/*
 * #%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.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.exception.TokenParamFormatInvalidRequestException;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
import ca.uhn.fhir.jpa.search.builder.models.MissingParameterQueryParams;
import ca.uhn.fhir.jpa.search.builder.models.MissingQueryParameterPredicateParams;
import ca.uhn.fhir.jpa.search.builder.models.PredicateBuilderCacheKey;
import ca.uhn.fhir.jpa.search.builder.models.PredicateBuilderCacheLookupResult;
import ca.uhn.fhir.jpa.search.builder.models.PredicateBuilderTypeEnum;
import ca.uhn.fhir.jpa.search.builder.predicate.BaseJoiningPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.BaseQuantityPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.BaseSearchParamPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.ComboNonUniqueSearchParameterPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.ComboUniqueSearchParameterPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.CoordsPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.DatePredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.ICanMakeMissingParamPredicate;
import ca.uhn.fhir.jpa.search.builder.predicate.ISourcePredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.NumberPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.ParsedLocationParam;
import ca.uhn.fhir.jpa.search.builder.predicate.ResourceIdPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.ResourceLinkPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.ResourceTablePredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.SearchParamPresentPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.TagPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.UriPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.sql.ColumnTupleObject;
import ca.uhn.fhir.jpa.search.builder.sql.PredicateBuilderFactory;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor;
import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
import ca.uhn.fhir.jpa.searchparam.util.SourceParam;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.SearchIncludeDeletedEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.NumberParam;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.SpecialParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import com.healthmarketscience.sqlbuilder.BinaryCondition;
import com.healthmarketscience.sqlbuilder.ComboCondition;
import com.healthmarketscience.sqlbuilder.Condition;
import com.healthmarketscience.sqlbuilder.Expression;
import com.healthmarketscience.sqlbuilder.InCondition;
import com.healthmarketscience.sqlbuilder.SelectQuery;
import com.healthmarketscience.sqlbuilder.SetOperationQuery;
import com.healthmarketscience.sqlbuilder.Subquery;
import com.healthmarketscience.sqlbuilder.UnionQuery;
import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.Triple;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.util.CollectionUtils;

import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.function.Supplier;
import java.util.regex.Pattern;
import java.util.stream.Collectors;

import static ca.uhn.fhir.jpa.search.builder.QueryStack.SearchForIdsParams.with;
import static ca.uhn.fhir.jpa.search.builder.predicate.ResourceIdPredicateBuilder.getResourceIdColumn;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.fromOperation;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.getChainedPart;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.getParamNameWithPrefix;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.toAndPredicate;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.toEqualToOrInPredicate;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.toOperation;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.toOrPredicate;
import static ca.uhn.fhir.rest.api.Constants.PARAM_HAS;
import static ca.uhn.fhir.rest.api.Constants.PARAM_ID;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.split;

public class QueryStack {

        private static final Logger ourLog = LoggerFactory.getLogger(QueryStack.class);
        public static final String LOCATION_POSITION = "Location.position";
        private static final Pattern PATTERN_DOT_AND_ALL_AFTER = Pattern.compile("\\..*");

        private final FhirContext myFhirContext;
        private final SearchQueryBuilder mySqlBuilder;
        private final SearchParameterMap mySearchParameters;
        private final ISearchParamRegistry mySearchParamRegistry;
        private final PartitionSettings myPartitionSettings;
        private final JpaStorageSettings myStorageSettings;
        private final EnumSet<PredicateBuilderTypeEnum> myReusePredicateBuilderTypes;
        private final RequestDetails myRequestDetails;
        private Map<PredicateBuilderCacheKey, BaseJoiningPredicateBuilder> myJoinMap;
        private Map<String, BaseJoiningPredicateBuilder> myParamNameToPredicateBuilderMap;
        // used for _offset queries with sort, should be removed once the fix is applied to the async path too.
        private boolean myUseAggregate;
        private boolean myGroupingAdded;

        /**
         * Constructor
         */
        public QueryStack(
                        RequestDetails theRequestDetails,
                        SearchParameterMap theSearchParameters,
                        JpaStorageSettings theStorageSettings,
                        FhirContext theFhirContext,
                        SearchQueryBuilder theSqlBuilder,
                        ISearchParamRegistry theSearchParamRegistry,
                        PartitionSettings thePartitionSettings) {
                this(
                                theRequestDetails,
                                theSearchParameters,
                                theStorageSettings,
                                theFhirContext,
                                theSqlBuilder,
                                theSearchParamRegistry,
                                thePartitionSettings,
                                EnumSet.of(PredicateBuilderTypeEnum.DATE));
        }

        /**
         * Constructor
         */
        private QueryStack(
                        RequestDetails theRequestDetails,
                        SearchParameterMap theSearchParameters,
                        JpaStorageSettings theStorageSettings,
                        FhirContext theFhirContext,
                        SearchQueryBuilder theSqlBuilder,
                        ISearchParamRegistry theSearchParamRegistry,
                        PartitionSettings thePartitionSettings,
                        EnumSet<PredicateBuilderTypeEnum> theReusePredicateBuilderTypes) {
                myRequestDetails = theRequestDetails;
                myPartitionSettings = thePartitionSettings;
                assert theSearchParameters != null;
                assert theStorageSettings != null;
                assert theFhirContext != null;
                assert theSqlBuilder != null;

                mySearchParameters = theSearchParameters;
                myStorageSettings = theStorageSettings;
                myFhirContext = theFhirContext;
                mySqlBuilder = theSqlBuilder;
                mySearchParamRegistry = theSearchParamRegistry;
                myReusePredicateBuilderTypes = theReusePredicateBuilderTypes;
        }

        public void addSortOnCoordsNear(String theParamName, boolean theAscending, SearchParameterMap theParams) {
                boolean handled = false;
                if (myParamNameToPredicateBuilderMap != null) {
                        BaseJoiningPredicateBuilder builder = myParamNameToPredicateBuilderMap.get(theParamName);
                        if (builder instanceof CoordsPredicateBuilder) {
                                CoordsPredicateBuilder coordsBuilder = (CoordsPredicateBuilder) builder;

