".equals(nextInclude.getValue());

                                // Account for _include=[resourceType]:*
                                String wantResourceType = null;
                                if (!matchAll) {
                                        if ("*".equals(nextInclude.getParamName())) {
                                                wantResourceType = nextInclude.getParamType();
                                                matchAll = true;
                                        }
                                }

                                if (matchAll) {
                                        loadIncludesMatchAll(
                                                        findPidFieldName,
                                                        findPartitionIdFieldName,
                                                        findResourceTypeFieldName,
                                                        findVersionFieldName,
                                                        searchPidFieldName,
                                                        searchPartitionIdFieldName,
                                                        wantResourceType,
                                                        reverseMode,
                                                        hasDesiredResourceTypes,
                                                        nextRoundMatches,
                                                        entityManager,
                                                        maxCount,
                                                        desiredResourceTypes,
                                                        pidsToInclude,
                                                        request);
                                } else {
                                        loadIncludesMatchSpecific(
                                                        nextInclude,
                                                        fhirContext,
                                                        findPidFieldName,
                                                        findPartitionIdFieldName,
                                                        findVersionFieldName,
                                                        searchPidFieldName,
                                                        searchPartitionIdFieldName,
                                                        reverseMode,
                                                        nextRoundMatches,
                                                        entityManager,
                                                        maxCount,
                                                        pidsToInclude,
                                                        request);
                                }
                        }

                        nextRoundMatches.clear();
                        for (JpaPid next : pidsToInclude) {
                                if (!original.contains(next) && !allAdded.contains(next)) {
                                        nextRoundMatches.add(next);
                                }
                        }

                        addedSomeThisRound = allAdded.addAll(pidsToInclude);

                        if (maxCount != null && allAdded.size() >= maxCount) {
                                break;
                        }

                } while (!includes.isEmpty() && !nextRoundMatches.isEmpty() && addedSomeThisRound);

                allAdded.removeAll(original);

                ourLog.info(
                                "Loaded {} {} in {} rounds and {} ms for search {}",
                                allAdded.size(),
                                reverseMode ? "_revincludes" : "_includes",
                                roundCounts,
                                w.getMillisAndRestart(),
                                searchIdOrDescription);

                if (compositeBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_RAW_SQL)) {
                        callRawSqlHookWithCurrentThreadQueries(request, compositeBroadcaster);
                }

                // Interceptor call: STORAGE_PREACCESS_RESOURCES
                // This can be used to remove results from the search result details before
                // the user has a chance to know that they were in the results
                if (!allAdded.isEmpty()) {

                        if (compositeBroadcaster.hasHooks(Pointcut.STORAGE_PREACCESS_RESOURCES)) {
                                List<JpaPid> includedPidList = new ArrayList<>(allAdded);
                                JpaPreResourceAccessDetails accessDetails =
                                                new JpaPreResourceAccessDetails(includedPidList, () -> this);
                                HookParams params = new HookParams()
                                                .add(IPreResourceAccessDetails.class, accessDetails)
                                                .add(RequestDetails.class, request)
                                                .addIfMatchesType(ServletRequestDetails.class, request);
                                compositeBroadcaster.callHooks(Pointcut.STORAGE_PREACCESS_RESOURCES, params);

                                for (int i = includedPidList.size() - 1; i >= 0; i--) {
                                        if (accessDetails.isDontReturnResourceAtIndex(i)) {
                                                JpaPid value = includedPidList.remove(i);
                                                if (value != null) {
                                                        allAdded.remove(value);
                                                }
                                        }
                                }
                        }
                }

                return allAdded;
        }

        private void loadIncludesMatchSpecific(
                        Include nextInclude,
                        FhirContext fhirContext,
                        String findPidFieldName,
                        String findPartitionFieldName,
                        String findVersionFieldName,
                        String searchPidFieldName,
                        String searchPartitionFieldName,
                        boolean reverseMode,
                        List<JpaPid> nextRoundMatches,
                        EntityManager entityManager,
                        Integer maxCount,
                        HashSet<JpaPid> pidsToInclude,
                        RequestDetails theRequest) {
                List<String> paths;

                // Start replace
                RuntimeSearchParam param;
                String resType = nextInclude.getParamType();
                if (isBlank(resType)) {
                        return;
                }
                RuntimeResourceDefinition def = fhirContext.getResourceDefinition(resType);
                if (def == null) {
                        ourLog.warn("Unknown resource type in include/revinclude=" + nextInclude.getValue());
                        return;
                }

                String paramName = nextInclude.getParamName();
                if (isNotBlank(paramName)) {
                        param = mySearchParamRegistry.getActiveSearchParam(
                                        resType, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                } else {
                        param = null;
                }
                if (param == null) {
                        ourLog.warn("Unknown param name in include/revinclude=" + nextInclude.getValue());
                        return;
                }

                paths = param.getPathsSplitForResourceType(resType);
                // end replace

                Set<String> targetResourceTypes = computeTargetResourceTypes(nextInclude, param);

                for (String nextPath : paths) {
                        String findPidFieldSqlColumn =
                                        findPidFieldName.equals(MY_SOURCE_RESOURCE_PID) ? "src_resource_id" : "target_resource_id";
                        String fieldsToLoad = "r." + findPidFieldSqlColumn + " AS " + RESOURCE_ID_ALIAS;
                        if (findVersionFieldName != null) {
                                fieldsToLoad += ", r.target_resource_version AS " + RESOURCE_VERSION_ALIAS;
                        }
                        if (myPartitionSettings.isDatabasePartitionMode()) {
                                fieldsToLoad += ", r.";
                                fieldsToLoad += findPartitionFieldName.equals(MY_SOURCE_RESOURCE_PARTITION_ID)
                                                ? "partition_id"
                                                : "target_res_partition_id";
                                fieldsToLoad += " as " + PARTITION_ID_ALIAS;
                        }

                        // Query for includes lookup has 2 cases
                        // Case 1: Where target_resource_id is available in hfj_res_link table for local references
                        // Case 2: Where target_resource_id is null in hfj_res_link table and referred by a canonical
                        // url in target_resource_url

                        // Case 1:
                        Map<String, Object> localReferenceQueryParams = new HashMap<>();

                        String searchPidFieldSqlColumn =
                                        searchPidFieldName.equals(MY_TARGET_RESOURCE_PID) ? "target_resource_id" : "src_resource_id";
                        StringBuilder localReferenceQuery = new StringBuilder();
                        localReferenceQuery.append("SELECT ").append(fieldsToLoad);
                        localReferenceQuery.append(" FROM hfj_res_link r ");
                        localReferenceQuery.append("WHERE r.src_path = :src_path");
                        if (!"target_resource_id".equals(searchPidFieldSqlColumn)) {
                                localReferenceQuery.append(" AND r.target_resource_id IS NOT NULL");
                        }
                        localReferenceQuery
                                        .append(" AND r.")
                                        .append(searchPidFieldSqlColumn)
                                        .append(" IN (:target_pids) ");
                        if (myPartitionSettings.isDatabasePartitionMode()) {
                                String partitionFieldToSearch = findPartitionFieldName.equals(MY_SOURCE_RESOURCE_PARTITION_ID)
                                                ? "target_res_partition_id"
                                                : "partition_id";
                                localReferenceQuery
                                                .append("AND r.")
                                                .append(partitionFieldToSearch)
                                                .append(" = :search_partition_id ");
                        }
                        localReferenceQueryParams.put("src_path", nextPath);
                        // we loop over target_pids later.
                        if (targetResourceTypes != null) {
                                if (targetResourceTypes.size() == 1) {
                                        localReferenceQuery.append("AND r.target_resource_type = :target_resource_type ");
                                        localReferenceQueryParams.put(
                                                        "target_resource_type",
                                                        targetResourceTypes.iterator().next());
                                } else {
                                        localReferenceQuery.append("AND r.target_resource_type in (:target_resource_types) ");
                                        localReferenceQueryParams.put("target_resource_types", targetResourceTypes);
                                }
                        }