                                List<List<IQueryParameterType>> params = theParams.get(theParamName);
                                if (!params.isEmpty() && !params.get(0).isEmpty()) {
                                        IQueryParameterType param = params.get(0).get(0);
                                        ParsedLocationParam location = ParsedLocationParam.from(theParams, param);
                                        double latitudeValue = location.getLatitudeValue();
                                        double longitudeValue = location.getLongitudeValue();
                                        mySqlBuilder.addSortCoordsNear(coordsBuilder, latitudeValue, longitudeValue, theAscending);
                                        handled = true;
                                }
                        }
                }

                if (!handled) {
                        String msg = myFhirContext
                                        .getLocalizer()
                                        .getMessageSanitized(QueryStack.class, "cantSortOnCoordParamWithoutValues", theParamName);
                        throw new InvalidRequestException(Msg.code(2307) + msg);
                }
        }

        public void addSortOnDate(String theResourceName, String theParamName, boolean theAscending) {
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                DatePredicateBuilder datePredicateBuilder = mySqlBuilder.createDatePredicateBuilder();

                Condition hashIdentityPredicate =
                                datePredicateBuilder.createHashIdentityPredicate(theResourceName, theParamName);

                addSortCustomJoin(firstPredicateBuilder, datePredicateBuilder, hashIdentityPredicate);

                mySqlBuilder.addSortDate(datePredicateBuilder.getColumnValueLow(), theAscending, myUseAggregate);
        }

        public void addSortOnLastUpdated(boolean theAscending) {
                ResourceTablePredicateBuilder resourceTablePredicateBuilder;
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                if (firstPredicateBuilder instanceof ResourceTablePredicateBuilder) {
                        resourceTablePredicateBuilder = (ResourceTablePredicateBuilder) firstPredicateBuilder;
                } else {
                        resourceTablePredicateBuilder =
                                        mySqlBuilder.addResourceTablePredicateBuilder(firstPredicateBuilder.getJoinColumns());
                }
                mySqlBuilder.addSortDate(resourceTablePredicateBuilder.getColumnLastUpdated(), theAscending, myUseAggregate);
        }

        public void addSortOnNumber(String theResourceName, String theParamName, boolean theAscending) {
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                NumberPredicateBuilder numberPredicateBuilder = mySqlBuilder.createNumberPredicateBuilder();

                Condition hashIdentityPredicate =
                                numberPredicateBuilder.createHashIdentityPredicate(theResourceName, theParamName);

                addSortCustomJoin(firstPredicateBuilder, numberPredicateBuilder, hashIdentityPredicate);

                mySqlBuilder.addSortNumeric(numberPredicateBuilder.getColumnValue(), theAscending, myUseAggregate);
        }

        public void addSortOnQuantity(String theResourceName, String theParamName, boolean theAscending) {
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();

                BaseQuantityPredicateBuilder quantityPredicateBuilder = mySqlBuilder.createQuantityPredicateBuilder();

                Condition hashIdentityPredicate =
                                quantityPredicateBuilder.createHashIdentityPredicate(theResourceName, theParamName);

                addSortCustomJoin(firstPredicateBuilder, quantityPredicateBuilder, hashIdentityPredicate);

                mySqlBuilder.addSortNumeric(quantityPredicateBuilder.getColumnValue(), theAscending, myUseAggregate);
        }

        public void addSortOnResourceId(boolean theAscending) {
                ResourceTablePredicateBuilder resourceTablePredicateBuilder;
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                if (firstPredicateBuilder instanceof ResourceTablePredicateBuilder) {
                        resourceTablePredicateBuilder = (ResourceTablePredicateBuilder) firstPredicateBuilder;
                } else {
                        resourceTablePredicateBuilder =
                                        mySqlBuilder.addResourceTablePredicateBuilder(firstPredicateBuilder.getJoinColumns());
                }
                mySqlBuilder.addSortString(resourceTablePredicateBuilder.getColumnFhirId(), theAscending, myUseAggregate);
        }

        /** Sort on RES_ID -- used to break ties for reliable sort */
        public void addSortOnResourcePID(boolean theAscending) {
                BaseJoiningPredicateBuilder predicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                mySqlBuilder.addSortString(predicateBuilder.getResourceIdColumn(), theAscending);
        }

        public void addSortOnResourceLink(
                        String theResourceName,
                        String theReferenceTargetType,
                        String theParamName,
                        String theChain,
                        boolean theAscending,
                        SearchParameterMap theParams) {
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                ResourceLinkPredicateBuilder resourceLinkPredicateBuilder = mySqlBuilder.createReferencePredicateBuilder(this);

                Condition pathPredicate =
                                resourceLinkPredicateBuilder.createPredicateSourcePaths(theResourceName, theParamName);

                addSortCustomJoin(firstPredicateBuilder, resourceLinkPredicateBuilder, pathPredicate);

                if (isBlank(theChain)) {
                        mySqlBuilder.addSortNumeric(
                                        resourceLinkPredicateBuilder.getColumnTargetResourceId(), theAscending, myUseAggregate);
                        return;
                }

                String targetType = null;
                RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
                                theResourceName, theParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                if (theReferenceTargetType != null) {
                        targetType = theReferenceTargetType;
                } else if (param.getTargets().size() > 1) {
                        throw new InvalidRequestException(Msg.code(2287) + "Unable to sort on a chained parameter from '"
                                        + theParamName + "' as this parameter has multiple target types. Please specify the target type.");
                } else if (param.getTargets().size() == 1) {
                        targetType = param.getTargets().iterator().next();
                }

                if (isBlank(targetType)) {
                        throw new InvalidRequestException(
                                        Msg.code(2288) + "Unable to sort on a chained parameter from '" + theParamName
                                                        + "' as this parameter as this parameter does not define a target type. Please specify the target type.");
                }

                RuntimeSearchParam targetSearchParameter = mySearchParamRegistry.getActiveSearchParam(
                                targetType, theChain, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                if (targetSearchParameter == null) {
                        Collection<String> validSearchParameterNames = mySearchParamRegistry
                                        .getActiveSearchParams(targetType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
                                        .values()
                                        .stream()
                                        .filter(t -> t.getParamType() == RestSearchParameterTypeEnum.STRING
                                                        || t.getParamType() == RestSearchParameterTypeEnum.TOKEN
                                                        || t.getParamType() == RestSearchParameterTypeEnum.DATE)
                                        .map(RuntimeSearchParam::getName)
                                        .sorted()
                                        .distinct()
                                        .collect(Collectors.toList());
                        String msg = myFhirContext
                                        .getLocalizer()
                                        .getMessageSanitized(
                                                        BaseStorageDao.class,
                                                        "invalidSortParameter",
                                                        theChain,
                                                        targetType,
                                                        validSearchParameterNames);
                        throw new InvalidRequestException(Msg.code(2289) + msg);
                }

                // add a left-outer join to a predicate for the target type, then sort on value columns(s).
                switch (targetSearchParameter.getParamType()) {
                        case STRING:
                                StringPredicateBuilder stringPredicateBuilder = mySqlBuilder.createStringPredicateBuilder();
                                addSortCustomJoin(
                                                resourceLinkPredicateBuilder.getJoinColumnsForTarget(),
                                                stringPredicateBuilder,
                                                stringPredicateBuilder.createHashIdentityPredicate(targetType, theChain));

                                mySqlBuilder.addSortString(
                                                stringPredicateBuilder.getColumnValueNormalized(), theAscending, myUseAggregate);
                                return;

                        case TOKEN:
                                TokenPredicateBuilder tokenPredicateBuilder = mySqlBuilder.createTokenPredicateBuilder();
                                addSortCustomJoin(
                                                resourceLinkPredicateBuilder.getJoinColumnsForTarget(),
                                                tokenPredicateBuilder,
                                                tokenPredicateBuilder.createHashIdentityPredicate(targetType, theChain));

                                mySqlBuilder.addSortString(tokenPredicateBuilder.getColumnSystem(), theAscending, myUseAggregate);
                                mySqlBuilder.addSortString(tokenPredicateBuilder.getColumnValue(), theAscending, myUseAggregate);
                                return;

                        case DATE:
                                DatePredicateBuilder datePredicateBuilder = mySqlBuilder.createDatePredicateBuilder();
                                addSortCustomJoin(
                                                resourceLinkPredicateBuilder.getJoinColumnsForTarget(),
                                                datePredicateBuilder,
                                                datePredicateBuilder.createHashIdentityPredicate(targetType, theChain));

                                mySqlBuilder.addSortDate(datePredicateBuilder.getColumnValueLow(), theAscending, myUseAggregate);
                                return;

                                /*
                                 * Note that many of the options below aren't implemented because they
                                 * don't seem useful to me, but they could theoretically be implemented
                                 * if someone ever needed them. I'm not sure why you'd want to do a chained
                                 * sort on a target that was a reference or a quantity, but if someone needed
                                 * that we could implement it here.
                                 */
                        case SPECIAL: {
                                if (LOCATION_POSITION.equals(targetSearchParameter.getPath())) {
                                        List<List<IQueryParameterType>> params = theParams.get(theParamName);
                                        if (params != null && !params.isEmpty() && !params.get(0).isEmpty()) {
                                                IQueryParameterType locationParam = params.get(0).get(0);
                                                final SpecialParam specialParam =
                                                                new SpecialParam().setValue(locationParam.getValueAsQueryToken(myFhirContext));
                                                ParsedLocationParam location = ParsedLocationParam.from(theParams, specialParam);
                                                double latitudeValue = location.getLatitudeValue();
                                                double longitudeValue = location.getLongitudeValue();
                                                final CoordsPredicateBuilder coordsPredicateBuilder = mySqlBuilder.addCoordsPredicateBuilder(
                                                                resourceLinkPredicateBuilder.getJoinColumnsForTarget());
                                                mySqlBuilder.addSortCoordsNear(
                                                                coordsPredicateBuilder, latitudeValue, longitudeValue, theAscending);
                                        } else {
                                                String msg = myFhirContext
                                                                .getLocalizer()
                                                                .getMessageSanitized(
                                                                                QueryStack.class, "cantSortOnCoordParamWithoutValues", theParamName);
                                                throw new InvalidRequestException(Msg.code(2497) + msg);
                                        }
                                        return;
                                }
                        }
                                //noinspection fallthrough
                        case NUMBER:
                        case REFERENCE:
                        case COMPOSITE:
                        case QUANTITY:
                        case URI:
                        case HAS:

                        default:
                                throw new InvalidRequestException(Msg.code(2290) + "Unable to sort on a chained parameter "
                                                + theParamName + "." + theChain + " as this parameter. Can not sort on chains of target type: "
                                                + targetSearchParameter.getParamType().name());
                }
        }

        public void addSortOnString(String theResourceName, String theParamName, boolean theAscending) {
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();

                StringPredicateBuilder stringPredicateBuilder = mySqlBuilder.createStringPredicateBuilder();
                Condition hashIdentityPredicate =
                                stringPredicateBuilder.createHashIdentityPredicate(theResourceName, theParamName);

                addSortCustomJoin(firstPredicateBuilder, stringPredicateBuilder, hashIdentityPredicate);

                mySqlBuilder.addSortString(stringPredicateBuilder.getColumnValueNormalized(), theAscending, myUseAggregate);
        }

        public void addSortOnToken(String theResourceName, String theParamName, boolean theAscending) {
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();

                TokenPredicateBuilder tokenPredicateBuilder = mySqlBuilder.createTokenPredicateBuilder();
                Condition hashIdentityPredicate =
                                tokenPredicateBuilder.createHashIdentityPredicate(theResourceName, theParamName);

                addSortCustomJoin(firstPredicateBuilder, tokenPredicateBuilder, hashIdentityPredicate);

                mySqlBuilder.addSortString(tokenPredicateBuilder.getColumnSystem(), theAscending, myUseAggregate);
                mySqlBuilder.addSortString(tokenPredicateBuilder.getColumnValue(), theAscending, myUseAggregate);
        }

        public void addSortOnUri(String theResourceName, String theParamName, boolean theAscending) {
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();

                UriPredicateBuilder uriPredicateBuilder = mySqlBuilder.createUriPredicateBuilder();
                Condition hashIdentityPredicate =
                                uriPredicateBuilder.createHashIdentityPredicate(theResourceName, theParamName);

                addSortCustomJoin(firstPredicateBuilder, uriPredicateBuilder, hashIdentityPredicate);

                mySqlBuilder.addSortString(uriPredicateBuilder.getColumnValue(), theAscending, myUseAggregate);
        }

        private void addSortCustomJoin(
                        BaseJoiningPredicateBuilder theFromJoiningPredicateBuilder,
                        BaseJoiningPredicateBuilder theToJoiningPredicateBuilder,
                        Condition theCondition) {
                addSortCustomJoin(theFromJoiningPredicateBuilder.getJoinColumns(), theToJoiningPredicateBuilder, theCondition);
        }

        private void addSortCustomJoin(
                        DbColumn[] theFromDbColumn,
                        BaseJoiningPredicateBuilder theToJoiningPredicateBuilder,
                        Condition theCondition) {