                        // Case 2:
                        Pair<String, Map<String, Object>> canonicalQuery =
                                        buildCanonicalUrlQuery(findVersionFieldName, targetResourceTypes, reverseMode, theRequest);

                        String sql = localReferenceQuery + "UNION " + canonicalQuery.getLeft();

                        Map<String, Object> limitParams = new HashMap<>();
                        if (maxCount != null) {
                                LinkedList<Object> bindVariables = new LinkedList<>();
                                sql = SearchQueryBuilder.applyLimitToSql(
                                                myDialectProvider.getDialect(), null, maxCount, sql, null, bindVariables);

                                // The dialect SQL limiter uses positional params, but we're using
                                // named params here, so we need to replace the positional params
                                // with equivalent named ones
                                StringBuilder sb = new StringBuilder();
                                for (int i = 0; i < sql.length(); i++) {
                                        char nextChar = sql.charAt(i);
                                        if (nextChar == '?') {
                                                String nextName = "limit" + i;
                                                sb.append(':').append(nextName);
                                                limitParams.put(nextName, bindVariables.removeFirst());
                                        } else {
                                                sb.append(nextChar);
                                        }
                                }
                                sql = sb.toString();
                        }

                        List<Collection<JpaPid>> partitions = partitionBySizeAndPartitionId(nextRoundMatches, getMaximumPageSize());
                        for (Collection<JpaPid> nextPartition : partitions) {
                                Query q = entityManager.createNativeQuery(sql, Tuple.class);
                                q.setParameter("target_pids", JpaPid.toLongList(nextPartition));
                                if (myPartitionSettings.isDatabasePartitionMode()) {
                                        q.setParameter(
                                                        "search_partition_id",
                                                        nextPartition.iterator().next().getPartitionId());
                                }
                                localReferenceQueryParams.forEach(q::setParameter);
                                canonicalQuery.getRight().forEach(q::setParameter);
                                limitParams.forEach(q::setParameter);

                                @SuppressWarnings("unchecked")
                                List<Tuple> results = q.getResultList();
                                for (Tuple result : results) {
                                        if (result != null) {
                                                Long resourceId = NumberUtils.createLong(String.valueOf(result.get(RESOURCE_ID_ALIAS)));
                                                Long resourceVersion = null;
                                                if (findVersionFieldName != null && result.get(RESOURCE_VERSION_ALIAS) != null) {
                                                        resourceVersion =
                                                                        NumberUtils.createLong(String.valueOf(result.get(RESOURCE_VERSION_ALIAS)));
                                                }
                                                Integer partitionId = null;
                                                if (myPartitionSettings.isDatabasePartitionMode()) {
                                                        partitionId = result.get(PARTITION_ID_ALIAS, Integer.class);
                                                }

                                                JpaPid pid = JpaPid.fromIdAndVersion(resourceId, resourceVersion);
                                                pid.setPartitionId(partitionId);
                                                pidsToInclude.add(pid);
                                        }
                                }
                        }
                }
        }

        private void loadIncludesMatchAll(
                        String findPidFieldName,
                        String findPartitionFieldName,
                        String findResourceTypeFieldName,
                        String findVersionFieldName,
                        String searchPidFieldName,
                        String searchPartitionFieldName,
                        String wantResourceType,
                        boolean reverseMode,
                        boolean hasDesiredResourceTypes,
                        List<JpaPid> nextRoundMatches,
                        EntityManager entityManager,
                        Integer maxCount,
                        List<String> desiredResourceTypes,
                        HashSet<JpaPid> pidsToInclude,
                        RequestDetails request) {
                StringBuilder sqlBuilder = new StringBuilder();
                sqlBuilder.append("SELECT r.").append(findPidFieldName);
                sqlBuilder.append(", r.").append(findResourceTypeFieldName);
                sqlBuilder.append(", r.myTargetResourceUrl");
                if (findVersionFieldName != null) {
                        sqlBuilder.append(", r.").append(findVersionFieldName);
                }
                if (myPartitionSettings.isDatabasePartitionMode()) {
                        sqlBuilder.append(", r.").append(findPartitionFieldName);
                }
                sqlBuilder.append(" FROM ResourceLink r WHERE ");

                if (myPartitionSettings.isDatabasePartitionMode()) {
                        sqlBuilder.append("r.").append(searchPartitionFieldName);
                        sqlBuilder.append(" = :target_partition_id AND ");
                }

                sqlBuilder.append("r.").append(searchPidFieldName);
                sqlBuilder.append(" IN (:target_pids)");

                /*
                 * We need to set the resource type in 2 cases only:
                 * 1) we are in $everything mode
                 *              (where we only want to fetch specific resource types, regardless of what is
                 *              available to fetch)
                 * 2) we are doing revincludes
                 *
                 *      Technically if the request is a qualified star (e.g. _include=Observation:*) we
                 * should always be checking the source resource type on the resource link. We don't
                 * actually index that column though by default, so in order to try and be efficient
                 * we don't actually include it for includes (but we do for revincludes). This is
                 * because for an include, it doesn't really make sense to include a different
                 * resource type than the one you are searching on.
                 */
                if (wantResourceType != null && (reverseMode || (myParams != null && myParams.getEverythingMode() != null))) {
                        // because mySourceResourceType is not part of the HFJ_RES_LINK
                        // index, this might not be the most optimal performance.
                        // but it is for an $everything operation (and maybe we should update the index)
                        sqlBuilder.append(" AND r.mySourceResourceType = :want_resource_type");
                } else {
                        wantResourceType = null;
                }

                // When calling $everything on a Patient instance, we don't want to recurse into new Patient
                // resources
                // (e.g. via Provenance, List, or Group) when in an $everything operation
                if (myParams != null
                                && myParams.getEverythingMode() == SearchParameterMap.EverythingModeEnum.PATIENT_INSTANCE) {
                        sqlBuilder.append(" AND r.myTargetResourceType != 'Patient'");
                        sqlBuilder.append(UNDESIRED_RESOURCE_LINKAGES_FOR_EVERYTHING_ON_PATIENT_INSTANCE.stream()
                                        .collect(Collectors.joining("', '", " AND r.mySourceResourceType NOT IN ('", "')")));
                }
                if (hasDesiredResourceTypes) {
                        sqlBuilder.append(" AND r.myTargetResourceType IN (:desired_target_resource_types)");
                }