                ComboCondition onCondition =
                                mySqlBuilder.createOnCondition(theFromDbColumn, theToJoiningPredicateBuilder.getJoinColumns());

                if (theCondition != null) {
                        onCondition.addCondition(theCondition);
                }

                mySqlBuilder.addCustomJoin(
                                SelectQuery.JoinType.LEFT_OUTER,
                                theFromDbColumn[0].getTable(),
                                theToJoiningPredicateBuilder.getTable(),
                                onCondition);
        }

        public void setUseAggregate(boolean theUseAggregate) {
                myUseAggregate = theUseAggregate;
        }

        @SuppressWarnings("unchecked")
        private <T extends BaseJoiningPredicateBuilder> PredicateBuilderCacheLookupResult<T> createOrReusePredicateBuilder(
                        PredicateBuilderTypeEnum theType,
                        DbColumn[] theSourceJoinColumn,
                        String theParamName,
                        Supplier<T> theFactoryMethod) {
                boolean cacheHit = false;
                BaseJoiningPredicateBuilder retVal;
                if (myReusePredicateBuilderTypes.contains(theType)) {
                        PredicateBuilderCacheKey key = new PredicateBuilderCacheKey(theSourceJoinColumn, theType, theParamName);
                        if (myJoinMap == null) {
                                myJoinMap = new HashMap<>();
                        }
                        retVal = myJoinMap.get(key);
                        if (retVal != null) {
                                cacheHit = true;
                        } else {
                                retVal = theFactoryMethod.get();
                                myJoinMap.put(key, retVal);
                        }
                } else {
                        retVal = theFactoryMethod.get();
                }

                if (theType == PredicateBuilderTypeEnum.COORDS) {
                        if (myParamNameToPredicateBuilderMap == null) {
                                myParamNameToPredicateBuilderMap = new HashMap<>();
                        }
                        myParamNameToPredicateBuilderMap.put(theParamName, retVal);
                }

                return new PredicateBuilderCacheLookupResult<>(cacheHit, (T) retVal);
        }

        private Condition createPredicateComposite(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSPNamePrefix,
                        RuntimeSearchParam theParamDef,
                        List<? extends IQueryParameterType> theNextAnd,
                        RequestPartitionId theRequestPartitionId) {
                return createPredicateComposite(
                                theSourceJoinColumn,
                                theResourceName,
                                theSPNamePrefix,
                                theParamDef,
                                theNextAnd,
                                theRequestPartitionId,
                                mySqlBuilder);
        }

        private Condition createPredicateComposite(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theParamDef,
                        List<? extends IQueryParameterType> theNextAnd,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {

                Condition orCondidtion = null;
                for (IQueryParameterType next : theNextAnd) {

                        if (!(next instanceof CompositeParam<?, ?>)) {
                                throw new InvalidRequestException(Msg.code(1203) + "Invalid type for composite param (must be "
                                                + CompositeParam.class.getSimpleName() + ": " + next.getClass());
                        }
                        CompositeParam<?, ?> cp = (CompositeParam<?, ?>) next;

                        List<RuntimeSearchParam> componentParams =
                                        JpaParamUtil.resolveCompositeComponentsDeclaredOrder(mySearchParamRegistry, theParamDef);
                        RuntimeSearchParam left = componentParams.get(0);
                        IQueryParameterType leftValue = cp.getLeftValue();
                        Condition leftPredicate = createPredicateCompositePart(
                                        theSourceJoinColumn,
                                        theResourceName,
                                        theSpnamePrefix,
                                        left,
                                        leftValue,
                                        theRequestPartitionId,
                                        theSqlBuilder);

                        RuntimeSearchParam right = componentParams.get(1);
                        IQueryParameterType rightValue = cp.getRightValue();
                        Condition rightPredicate = createPredicateCompositePart(
                                        theSourceJoinColumn,
                                        theResourceName,
                                        theSpnamePrefix,
                                        right,
                                        rightValue,
                                        theRequestPartitionId,
                                        theSqlBuilder);

                        Condition andCondition = toAndPredicate(leftPredicate, rightPredicate);

                        if (orCondidtion == null) {
                                orCondidtion = toOrPredicate(andCondition);
                        } else {
                                orCondidtion = toOrPredicate(orCondidtion, andCondition);
                        }
                }

                return orCondidtion;
        }

        private Condition createPredicateCompositePart(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theParam,
                        IQueryParameterType theParamValue,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {

                switch (theParam.getParamType()) {
                        case STRING: {
                                return createPredicateString(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParam,
                                                Collections.singletonList(theParamValue),
                                                null,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                        }
                        case TOKEN: {
                                return createPredicateToken(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParam,
                                                Collections.singletonList(theParamValue),
                                                null,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                        }
                        case DATE: {
                                return createPredicateDate(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParam,
                                                Collections.singletonList(theParamValue),
                                                toOperation(((DateParam) theParamValue).getPrefix()),
                                                theRequestPartitionId,
                                                theSqlBuilder);
                        }
                        case QUANTITY: {
                                return createPredicateQuantity(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParam,
                                                Collections.singletonList(theParamValue),
                                                null,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                        }
                        case NUMBER:
                        case REFERENCE:
                        case COMPOSITE:
                        case URI:
                        case HAS:
                        case SPECIAL:
                        default:
                                throw new InvalidRequestException(Msg.code(1204)
                                                + "Don't know how to handle composite parameter with type of " + theParam.getParamType());
                }
        }

        private Condition createMissingParameterQuery(MissingParameterQueryParams theParams) {
                if (theParams.getParamType() == RestSearchParameterTypeEnum.COMPOSITE) {
                        ourLog.error("Cannot create missing parameter query for a composite parameter.");
                        return null;
                } else if (theParams.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
                        if (isEligibleForEmbeddedChainedResourceSearch(
                                                        theParams.getResourceType(), theParams.getParamName(), theParams.getQueryParameterTypes())
                                        .supportsUplifted()) {
                                ourLog.error("Cannot construct missing query parameter search for ContainedResource REFERENCE search.");
                                return null;
                        }
                }