                String sql = sqlBuilder.toString();
                List<Collection<JpaPid>> partitions = partitionBySizeAndPartitionId(nextRoundMatches, getMaximumPageSize());
                for (Collection<JpaPid> nextPartition : partitions) {
                        TypedQuery<?> q = entityManager.createQuery(sql, Object[].class);
                        q.setParameter("target_pids", JpaPid.toLongList(nextPartition));
                        if (myPartitionSettings.isDatabasePartitionMode()) {
                                q.setParameter(
                                                "target_partition_id", nextPartition.iterator().next().getPartitionId());
                        }
                        if (wantResourceType != null) {
                                q.setParameter("want_resource_type", wantResourceType);
                        }
                        if (maxCount != null) {
                                q.setMaxResults(maxCount);
                        }
                        if (hasDesiredResourceTypes) {
                                q.setParameter("desired_target_resource_types", desiredResourceTypes);
                        }
                        List<?> results = q.getResultList();
                        Set<String> canonicalUrls = null;
                        for (Object nextRow : results) {
                                if (nextRow == null) {
                                        // This can happen if there are outgoing references which are canonical or point to
                                        // other servers
                                        continue;
                                }

                                Long version = null;
                                Long resourceId = (Long) ((Object[]) nextRow)[0];
                                String resourceType = (String) ((Object[]) nextRow)[1];
                                String resourceCanonicalUrl = (String) ((Object[]) nextRow)[2];
                                Integer partitionId = null;
                                int offset = 0;
                                if (findVersionFieldName != null) {
                                        version = (Long) ((Object[]) nextRow)[3];
                                        offset++;
                                }
                                if (myPartitionSettings.isDatabasePartitionMode()) {
                                        partitionId = ((Integer) ((Object[]) nextRow)[3 + offset]);
                                }

                                if (resourceId != null) {
                                        JpaPid pid = JpaPid.fromIdAndVersionAndResourceType(resourceId, version, resourceType);
                                        pid.setPartitionId(partitionId);
                                        pidsToInclude.add(pid);
                                } else if (resourceCanonicalUrl != null) {
                                        if (canonicalUrls == null) {
                                                canonicalUrls = new HashSet<>();
                                        }
                                        canonicalUrls.add(resourceCanonicalUrl);
                                }
                        }

                        if (canonicalUrls != null) {
                                String message =
                                                "Search with _include=* can be inefficient when references using canonical URLs are detected. Use more specific _include values instead.";
                                firePerformanceWarning(request, message);
                                loadCanonicalUrls(request, canonicalUrls, entityManager, pidsToInclude, reverseMode);
                        }
                }
        }

        private void loadCanonicalUrls(
                        RequestDetails theRequestDetails,
                        Set<String> theCanonicalUrls,
                        EntityManager theEntityManager,
                        HashSet<JpaPid> thePidsToInclude,
                        boolean theReverse) {
                StringBuilder sqlBuilder;
                CanonicalUrlTargets canonicalUrlTargets =
                                calculateIndexUriIdentityHashesForResourceTypes(theRequestDetails, null, theReverse);
                List<List<String>> canonicalUrlPartitions = ListUtils.partition(
                                List.copyOf(theCanonicalUrls), getMaximumPageSize() - canonicalUrlTargets.myHashIdentityValues.size());

                sqlBuilder = new StringBuilder();
                sqlBuilder.append("SELECT ");
                if (myPartitionSettings.isPartitioningEnabled()) {
                        sqlBuilder.append("i.myPartitionIdValue, ");
                }
                sqlBuilder.append("i.myResourcePid ");

                sqlBuilder.append("FROM ResourceIndexedSearchParamUri i ");
                sqlBuilder.append("WHERE i.myHashIdentity IN (:hash_identity) ");
                sqlBuilder.append("AND i.myUri IN (:uris)");

                String canonicalResSql = sqlBuilder.toString();

                for (Collection<String> nextCanonicalUrlList : canonicalUrlPartitions) {
                        TypedQuery<Object[]> canonicalResIdQuery = theEntityManager.createQuery(canonicalResSql, Object[].class);
                        canonicalResIdQuery.setParameter("hash_identity", canonicalUrlTargets.myHashIdentityValues);
                        canonicalResIdQuery.setParameter("uris", nextCanonicalUrlList);
                        List<Object[]> results = canonicalResIdQuery.getResultList();
                        for (var next : results) {
                                if (next != null) {
                                        Integer partitionId = null;
                                        Long pid;
                                        if (next.length == 1) {
                                                pid = (Long) next[0];
                                        } else {
                                                partitionId = (Integer) ((Object[]) next)[0];
                                                pid = (Long) ((Object[]) next)[1];
                                        }
                                        if (pid != null) {
                                                thePidsToInclude.add(JpaPid.fromId(pid, partitionId));
                                        }
                                }
                        }
                }
        }

        /**
         * Calls Performance Trace Hook
         *
         * @param request                 the request deatils
         *                                Sends a raw SQL query to the Pointcut for raw SQL queries.
         */
        private void callRawSqlHookWithCurrentThreadQueries(
                        RequestDetails request, IInterceptorBroadcaster theCompositeBroadcaster) {
                SqlQueryList capturedQueries = CurrentThreadCaptureQueriesListener.getCurrentQueueAndStopCapturing();
                HookParams params = new HookParams()
                                .add(RequestDetails.class, request)
                                .addIfMatchesType(ServletRequestDetails.class, request)
                                .add(SqlQueryList.class, capturedQueries);
                theCompositeBroadcaster.callHooks(Pointcut.JPA_PERFTRACE_RAW_SQL, params);
        }

        @Nullable
        private static Set<String> computeTargetResourceTypes(Include nextInclude, RuntimeSearchParam param) {
                String targetResourceType = defaultString(nextInclude.getParamTargetType(), null);
                boolean haveTargetTypesDefinedByParam = param.hasTargets();
                Set<String> targetResourceTypes;
                if (targetResourceType != null) {
                        targetResourceTypes = Set.of(targetResourceType);
                } else if (haveTargetTypesDefinedByParam) {
                        targetResourceTypes = param.getTargets();
                } else {
                        // all types!
                        targetResourceTypes = null;
                }
                return targetResourceTypes;
        }

        @Nonnull
        private Pair<String, Map<String, Object>> buildCanonicalUrlQuery(
                        String theVersionFieldName,
                        Set<String> theTargetResourceTypes,
                        boolean theReverse,
                        RequestDetails theRequest) {
                String fieldsToLoadFromSpidxUriTable = theReverse ? "r.src_resource_id" : "rUri.res_id";
                if (theVersionFieldName != null) {
                        // canonical-uri references aren't versioned, but we need to match the column count for the UNION
                        fieldsToLoadFromSpidxUriTable += ", NULL";
                }

                if (myPartitionSettings.isDatabasePartitionMode()) {
                        if (theReverse) {
                                fieldsToLoadFromSpidxUriTable += ", r.partition_id as " + PARTITION_ID_ALIAS;
                        } else {
                                fieldsToLoadFromSpidxUriTable += ", rUri.partition_id as " + PARTITION_ID_ALIAS;
                        }
                }

                // The logical join will be by hfj_spidx_uri on sp_name='uri' and sp_uri=target_resource_url.
                // But sp_name isn't indexed, so we use hash_identity instead.
                CanonicalUrlTargets canonicalUrlTargets =
                                calculateIndexUriIdentityHashesForResourceTypes(theRequest, theTargetResourceTypes, theReverse);