                // TODO - Change this when we have HFJ_SPIDX_MISSING table
                /*
                 * How we search depends on if the
                 * {@link JpaStorageSettings#getIndexMissingFields()} property
                 * is Enabled or Disabled.
                 *
                 * If it is, we will use the SP_MISSING values set into the various
                 * SP_INDX_X tables and search on those ("old" search).
                 *
                 * If it is not set, however, we will try and construct a query that
                 * looks for missing SearchParameters in the SP_IDX_* tables ("new" search).
                 *
                 * You cannot mix and match, however (SP_MISSING is not in HASH_IDENTITY information).
                 * So setting (or unsetting) the IndexMissingFields
                 * property should always be followed up with a /$reindex call.
                 *
                 * ---
                 *
                 * Current limitations:
                 * Checking if a row exists ("new" search) for a given missing field in an SP_INDX_* table
                 * (ie, :missing=true) is slow when there are many resources in the table. (Defaults to
                 * a table scan, since HASH_IDENTITY isn't part of the index).
                 *
                 * However, the "old" search method was slow for the reverse: when looking for resources
                 * that do not have a missing field (:missing=false) for much the same reason.
                 */
                SearchQueryBuilder sqlBuilder = theParams.getSqlBuilder();
                if (myStorageSettings.getIndexMissingFields() == JpaStorageSettings.IndexEnabledEnum.DISABLED) {
                        // new search
                        return createMissingPredicateForUnindexedMissingFields(theParams, sqlBuilder);
                } else {
                        // old search
                        return createMissingPredicateForIndexedMissingFields(theParams, sqlBuilder);
                }
        }

        /**
         * Old way of searching.
         * Missing values must be indexed!
         */
        private Condition createMissingPredicateForIndexedMissingFields(
                        MissingParameterQueryParams theParams, SearchQueryBuilder sqlBuilder) {
                PredicateBuilderTypeEnum predicateType = null;
                Supplier<? extends BaseJoiningPredicateBuilder> supplier = null;
                switch (theParams.getParamType()) {
                        case STRING:
                                predicateType = PredicateBuilderTypeEnum.STRING;
                                supplier = () -> sqlBuilder.addStringPredicateBuilder(theParams.getSourceJoinColumn());
                                break;
                        case NUMBER:
                                predicateType = PredicateBuilderTypeEnum.NUMBER;
                                supplier = () -> sqlBuilder.addNumberPredicateBuilder(theParams.getSourceJoinColumn());
                                break;
                        case DATE:
                                predicateType = PredicateBuilderTypeEnum.DATE;
                                supplier = () -> sqlBuilder.addDatePredicateBuilder(theParams.getSourceJoinColumn());
                                break;
                        case TOKEN:
                                predicateType = PredicateBuilderTypeEnum.TOKEN;
                                supplier = () -> sqlBuilder.addTokenPredicateBuilder(theParams.getSourceJoinColumn());
                                break;
                        case QUANTITY:
                                predicateType = PredicateBuilderTypeEnum.QUANTITY;
                                supplier = () -> sqlBuilder.addQuantityPredicateBuilder(theParams.getSourceJoinColumn());
                                break;
                        case REFERENCE:
                        case URI:
                                // we expect these values, but the pattern is slightly different;
                                // see below
                                break;
                        case HAS:
                        case SPECIAL:
                                predicateType = PredicateBuilderTypeEnum.COORDS;
                                supplier = () -> sqlBuilder.addCoordsPredicateBuilder(theParams.getSourceJoinColumn());
                                break;
                        case COMPOSITE:
                        default:
                                break;
                }

                if (supplier != null) {
                        BaseSearchParamPredicateBuilder join = (BaseSearchParamPredicateBuilder) createOrReusePredicateBuilder(
                                                        predicateType, theParams.getSourceJoinColumn(), theParams.getParamName(), supplier)
                                        .getResult();

                        return join.createPredicateParamMissingForNonReference(
                                        theParams.getResourceType(),
                                        theParams.getParamName(),
                                        theParams.isMissing(),
                                        theParams.getRequestPartitionId());
                } else {
                        if (theParams.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
                                SearchParamPresentPredicateBuilder join =
                                                sqlBuilder.addSearchParamPresentPredicateBuilder(theParams.getSourceJoinColumn());
                                return join.createPredicateParamMissingForReference(
                                                theParams.getResourceType(),
                                                theParams.getParamName(),
                                                theParams.isMissing(),
                                                theParams.getRequestPartitionId());
                        } else if (theParams.getParamType() == RestSearchParameterTypeEnum.URI) {
                                UriPredicateBuilder join = sqlBuilder.addUriPredicateBuilder(theParams.getSourceJoinColumn());
                                return join.createPredicateParamMissingForNonReference(
                                                theParams.getResourceType(),
                                                theParams.getParamName(),
                                                theParams.isMissing(),
                                                theParams.getRequestPartitionId());
                        } else {
                                // we don't expect to see this
                                ourLog.error("Invalid param type " + theParams.getParamType().name());
                                return null;
                        }
                }
        }

        /**
         * New way of searching for missing fields.
         * Missing values must not indexed!
         */
        private Condition createMissingPredicateForUnindexedMissingFields(
                        MissingParameterQueryParams theParams, SearchQueryBuilder sqlBuilder) {
                ResourceTablePredicateBuilder table = sqlBuilder.getOrCreateResourceTablePredicateBuilder();

                ICanMakeMissingParamPredicate innerQuery = PredicateBuilderFactory.createPredicateBuilderForParamType(
                                theParams.getParamType(), theParams.getSqlBuilder(), this);
                return innerQuery.createPredicateParamMissingValue(new MissingQueryParameterPredicateParams(
                                table, theParams.isMissing(), theParams.getParamName(), theParams.getRequestPartitionId()));
        }

        public Condition createPredicateCoords(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {
                Boolean isMissing = theList.get(0).getMissing();
                if (isMissing != null) {
                        String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());

                        return createMissingParameterQuery(new MissingParameterQueryParams(
                                        theSqlBuilder,
                                        theSearchParam.getParamType(),
                                        theList,
                                        paramName,
                                        theResourceName,
                                        theSourceJoinColumn,
                                        theRequestPartitionId));
                } else {
                        CoordsPredicateBuilder predicateBuilder = createOrReusePredicateBuilder(
                                                        PredicateBuilderTypeEnum.COORDS,
                                                        theSourceJoinColumn,
                                                        theSearchParam.getName(),
                                                        () -> mySqlBuilder.addCoordsPredicateBuilder(theSourceJoinColumn))
                                        .getResult();