                Map<String, Object> canonicalUriQueryParams = new HashMap<>();
                StringBuilder canonicalUrlQuery = new StringBuilder();
                canonicalUrlQuery
                                .append("SELECT ")
                                .append(fieldsToLoadFromSpidxUriTable)
                                .append(' ');
                canonicalUrlQuery.append("FROM hfj_res_link r ");

                // join on hash_identity and sp_uri - indexed in IDX_SP_URI_HASH_IDENTITY_V2
                canonicalUrlQuery.append("JOIN hfj_spidx_uri rUri ON (");
                if (myPartitionSettings.isDatabasePartitionMode()) {
                        canonicalUrlQuery.append("rUri.partition_id IN (:uri_partition_id) AND ");
                        canonicalUriQueryParams.put("uri_partition_id", canonicalUrlTargets.myPartitionIds);
                }
                if (canonicalUrlTargets.myHashIdentityValues.size() == 1) {
                        canonicalUrlQuery.append("rUri.hash_identity = :uri_identity_hash");
                        canonicalUriQueryParams.put(
                                        "uri_identity_hash",
                                        canonicalUrlTargets.myHashIdentityValues.iterator().next());
                } else {
                        canonicalUrlQuery.append("rUri.hash_identity in (:uri_identity_hashes)");
                        canonicalUriQueryParams.put("uri_identity_hashes", canonicalUrlTargets.myHashIdentityValues);
                }
                canonicalUrlQuery.append(" AND r.target_resource_url = rUri.sp_uri");
                canonicalUrlQuery.append(")");

                canonicalUrlQuery.append(" WHERE r.src_path = :src_path AND");
                canonicalUrlQuery.append(" r.target_resource_id IS NULL");
                canonicalUrlQuery.append(" AND");
                if (myPartitionSettings.isDatabasePartitionMode()) {
                        if (theReverse) {
                                canonicalUrlQuery.append(" rUri.partition_id");
                        } else {
                                canonicalUrlQuery.append(" r.partition_id");
                        }
                        canonicalUrlQuery.append(" = :search_partition_id");
                        canonicalUrlQuery.append(" AND");
                }
                if (theReverse) {
                        canonicalUrlQuery.append(" rUri.res_id");
                } else {
                        canonicalUrlQuery.append(" r.src_resource_id");
                }
                canonicalUrlQuery.append(" IN (:target_pids)");

                return Pair.of(canonicalUrlQuery.toString(), canonicalUriQueryParams);
        }

        @Nonnull
        CanonicalUrlTargets calculateIndexUriIdentityHashesForResourceTypes(
                        RequestDetails theRequestDetails, Set<String> theTargetResourceTypes, boolean theReverse) {
                Set<String> targetResourceTypes = theTargetResourceTypes;
                if (targetResourceTypes == null) {
                        /*
                         * If we don't have a list of valid target types, we need to figure out a list of all
                         * possible target types in order to perform the search of the URI index table. This is
                         * because the hash_identity column encodes the resource type, so we'll need a hash
                         * value for each possible target type.
                         */
                        targetResourceTypes = new HashSet<>();
                        Set<String> possibleTypes = myDaoRegistry.getRegisteredDaoTypes();
                        if (theReverse) {
                                // For reverse includes, it is really hard to figure out what types
                                // are actually potentially pointing to the type we're searching for
                                // in this context, so let's just assume it could be anything.
                                targetResourceTypes = possibleTypes;
                        } else {
                                for (var next : mySearchParamRegistry
                                                .getActiveSearchParams(myResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
                                                .values()
                                                .stream()
                                                .filter(t -> t.getParamType().equals(RestSearchParameterTypeEnum.REFERENCE))
                                                .collect(Collectors.toList())) {

                                        // If the reference points to a Reference (ie not a canonical or CanonicalReference)
                                        // then it doesn't matter here anyhow. The logic here only works for elements at the
                                        // root level of the document (e.g. QuestionnaireResponse.subject or
                                        // QuestionnaireResponse.subject.where(...)) but this is just an optimization
                                        // anyhow.
                                        if (next.getPath().startsWith(myResourceName + ".")) {
                                                String elementName =
                                                                next.getPath().substring(next.getPath().indexOf('.') + 1);
                                                int secondDotIndex = elementName.indexOf('.');
                                                if (secondDotIndex != -1) {
                                                        elementName = elementName.substring(0, secondDotIndex);
                                                }
                                                BaseRuntimeChildDefinition child =
                                                                myContext.getResourceDefinition(myResourceName).getChildByName(elementName);
                                                if (child != null) {
                                                        BaseRuntimeElementDefinition<?> childDef = child.getChildByName(elementName);
                                                        if (childDef != null) {
                                                                if (childDef.getName().equals("Reference")) {
                                                                        continue;
                                                                }
                                                        }
                                                }
                                        }

                                        if (!next.getTargets().isEmpty()) {
                                                // For each reference parameter on the resource type we're searching for,
                                                // add all the potential target types to the list of possible target
                                                // resource types we can look up.
                                                for (var nextTarget : next.getTargets()) {
                                                        if (possibleTypes.contains(nextTarget)) {
                                                                targetResourceTypes.add(nextTarget);
                                                        }
                                                }
                                        } else {
                                                // If we have any references that don't define any target types, then
                                                // we need to assume that all enabled resource types are possible target
                                                // types
                                                targetResourceTypes.addAll(possibleTypes);
                                                break;
                                        }
                                }
                        }
                }
                assert !targetResourceTypes.isEmpty();

                Set<Long> hashIdentityValues = new HashSet<>();
                Set<Integer> partitionIds = new HashSet<>();
                for (String type : targetResourceTypes) {

                        RequestPartitionId readPartition;
                        if (myPartitionSettings.isPartitioningEnabled()) {
                                readPartition =
                                                myPartitionHelperSvc.determineReadPartitionForRequestForSearchType(theRequestDetails, type);
                        } else {
                                readPartition = RequestPartitionId.defaultPartition();
                        }
                        if (readPartition.hasPartitionIds()) {
                                partitionIds.addAll(readPartition.getPartitionIds());
                        }

                        Long hashIdentity = BaseResourceIndexedSearchParam.calculateHashIdentity(
                                        myPartitionSettings, readPartition, type, "url");
                        hashIdentityValues.add(hashIdentity);
                }

                return new CanonicalUrlTargets(hashIdentityValues, partitionIds);
        }

        static class CanonicalUrlTargets {

                @Nonnull
                final Set<Long> myHashIdentityValues;

                @Nonnull
                final Set<Integer> myPartitionIds;

                public CanonicalUrlTargets(@Nonnull Set<Long> theHashIdentityValues, @Nonnull Set<Integer> thePartitionIds) {
                        myHashIdentityValues = theHashIdentityValues;
                        myPartitionIds = thePartitionIds;
                }
        }

        /**
         * This method takes in a list of {@link JpaPid}'s and returns a series of sublists containing
         * those pids where:
         * <ul>
         *     <li>No single list is most than {@literal theMaxLoad} entries</li>
         *     <li>Each list only contains JpaPids with the same partition ID</li>
         * </ul>
         */
        static List<Collection<JpaPid>> partitionBySizeAndPartitionId(List<JpaPid> theNextRoundMatches, int theMaxLoad) {

                if (theNextRoundMatches.size() <= theMaxLoad) {
                        boolean allSamePartition = true;
                        for (int i = 1; i < theNextRoundMatches.size(); i++) {
                                if (!Objects.equals(
                                                theNextRoundMatches.get(i - 1).getPartitionId(),
                                                theNextRoundMatches.get(i).getPartitionId())) {
                                        allSamePartition = false;
                                        break;
                                }
                        }
                        if (allSamePartition) {
                                return Collections.singletonList(theNextRoundMatches);
                        }
                }

                // Break into partitioned sublists
                ListMultimap<String, JpaPid> lists =
                                MultimapBuilder.hashKeys().arrayListValues().build();
                for (JpaPid nextRoundMatch : theNextRoundMatches) {
                        String partitionId = nextRoundMatch.getPartitionId() != null
                                        ? nextRoundMatch.getPartitionId().toString()
                                        : "";
                        lists.put(partitionId, nextRoundMatch);
                }

                List<Collection<JpaPid>> retVal = new ArrayList<>();
                for (String key : lists.keySet()) {
                        List<List<JpaPid>> nextPartition = Lists.partition(lists.get(key), theMaxLoad);
                        retVal.addAll(nextPartition);
                }

                // In unit test mode, we sort the results just for unit test predictability
                if (HapiSystemProperties.isUnitTestModeEnabled()) {
                        retVal = retVal.stream()
                                        .map(t -> t.stream().sorted().collect(Collectors.toList()))
                                        .collect(Collectors.toList());
                }

                return retVal;
        }

        private void attemptComboUniqueSpProcessing(
                        QueryStack theQueryStack, @Nonnull SearchParameterMap theParams, RequestDetails theRequest) {
                RuntimeSearchParam comboParam = null;
                List<String> comboParamNames = null;
                List<RuntimeSearchParam> exactMatchParams = mySearchParamRegistry.getActiveComboSearchParams(
                                myResourceName, theParams.keySet(), ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                if (!exactMatchParams.isEmpty()) {
                        comboParam = exactMatchParams.get(0);
                        comboParamNames = new ArrayList<>(theParams.keySet());
                }

                if (comboParam == null) {
                        List<RuntimeSearchParam> candidateComboParams = mySearchParamRegistry.getActiveComboSearchParams(
                                        myResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                        for (RuntimeSearchParam nextCandidate : candidateComboParams) {
                                List<String> nextCandidateParamNames =
                                                JpaParamUtil.resolveComponentParameters(mySearchParamRegistry, nextCandidate).stream()
                                                                .map(RuntimeSearchParam::getName)
                                                                .collect(Collectors.toList());
                                if (theParams.keySet().containsAll(nextCandidateParamNames)) {
                                        comboParam = nextCandidate;
                                        comboParamNames = nextCandidateParamNames;
                                        break;
                                }
                        }
                }

                if (comboParam != null) {
                        Collections.sort(comboParamNames);

                        // Since we're going to remove elements below
                        theParams.values().forEach(this::ensureSubListsAreWritable);

                        /*
                         * Apply search against the combo param index in a loop:
                         *
                         * 1. First we check whether the actual parameter values in the
                         * parameter map are actually usable for searching against the combo
                         * param index. E.g. no search modifiers, date comparators, etc.,
                         * since these mean you can't use the combo index.
                         *
                         * 2. Apply and create the join SQl. We remove parameter values from
                         * the map as we apply them, so any parameter values remaining in the
                         * map after each loop haven't yet been factored into the SQL.
                         *
                         * The loop allows us to create multiple combo index joins if there
                         * are multiple AND expressions for the related parameters.
                         */
                        while (validateParamValuesAreValidForComboParam(theRequest, theParams, comboParamNames, comboParam)) {
                                applyComboSearchParam(theQueryStack, theParams, theRequest, comboParamNames, comboParam);
                        }
                }
        }

        private void applyComboSearchParam(
                        QueryStack theQueryStack,
                        @Nonnull SearchParameterMap theParams,
                        RequestDetails theRequest,
                        List<String> theComboParamNames,
                        RuntimeSearchParam theComboParam) {

                List<List<IQueryParameterType>> inputs = new ArrayList<>();
                for (String nextParamName : theComboParamNames) {
                        List<IQueryParameterType> nextValues = theParams.get(nextParamName).remove(0);
                        inputs.add(nextValues);
                }

                List<List<IQueryParameterType>> inputPermutations = Lists.cartesianProduct(inputs);
                List<String> indexStrings = new ArrayList<>(CartesianProductUtil.calculateCartesianProductSize(inputs));
                for (List<IQueryParameterType> nextPermutation : inputPermutations) {

                        StringBuilder searchStringBuilder = new StringBuilder();
                        searchStringBuilder.append(myResourceName);
                        searchStringBuilder.append("?");

                        boolean first = true;
                        for (int paramIndex = 0; paramIndex < theComboParamNames.size(); paramIndex++) {

                                String nextParamName = theComboParamNames.get(paramIndex);
                                IQueryParameterType nextOr = nextPermutation.get(paramIndex);
                                // The only prefix accepted when combo searching is 'eq' (see validateParamValuesAreValidForComboParam).
                                // As a result, we strip the prefix if present.
                                String nextOrValue = stripStart(nextOr.getValueAsQueryToken(myContext), EQUAL.getValue());

                                RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(
                                                myResourceName, nextParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                                if (theComboParam.getComboSearchParamType() == ComboSearchParamType.NON_UNIQUE) {
                                        if (nextParamDef.getParamType() == RestSearchParameterTypeEnum.STRING) {
                                                nextOrValue = StringUtil.normalizeStringForSearchIndexing(nextOrValue);
                                        }
                                }

                                if (first) {
                                        first = false;
                                } else {
                                        searchStringBuilder.append('&');
                                }

                                nextParamName = UrlUtil.escapeUrlParam(nextParamName);
                                nextOrValue = UrlUtil.escapeUrlParam(nextOrValue);

                                searchStringBuilder.append(nextParamName).append('=').append(nextOrValue);
                        }

                        String indexString = searchStringBuilder.toString();
                        ourLog.debug(
                                        "Checking for {} combo index for query: {}", theComboParam.getComboSearchParamType(), indexString);

                        indexStrings.add(indexString);
                }

                // Just to make sure we're stable for tests
                indexStrings.sort(Comparator.naturalOrder());

                // Interceptor broadcast: JPA_PERFTRACE_INFO
                IInterceptorBroadcaster compositeBroadcaster =
                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest);
                if (compositeBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO)) {
                        String indexStringForLog = indexStrings.size() > 1 ? indexStrings.toString() : indexStrings.get(0);
                        StorageProcessingMessage msg = new StorageProcessingMessage()
                                        .setMessage("Using " + theComboParam.getComboSearchParamType() + " index(es) for query for search: "
                                                        + indexStringForLog);
                        HookParams params = new HookParams()
                                        .add(RequestDetails.class, theRequest)
                                        .addIfMatchesType(ServletRequestDetails.class, theRequest)
                                        .add(StorageProcessingMessage.class, msg);
                        compositeBroadcaster.callHooks(Pointcut.JPA_PERFTRACE_INFO, params);
                }

                switch (requireNonNull(theComboParam.getComboSearchParamType())) {
                        case UNIQUE:
                                theQueryStack.addPredicateCompositeUnique(indexStrings, myRequestPartitionId);
                                break;
                        case NON_UNIQUE:
                                theQueryStack.addPredicateCompositeNonUnique(indexStrings, myRequestPartitionId);
                                break;
                }