                        List<Condition> codePredicates = new ArrayList<>();
                        for (IQueryParameterType nextOr : theList) {
                                Condition singleCode = predicateBuilder.createPredicateCoords(
                                                mySearchParameters,
                                                nextOr,
                                                theResourceName,
                                                theSearchParam,
                                                predicateBuilder,
                                                theRequestPartitionId);
                                codePredicates.add(singleCode);
                        }

                        return predicateBuilder.combineWithRequestPartitionIdPredicate(
                                        theRequestPartitionId, ComboCondition.or(codePredicates.toArray(new Condition[0])));
                }
        }

        public Condition createPredicateDate(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId) {
                return createPredicateDate(
                                theSourceJoinColumn,
                                theResourceName,
                                theSpnamePrefix,
                                theSearchParam,
                                theList,
                                theOperation,
                                theRequestPartitionId,
                                mySqlBuilder);
        }

        public Condition createPredicateDate(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {
                String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());

                Boolean isMissing = theList.get(0).getMissing();
                if (isMissing != null) {
                        return createMissingParameterQuery(new MissingParameterQueryParams(
                                        theSqlBuilder,
                                        theSearchParam.getParamType(),
                                        theList,
                                        paramName,
                                        theResourceName,
                                        theSourceJoinColumn,
                                        theRequestPartitionId));
                } else {
                        PredicateBuilderCacheLookupResult<DatePredicateBuilder> predicateBuilderLookupResult =
                                        createOrReusePredicateBuilder(
                                                        PredicateBuilderTypeEnum.DATE,
                                                        theSourceJoinColumn,
                                                        paramName,
                                                        () -> theSqlBuilder.addDatePredicateBuilder(theSourceJoinColumn));
                        DatePredicateBuilder predicateBuilder = predicateBuilderLookupResult.getResult();
                        boolean cacheHit = predicateBuilderLookupResult.isCacheHit();

                        List<Condition> codePredicates = new ArrayList<>();

                        for (IQueryParameterType nextOr : theList) {
                                Condition p = predicateBuilder.createPredicateDateWithoutIdentityPredicate(nextOr, theOperation);
                                codePredicates.add(p);
                        }

                        Condition predicate = toOrPredicate(codePredicates);

                        if (!cacheHit) {
                                predicate = predicateBuilder.combineWithHashIdentityPredicate(theResourceName, paramName, predicate);
                                predicate = predicateBuilder.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
                        }

                        return predicate;
                }
        }

        private Condition createPredicateFilter(
                        QueryStack theQueryStack3,
                        SearchFilterParser.BaseFilter theFilter,
                        String theResourceName,
                        RequestPartitionId theRequestPartitionId) {

                if (theFilter instanceof SearchFilterParser.FilterParameter) {
                        return createPredicateFilter(
                                        theQueryStack3,
                                        (SearchFilterParser.FilterParameter) theFilter,
                                        theResourceName,
                                        theRequestPartitionId);
                } else if (theFilter instanceof SearchFilterParser.FilterLogical) {
                        // Left side
                        Condition xPredicate = createPredicateFilter(
                                        theQueryStack3,
                                        ((SearchFilterParser.FilterLogical) theFilter).getFilter1(),
                                        theResourceName,
                                        theRequestPartitionId);

                        // Right side
                        Condition yPredicate = createPredicateFilter(
                                        theQueryStack3,
                                        ((SearchFilterParser.FilterLogical) theFilter).getFilter2(),
                                        theResourceName,
                                        theRequestPartitionId);

                        if (((SearchFilterParser.FilterLogical) theFilter).getOperation()
                                        == SearchFilterParser.FilterLogicalOperation.and) {
                                return ComboCondition.and(xPredicate, yPredicate);
                        } else if (((SearchFilterParser.FilterLogical) theFilter).getOperation()
                                        == SearchFilterParser.FilterLogicalOperation.or) {
                                return ComboCondition.or(xPredicate, yPredicate);
                        } else {
                                // Shouldn't happen
                                throw new InvalidRequestException(Msg.code(1205) + "Don't know how to handle operation "
                                                + ((SearchFilterParser.FilterLogical) theFilter).getOperation());
                        }
                } else {
                        return createPredicateFilter(
                                        theQueryStack3,
                                        ((SearchFilterParser.FilterParameterGroup) theFilter).getContained(),
                                        theResourceName,
                                        theRequestPartitionId);
                }
        }

        private Condition createPredicateFilter(
                        QueryStack theQueryStack3,
                        SearchFilterParser.FilterParameter theFilter,
                        String theResourceName,
                        RequestPartitionId theRequestPartitionId) {

                String paramName = theFilter.getParamPath().getName();

                switch (paramName) {
                        case IAnyResource.SP_RES_ID: {
                                TokenParam param = new TokenParam();
                                param.setValueAsQueryToken(null, null, null, theFilter.getValue());