                // Remove any empty parameters remaining after this
                theParams.clean();
        }

        /**
         * Returns {@literal true} if the actual parameter instances in a given query are actually usable for
         * searching against a combo param with the given parameter names. This might be {@literal false} if
         * parameters have modifiers (e.g. <code>?name:exact=SIMPSON</code>), prefixes
         * (e.g. <code>?date=gt2024-02-01</code>), etc.
         */
        private boolean validateParamValuesAreValidForComboParam(
                        RequestDetails theRequest,
                        @Nonnull SearchParameterMap theParams,
                        List<String> theComboParamNames,
                        RuntimeSearchParam theComboParam) {
                boolean paramValuesAreValidForCombo = true;
                List<List<IQueryParameterType>> paramOrValues = new ArrayList<>(theComboParamNames.size());

                for (String nextParamName : theComboParamNames) {
                        List<List<IQueryParameterType>> nextValues = theParams.get(nextParamName);

                        if (nextValues == null || nextValues.isEmpty()) {
                                paramValuesAreValidForCombo = false;
                                break;
                        }

                        List<IQueryParameterType> nextAndValue = nextValues.get(0);
                        paramOrValues.add(nextAndValue);

                        for (IQueryParameterType nextOrValue : nextAndValue) {
                                if (nextOrValue instanceof DateParam) {
                                        DateParam dateParam = (DateParam) nextOrValue;
                                        if (dateParam.getPrecision() != TemporalPrecisionEnum.DAY) {
                                                String message = "Search with params " + theComboParamNames
                                                                + " is not a candidate for combo searching - Date search with non-DAY precision for parameter '"
                                                                + nextParamName + "'";
                                                firePerformanceInfo(theRequest, message);
                                                paramValuesAreValidForCombo = false;
                                                break;
                                        }
                                }
                                if (nextOrValue instanceof BaseParamWithPrefix) {
                                        BaseParamWithPrefix<?> paramWithPrefix = (BaseParamWithPrefix<?>) nextOrValue;
                                        ParamPrefixEnum prefix = paramWithPrefix.getPrefix();
                                        // A parameter with the 'eq' prefix is the only accepted prefix when combo searching since
                                        // birthdate=2025-01-01 and birthdate=eq2025-01-01 are equivalent searches.
                                        if (prefix != null && prefix != EQUAL) {
                                                String message = "Search with params " + theComboParamNames
                                                                + " is not a candidate for combo searching - Parameter '" + nextParamName
                                                                + "' has prefix: '"
                                                                + paramWithPrefix.getPrefix().getValue() + "'";
                                                firePerformanceInfo(theRequest, message);
                                                paramValuesAreValidForCombo = false;
                                                break;
                                        }
                                }
                                if (isNotBlank(nextOrValue.getQueryParameterQualifier())) {
                                        String message = "Search with params " + theComboParamNames
                                                        + " is not a candidate for combo searching - Parameter '" + nextParamName
                                                        + "' has modifier: '" + nextOrValue.getQueryParameterQualifier() + "'";
                                        firePerformanceInfo(theRequest, message);
                                        paramValuesAreValidForCombo = false;
                                        break;
                                }
                        }

                        // Reference params are only eligible for using a composite index if they
                        // are qualified
                        RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(
                                        myResourceName, nextParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                        if (nextParamDef.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
                                ReferenceParam param = (ReferenceParam) nextValues.get(0).get(0);
                                if (isBlank(param.getResourceType())) {
                                        ourLog.debug(
                                                        "Search is not a candidate for unique combo searching - Reference with no type specified");
                                        paramValuesAreValidForCombo = false;
                                        break;
                                }
                        }

                        // Date params are not eligible for using composite unique index
                        // as index could contain date with different precision (e.g. DAY, SECOND)
                        if (nextParamDef.getParamType() == RestSearchParameterTypeEnum.DATE
                                        && theComboParam.getComboSearchParamType() == ComboSearchParamType.UNIQUE) {
                                ourLog.debug(
                                                "Search with params {} is not a candidate for combo searching - "
                                                                + "Unique combo search parameter '{}' has DATE type",
                                                theComboParamNames,
                                                nextParamName);
                                paramValuesAreValidForCombo = false;
                                break;
                        }
                }

                if (CartesianProductUtil.calculateCartesianProductSize(paramOrValues) > 500) {
                        ourLog.debug(
                                        "Search is not a candidate for unique combo searching - Too many OR values would result in too many permutations");
                        paramValuesAreValidForCombo = false;
                }

                return paramValuesAreValidForCombo;
        }

        private <T> void ensureSubListsAreWritable(List<List<T>> theListOfLists) {
                for (int i = 0; i < theListOfLists.size(); i++) {
                        List<T> oldSubList = theListOfLists.get(i);
                        if (!(oldSubList instanceof ArrayList)) {
                                List<T> newSubList = new ArrayList<>(oldSubList);
                                theListOfLists.set(i, newSubList);
                        }
                }
        }

        @Override
        public void setFetchSize(int theFetchSize) {
                myFetchSize = theFetchSize;
        }

        public SearchParameterMap getParams() {
                return myParams;
        }

        public CriteriaBuilder getBuilder() {
                return myCriteriaBuilder;
        }

        public Class<? extends IBaseResource> getResourceType() {
                return myResourceType;
        }

        public String getResourceName() {
                return myResourceName;
        }

        /**
         * IncludesIterator, used to recursively fetch resources from the provided list of PIDs
         */
        public class IncludesIterator extends BaseIterator<JpaPid> implements Iterator<JpaPid> {

                private final RequestDetails myRequest;
                private final Set<JpaPid> myCurrentPids;
                private Iterator<JpaPid> myCurrentIterator;
                private JpaPid myNext;

                IncludesIterator(Set<JpaPid> thePidSet, RequestDetails theRequest) {
                        myCurrentPids = new HashSet<>(thePidSet);
                        myCurrentIterator = null;
                        myRequest = theRequest;
                }

                private void fetchNext() {
                        while (myNext == null) {

                                if (myCurrentIterator == null) {
                                        Set<Include> includes = new HashSet<>();
                                        if (myParams.containsKey(Constants.PARAM_TYPE)) {
                                                for (List<IQueryParameterType> typeList : myParams.get(Constants.PARAM_TYPE)) {
                                                        for (IQueryParameterType type : typeList) {
                                                                String queryString = ParameterUtil.unescape(type.getValueAsQueryToken(myContext));
                                                                for (String resourceType : queryString.split(",")) {
                                                                        String rt = resourceType.trim();
                                                                        if (isNotBlank(rt)) {
                                                                                includes.add(new Include(rt + ":*", true));
                                                                        }
                                                                }
                                                        }
                                                }
                                        }
                                        if (includes.isEmpty()) {
                                                includes.add(new Include("*", true));
                                        }
                                        Set<JpaPid> newPids = loadIncludes(
                                                        myContext,
                                                        myEntityManager,
                                                        myCurrentPids,
                                                        includes,
                                                        false,
                                                        getParams().getLastUpdated(),
                                                        mySearchUuid,
                                                        myRequest,
                                                        null);
                                        myCurrentIterator = newPids.iterator();
                                }

                                if (myCurrentIterator.hasNext()) {
                                        myNext = myCurrentIterator.next();
                                } else {
                                        myNext = NO_MORE;
                                }
                        }
                }

                @Override
                public boolean hasNext() {
                        fetchNext();
                        return !NO_MORE.equals(myNext);
                }

                @Override
                public JpaPid next() {
                        fetchNext();
                        JpaPid retVal = myNext;
                        myNext = null;
                        return retVal;
                }
        }

        /**
         * Basic Query iterator, used to fetch the results of a query.
         */
        private final class QueryIterator extends BaseIterator<JpaPid> implements IResultIterator<JpaPid> {

                private final SearchRuntimeDetails mySearchRuntimeDetails;
                private final RequestDetails myRequest;
                private final boolean myHaveRawSqlHooks;
                private final boolean myHavePerfTraceFoundIdHook;
                private final SortSpec mySort;
                private final Integer myOffset;
                private final IInterceptorBroadcaster myCompositeBroadcaster;
                private boolean myFirst = true;
                private IncludesIterator myIncludesIterator;
                /**
                 * The next JpaPid value of the next result in this query.
                 * Will not be null if fetched using getNext()
                 */
                private JpaPid myNext;
                /**
                 * The current query result iterator running sql and supplying PIDs
                 * @see #myQueryList
                 */
                private ISearchQueryExecutor myResultsIterator;

                private boolean myFetchIncludesForEverythingOperation;
                /**
                 * The count of resources skipped because they were seen in earlier results
                 */
                private int mySkipCount = 0;
                /**
                 * The count of resources that are new in this search
                 * (ie, not cached in previous searches)
                 */
                private int myNonSkipCount = 0;

                /**
                 * The list of queries to use to find all results.
                 * Normal JPA queries will normally have a single entry.
                 * Queries that involve Hibernate Search/Elastisearch may have
                 * multiple queries because of chunking.
                 * The $everything operation also jams some extra results in.
                 */
                private List<ISearchQueryExecutor> myQueryList = new ArrayList<>();

                private QueryIterator(SearchRuntimeDetails theSearchRuntimeDetails, RequestDetails theRequest) {
                        mySearchRuntimeDetails = theSearchRuntimeDetails;
                        mySort = myParams.getSort();
                        myOffset = myParams.getOffset();
                        myRequest = theRequest;
                        myCompositeBroadcaster =
                                        CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest);

                        // everything requires fetching recursively all related resources
                        if (myParams.getEverythingMode() != null) {
                                myFetchIncludesForEverythingOperation = true;
                        }

                        myHavePerfTraceFoundIdHook = myCompositeBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_SEARCH_FOUND_ID);
                        myHaveRawSqlHooks = myCompositeBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_RAW_SQL);
                }

                private void fetchNext() {
                        try {
                                if (myHaveRawSqlHooks) {
                                        CurrentThreadCaptureQueriesListener.startCapturing();
                                }

                                // If we don't have a query yet, create one
                                if (myResultsIterator == null) {
                                        if (!mySearchProperties.hasMaxResultsRequested()) {
                                                mySearchProperties.setMaxResultsRequested(calculateMaxResultsToFetch());
                                        }

                                        /*
                                         * assigns the results iterator
                                         * and populates the myQueryList.
                                         */
                                        initializeIteratorQuery(myOffset, mySearchProperties.getMaxResultsRequested());
                                }

                                if (myNext == null) {
                                        // no next means we need a new query (if one is available)
                                        while (myResultsIterator.hasNext() || !myQueryList.isEmpty()) {
                                                /*
                                                 * Because we combine our DB searches with Lucene
                                                 * sometimes we can have multiple results iterators
                                                 * (with only some having data in them to extract).
                                                 *
                                                 * We'll iterate our results iterators until we
                                                 * either run out of results iterators, or we
                                                 * have one that actually has data in it.
                                                 */
                                                while (!myResultsIterator.hasNext() && !myQueryList.isEmpty()) {
                                                        retrieveNextIteratorQuery();
                                                }

                                                if (!myResultsIterator.hasNext()) {
                                                        // we couldn't find a results iterator;
                                                        // we're done here
                                                        break;
                                                }

                                                JpaPid nextPid = myResultsIterator.next();
                                                if (myHavePerfTraceFoundIdHook) {
                                                        callPerformanceTracingHook(nextPid);
                                                }

                                                if (nextPid != null) {
                                                        if (!myPidSet.contains(nextPid)) {
                                                                if (!mySearchProperties.isDeduplicateInDatabase()) {
                                                                        /*
                                                                         * We only add to the map if we aren't fetching "everything";
                                                                         * otherwise, we let the de-duplication happen in the database
                                                                         * (see createChunkedQueryNormalSearch above), because it
                                                                         * saves memory that way.
                                                                         */
                                                                        myPidSet.add(nextPid);
                                                                }
                                                                if (doNotSkipNextPidForEverything()) {
                                                                        myNext = nextPid;
                                                                        myNonSkipCount++;
                                                                        break;
                                                                }
                                                        } else {
                                                                mySkipCount++;
                                                        }
                                                }

                                                if (!myResultsIterator.hasNext()) {
                                                        if (mySearchProperties.hasMaxResultsRequested()
                                                                        && (mySkipCount + myNonSkipCount == mySearchProperties.getMaxResultsRequested())) {
                                                                if (mySkipCount > 0 && myNonSkipCount == 0) {
                                                                        sendProcessingMsgAndFirePerformanceHook();
                                                                        // need the next iterator; increase the maxsize
                                                                        // (we should always do this)
                                                                        int maxResults = mySearchProperties.getMaxResultsRequested() + 1000;
                                                                        mySearchProperties.setMaxResultsRequested(maxResults);

                                                                        if (!mySearchProperties.isDeduplicateInDatabase()) {
                                                                                // if we're not using the database to deduplicate
                                                                                // we should recheck our memory usage
                                                                                // the prefetch size check is future proofing
                                                                                int prefetchSize = myStorageSettings
                                                                                                .getSearchPreFetchThresholds()
                                                                                                .size();
                                                                                if (prefetchSize > 0) {
                                                                                        if (myStorageSettings
                                                                                                                        .getSearchPreFetchThresholds()
                                                                                                                        .get(prefetchSize - 1)
                                                                                                        < mySearchProperties.getMaxResultsRequested()) {
                                                                                                mySearchProperties.setDeduplicateInDatabase(true);
                                                                                        }
                                                                                }
                                                                        }

                                                                        initializeIteratorQuery(myOffset, mySearchProperties.getMaxResultsRequested());
                                                                }
                                                        }
                                                }
                                        }
                                }

                                if (myNext == null) {
                                        // if we got here, it means the current JpaPid has already been processed,
                                        // and we will decide (here) if we need to fetch related resources recursively
                                        if (myFetchIncludesForEverythingOperation) {
                                                myIncludesIterator = new IncludesIterator(myPidSet, myRequest);
                                                myFetchIncludesForEverythingOperation = false;
                                        }
                                        if (myIncludesIterator != null) {
                                                while (myIncludesIterator.hasNext()) {
                                                        JpaPid next = myIncludesIterator.next();
                                                        if (next != null && myPidSet.add(next) && doNotSkipNextPidForEverything()) {
                                                                myNext = next;
                                                                break;
                                                        }
                                                }
                                                if (myNext == null) {
                                                        myNext = NO_MORE;
                                                }
                                        } else {
                                                myNext = NO_MORE;
                                        }
                                }