                                SearchForIdsParams searchForIdsParams = with().setAndOrParams(
                                                                Collections.singletonList(Collections.singletonList(param)))
                                                .setResourceName(theResourceName)
                                                .setOperation(theFilter.getOperation())
                                                .setRequestPartitionId(theRequestPartitionId);
                                return theQueryStack3.createPredicateResourceId(searchForIdsParams);
                        }
                        case Constants.PARAM_SOURCE: {
                                TokenParam param = new TokenParam();
                                param.setValueAsQueryToken(null, null, null, theFilter.getValue());
                                return createPredicateSource(null, Collections.singletonList(param));
                        }
                        default:
                                RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(
                                                theResourceName, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                                if (searchParam == null) {
                                        Collection<String> validNames = mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(
                                                        theResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                                        String msg = myFhirContext
                                                        .getLocalizer()
                                                        .getMessageSanitized(
                                                                        BaseStorageDao.class,
                                                                        "invalidSearchParameter",
                                                                        paramName,
                                                                        theResourceName,
                                                                        validNames);
                                        throw new InvalidRequestException(Msg.code(1206) + msg);
                                }
                                RestSearchParameterTypeEnum typeEnum = searchParam.getParamType();
                                if (typeEnum == RestSearchParameterTypeEnum.URI) {
                                        return theQueryStack3.createPredicateUri(
                                                        null,
                                                        theResourceName,
                                                        null,
                                                        searchParam,
                                                        Collections.singletonList(new UriParam(theFilter.getValue())),
                                                        theFilter.getOperation(),
                                                        theRequestPartitionId);
                                } else if (typeEnum == RestSearchParameterTypeEnum.STRING) {
                                        return theQueryStack3.createPredicateString(
                                                        null,
                                                        theResourceName,
                                                        null,
                                                        searchParam,
                                                        Collections.singletonList(new StringParam(theFilter.getValue())),
                                                        theFilter.getOperation(),
                                                        theRequestPartitionId);
                                } else if (typeEnum == RestSearchParameterTypeEnum.DATE) {
                                        return theQueryStack3.createPredicateDate(
                                                        null,
                                                        theResourceName,
                                                        null,
                                                        searchParam,
                                                        Collections.singletonList(
                                                                        new DateParam(fromOperation(theFilter.getOperation()), theFilter.getValue())),
                                                        theFilter.getOperation(),
                                                        theRequestPartitionId);
                                } else if (typeEnum == RestSearchParameterTypeEnum.NUMBER) {
                                        return theQueryStack3.createPredicateNumber(
                                                        null,
                                                        theResourceName,
                                                        null,
                                                        searchParam,
                                                        Collections.singletonList(new NumberParam(theFilter.getValue())),
                                                        theFilter.getOperation(),
                                                        theRequestPartitionId);
                                } else if (typeEnum == RestSearchParameterTypeEnum.REFERENCE) {
                                        SearchFilterParser.CompareOperation operation = theFilter.getOperation();
                                        String resourceType =
                                                        null; // The value can either have (Patient/123) or not have (123) a resource type, either
                                        // way it's not needed here
                                        String chain = (theFilter.getParamPath().getNext() != null)
                                                        ? theFilter.getParamPath().getNext().toString()
                                                        : null;
                                        String value = theFilter.getValue();
                                        ReferenceParam referenceParam = new ReferenceParam(resourceType, chain, value);
                                        return theQueryStack3.createPredicateReference(
                                                        null,
                                                        theResourceName,
                                                        paramName,
                                                        new ArrayList<>(),
                                                        Collections.singletonList(referenceParam),
                                                        operation,
                                                        theRequestPartitionId);
                                } else if (typeEnum == RestSearchParameterTypeEnum.QUANTITY) {
                                        return theQueryStack3.createPredicateQuantity(
                                                        null,
                                                        theResourceName,
                                                        null,
                                                        searchParam,
                                                        Collections.singletonList(new QuantityParam(theFilter.getValue())),
                                                        theFilter.getOperation(),
                                                        theRequestPartitionId);
                                } else if (typeEnum == RestSearchParameterTypeEnum.COMPOSITE) {
                                        throw new InvalidRequestException(Msg.code(1207)
                                                        + "Composite search parameters not currently supported with _filter clauses");
                                } else if (typeEnum == RestSearchParameterTypeEnum.TOKEN) {
                                        TokenParam param = new TokenParam();
                                        param.setValueAsQueryToken(null, null, null, theFilter.getValue());
                                        return theQueryStack3.createPredicateToken(
                                                        null,
                                                        theResourceName,
                                                        null,
                                                        searchParam,
                                                        Collections.singletonList(param),
                                                        theFilter.getOperation(),
                                                        theRequestPartitionId);
                                }
                                break;
                }
                return null;
        }

        private Condition createPredicateHas(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceType,
                        List<List<IQueryParameterType>> theHasParameters,
                        RequestDetails theRequest,
                        RequestPartitionId theRequestPartitionId) {

                List<Condition> andPredicates = new ArrayList<>();
                for (List<? extends IQueryParameterType> nextOrList : theHasParameters) {

                        String targetResourceType = null;
                        String paramReference = null;
                        String parameterName = null;

                        String paramName = null;
                        List<QualifiedParamList> parameters = new ArrayList<>();
                        for (IQueryParameterType nextParam : nextOrList) {
                                HasParam next = (HasParam) nextParam;
                                targetResourceType = next.getTargetResourceType();
                                paramReference = next.getReferenceFieldName();
                                parameterName = next.getParameterName();
                                paramName = PATTERN_DOT_AND_ALL_AFTER.matcher(parameterName).replaceAll("");
                                parameters.add(QualifiedParamList.singleton(null, next.getValueAsQueryToken(myFhirContext)));
                        }

                        if (paramName == null) {
                                continue;
                        }

                        try {
                                myFhirContext.getResourceDefinition(targetResourceType);
                        } catch (DataFormatException e) {
                                throw new InvalidRequestException(Msg.code(1208) + "Invalid resource type: " + targetResourceType);
                        }

                        ArrayList<IQueryParameterType> orValues = Lists.newArrayList();

                        if (paramName.startsWith("_has:")) {

                                ourLog.trace("Handling double _has query: {}", paramName);

                                String qualifier = paramName.substring(4);
                                for (IQueryParameterType next : nextOrList) {
                                        HasParam nextHasParam = new HasParam();
                                        nextHasParam.setValueAsQueryToken(
                                                        myFhirContext, PARAM_HAS, qualifier, next.getValueAsQueryToken(myFhirContext));
                                        orValues.add(nextHasParam);
                                }

                        } else if (paramName.equals(PARAM_ID)) {

                                for (IQueryParameterType next : nextOrList) {
                                        orValues.add(new TokenParam(next.getValueAsQueryToken(myFhirContext)));
                                }

                        } else {

                                // Ensure that the name of the search param
                                // (e.g. the `code` in Patient?_has:Observation:subject:code=sys|val)
                                // exists on the target resource type.
                                RuntimeSearchParam owningParameterDef = mySearchParamRegistry.getRuntimeSearchParam(
                                                targetResourceType, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);

                                // Ensure that the name of the back-referenced search param on the target (e.g. the `subject` in
                                // Patient?_has:Observation:subject:code=sys|val)
                                // exists on the target resource, or in the top-level Resource resource.
                                mySearchParamRegistry.getRuntimeSearchParam(
                                                targetResourceType, paramReference, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);

                                IQueryParameterAnd<?> parsedParam = JpaParamUtil.parseQueryParams(
                                                mySearchParamRegistry, myFhirContext, owningParameterDef, paramName, parameters);

                                for (IQueryParameterOr<?> next : parsedParam.getValuesAsQueryTokens()) {
                                        orValues.addAll(next.getValuesAsQueryTokens());
                                }
                        }