                                if (!mySearchProperties.hasMaxResultsRequested()) {
                                        mySearchRuntimeDetails.setFoundIndexMatchesCount(myNonSkipCount);
                                } else {
                                        mySearchRuntimeDetails.setFoundMatchesCount(myPidSet.size());
                                }

                        } finally {
                                // search finished - fire hooks
                                if (myHaveRawSqlHooks) {
                                        callRawSqlHookWithCurrentThreadQueries(myRequest, myCompositeBroadcaster);
                                }
                        }

                        if (myFirst) {
                                HookParams params = new HookParams()
                                                .add(RequestDetails.class, myRequest)
                                                .addIfMatchesType(ServletRequestDetails.class, myRequest)
                                                .add(SearchRuntimeDetails.class, mySearchRuntimeDetails);
                                myCompositeBroadcaster.callHooks(Pointcut.JPA_PERFTRACE_SEARCH_FIRST_RESULT_LOADED, params);
                                myFirst = false;
                        }

                        if (NO_MORE.equals(myNext)) {
                                HookParams params = new HookParams()
                                                .add(RequestDetails.class, myRequest)
                                                .addIfMatchesType(ServletRequestDetails.class, myRequest)
                                                .add(SearchRuntimeDetails.class, mySearchRuntimeDetails);
                                myCompositeBroadcaster.callHooks(Pointcut.JPA_PERFTRACE_SEARCH_SELECT_COMPLETE, params);
                        }
                }

                private Integer calculateMaxResultsToFetch() {
                        if (myParams.getLoadSynchronousUpTo() != null) {
                                return myParams.getLoadSynchronousUpTo();
                        } else if (myParams.getOffset() != null && myParams.getCount() != null) {
                                return myParams.getEverythingMode() != null
                                                ? myParams.getOffset() + myParams.getCount()
                                                : myParams.getCount();
                        } else {
                                return myStorageSettings.getFetchSizeDefaultMaximum();
                        }
                }

                private boolean doNotSkipNextPidForEverything() {
                        return !(myParams.getEverythingMode() != null && (myOffset != null && myOffset >= myPidSet.size()));
                }

                private void callPerformanceTracingHook(JpaPid theNextPid) {
                        HookParams params = new HookParams()
                                        .add(Integer.class, System.identityHashCode(this))
                                        .add(Object.class, theNextPid);
                        myCompositeBroadcaster.callHooks(Pointcut.JPA_PERFTRACE_SEARCH_FOUND_ID, params);
                }

                private void sendProcessingMsgAndFirePerformanceHook() {
                        String msg = "Pass completed with no matching results seeking rows "
                                        + myPidSet.size() + "-" + mySkipCount
                                        + ". This indicates an inefficient query! Retrying with new max count of "
                                        + mySearchProperties.getMaxResultsRequested();
                        firePerformanceWarning(myRequest, msg);
                }

                private void initializeIteratorQuery(Integer theOffset, Integer theMaxResultsToFetch) {
                        Integer offset = theOffset;
                        if (myQueryList.isEmpty()) {
                                // Capture times for Lucene/Elasticsearch queries as well
                                mySearchRuntimeDetails.setQueryStopwatch(new StopWatch());

                                // setting offset to 0 to fetch all resource ids to guarantee
                                // correct output result for everything operation during paging
                                if (myParams.getEverythingMode() != null) {
                                        offset = 0;
                                }

                                SearchQueryProperties properties = mySearchProperties.clone();
                                properties
                                                .setOffset(offset)
                                                .setMaxResultsRequested(theMaxResultsToFetch)
                                                .setDoCountOnlyFlag(false)
                                                .setDeduplicateInDatabase(properties.isDeduplicateInDatabase() || offset != null);
                                myQueryList = createQuery(myParams, properties, myRequest, mySearchRuntimeDetails);
                        }

                        mySearchRuntimeDetails.setQueryStopwatch(new StopWatch());

                        retrieveNextIteratorQuery();

                        mySkipCount = 0;
                        myNonSkipCount = 0;
                }

                private void retrieveNextIteratorQuery() {
                        close();
                        if (isNotEmpty(myQueryList)) {
                                myResultsIterator = myQueryList.remove(0);
                                myHasNextIteratorQuery = true;
                        } else {
                                myResultsIterator = SearchQueryExecutor.emptyExecutor();
                                myHasNextIteratorQuery = false;
                        }
                }

                @Override
                public boolean hasNext() {
                        if (myNext == null) {
                                fetchNext();
                        }
                        return !NO_MORE.equals(myNext);
                }

                @Override
                public JpaPid next() {
                        fetchNext();
                        JpaPid retVal = myNext;
                        myNext = null;
                        Validate.isTrue(!NO_MORE.equals(retVal), "No more elements");
                        return retVal;
                }

                @Override
                public int getSkippedCount() {
                        return mySkipCount;
                }

                @Override
                public int getNonSkippedCount() {
                        return myNonSkipCount;
                }

                @Override
                public Collection<JpaPid> getNextResultBatch(long theBatchSize) {
                        Collection<JpaPid> batch = new ArrayList<>();
                        while (this.hasNext() && batch.size() < theBatchSize) {
                                batch.add(this.next());
                        }
                        return batch;
                }

                @Override
                public void close() {
                        if (myResultsIterator != null) {
                                myResultsIterator.close();
                        }
                        myResultsIterator = null;
                }
        }

        private void firePerformanceInfo(RequestDetails theRequest, String theMessage) {
                // Only log at debug level since these messages aren't considered important enough
                // that we should be cluttering the system log, but they are important to the
                // specific query being executed to we'll INFO level them there
                ourLog.debug(theMessage);
                firePerformanceMessage(theRequest, theMessage, Pointcut.JPA_PERFTRACE_INFO);
        }

        private void firePerformanceWarning(RequestDetails theRequest, String theMessage) {
                ourLog.warn(theMessage);
                firePerformanceMessage(theRequest, theMessage, Pointcut.JPA_PERFTRACE_WARNING);
        }

        private void firePerformanceMessage(RequestDetails theRequest, String theMessage, Pointcut thePointcut) {
                IInterceptorBroadcaster compositeBroadcaster =
                                CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest);
                if (compositeBroadcaster.hasHooks(thePointcut)) {
                        StorageProcessingMessage message = new StorageProcessingMessage();
                        message.setMessage(theMessage);
                        HookParams params = new HookParams()
                                        .add(RequestDetails.class, theRequest)
                                        .addIfMatchesType(ServletRequestDetails.class, theRequest)
                                        .add(StorageProcessingMessage.class, message);
                        compositeBroadcaster.callHooks(thePointcut, params);
                }
        }

        public static int getMaximumPageSize() {
                if (myMaxPageSizeForTests != null) {
                        return myMaxPageSizeForTests;
                }
                return MAXIMUM_PAGE_SIZE;
        }

        public static void setMaxPageSizeForTest(Integer theTestSize) {
                myMaxPageSizeForTests = theTestSize;
        }
}