                        // Handle internal chain inside the has.
                        if (parameterName.contains(".")) {
                                // Previously, for some unknown reason, we were calling getChainedPart() twice.  This broke the _has
                                // then chain, then _has use case by effectively cutting off the second part of the chain and
                                // missing one iteration of the recursive call to build the query.
                                // So, for example, for
                                // Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor._has:List:item:_id=list1
                                // instead of passing " payor._has:List:item:_id=list1" to the next recursion, the second call to
                                // getChainedPart() was wrongly removing "payor." and passing down "_has:List:item:_id=list1" instead.
                                // This resulted in running incorrect SQL with nonsensical join that resulted in 0 results.
                                // However, after running the pipeline,  I've concluded there's no use case at all for the
                                // double call to "getChainedPart()", which is why there's no conditional logic at all to make a double
                                // call to getChainedPart().
                                final String chainedPart = getChainedPart(parameterName);

                                orValues.stream()
                                                .filter(qp -> qp instanceof ReferenceParam)
                                                .map(qp -> (ReferenceParam) qp)
                                                .forEach(rp -> rp.setChain(chainedPart));

                                parameterName = parameterName.substring(0, parameterName.indexOf('.'));
                        }

                        int colonIndex = parameterName.indexOf(':');
                        if (colonIndex != -1) {
                                parameterName = parameterName.substring(0, colonIndex);
                        }

                        ResourceLinkPredicateBuilder resourceLinkTableJoin =
                                        mySqlBuilder.addReferencePredicateBuilderReversed(this, theSourceJoinColumn);

                        List<String> paths = resourceLinkTableJoin.createResourceLinkPaths(
                                        targetResourceType, paramReference, new ArrayList<>());
                        if (CollectionUtils.isEmpty(paths)) {
                                throw new InvalidRequestException(Msg.code(2305) + "Reference field does not exist: " + paramReference);
                        }

                        Condition typePredicate = BinaryCondition.equalTo(
                                        resourceLinkTableJoin.getColumnTargetResourceType(),
                                        mySqlBuilder.generatePlaceholder(theResourceType));
                        Condition pathPredicate = toEqualToOrInPredicate(
                                        resourceLinkTableJoin.getColumnSourcePath(), mySqlBuilder.generatePlaceholders(paths));

                        Condition linkedPredicate =
                                        searchForIdsWithAndOr(with().setSourceJoinColumn(resourceLinkTableJoin.getJoinColumnsForSource())
                                                        .setResourceName(targetResourceType)
                                                        .setParamName(parameterName)
                                                        .setAndOrParams(Collections.singletonList(orValues))
                                                        .setRequest(theRequest)
                                                        .setRequestPartitionId(theRequestPartitionId));

                        if (myPartitionSettings.isDatabasePartitionMode()) {
                                andPredicates.add(toAndPredicate(pathPredicate, typePredicate, linkedPredicate));
                        } else {
                                Condition partitionPredicate = resourceLinkTableJoin.createPartitionIdPredicate(theRequestPartitionId);
                                andPredicates.add(toAndPredicate(partitionPredicate, pathPredicate, typePredicate, linkedPredicate));
                        }
                }

                return toAndPredicate(andPredicates);
        }

        public Condition createPredicateNumber(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId) {
                return createPredicateNumber(
                                theSourceJoinColumn,
                                theResourceName,
                                theSpnamePrefix,
                                theSearchParam,
                                theList,
                                theOperation,
                                theRequestPartitionId,
                                mySqlBuilder);
        }

        public Condition createPredicateNumber(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {

                String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());

                Boolean isMissing = theList.get(0).getMissing();
                if (isMissing != null) {
                        return createMissingParameterQuery(new MissingParameterQueryParams(
                                        theSqlBuilder,
                                        theSearchParam.getParamType(),
                                        theList,
                                        paramName,
                                        theResourceName,
                                        theSourceJoinColumn,
                                        theRequestPartitionId));
                } else {
                        NumberPredicateBuilder join = createOrReusePredicateBuilder(
                                                        PredicateBuilderTypeEnum.NUMBER,
                                                        theSourceJoinColumn,
                                                        paramName,
                                                        () -> theSqlBuilder.addNumberPredicateBuilder(theSourceJoinColumn))
                                        .getResult();

                        List<Condition> codePredicates = new ArrayList<>();
                        for (IQueryParameterType nextOr : theList) {

                                if (nextOr instanceof NumberParam) {
                                        NumberParam param = (NumberParam) nextOr;

                                        BigDecimal value = param.getValue();
                                        if (value == null) {
                                                continue;
                                        }

                                        SearchFilterParser.CompareOperation operation = theOperation;
                                        if (operation == null) {
                                                operation = toOperation(param.getPrefix());
                                        }

                                        Condition predicate = join.createPredicateNumeric(
                                                        theResourceName, paramName, operation, value, theRequestPartitionId, nextOr);
                                        codePredicates.add(predicate);

                                } else {
                                        throw new IllegalArgumentException(Msg.code(1211) + "Invalid token type: " + nextOr.getClass());
                                }
                        }

                        return join.combineWithRequestPartitionIdPredicate(
                                        theRequestPartitionId, ComboCondition.or(codePredicates.toArray(new Condition[0])));
                }
        }

        public Condition createPredicateQuantity(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId) {
                return createPredicateQuantity(
                                theSourceJoinColumn,
                                theResourceName,
                                theSpnamePrefix,
                                theSearchParam,
                                theList,
                                theOperation,
                                theRequestPartitionId,
                                mySqlBuilder);
        }

        public Condition createPredicateQuantity(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {

                String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());

                Boolean isMissing = theList.get(0).getMissing();
                if (isMissing != null) {
                        return createMissingParameterQuery(new MissingParameterQueryParams(
                                        theSqlBuilder,
                                        theSearchParam.getParamType(),
                                        theList,
                                        paramName,
                                        theResourceName,
                                        theSourceJoinColumn,
                                        theRequestPartitionId));
                } else {
                        List<QuantityParam> quantityParams =
                                        theList.stream().map(QuantityParam::toQuantityParam).collect(Collectors.toList());

                        BaseQuantityPredicateBuilder join = null;
                        boolean normalizedSearchEnabled = myStorageSettings
                                        .getNormalizedQuantitySearchLevel()
                                        .equals(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED);
                        if (normalizedSearchEnabled) {
                                List<QuantityParam> normalizedQuantityParams = quantityParams.stream()
                                                .map(UcumServiceUtil::toCanonicalQuantityOrNull)
                                                .filter(Objects::nonNull)
                                                .collect(Collectors.toList());

                                if (normalizedQuantityParams.size() == quantityParams.size()) {
                                        join = createOrReusePredicateBuilder(
                                                                        PredicateBuilderTypeEnum.QUANTITY,
                                                                        theSourceJoinColumn,
                                                                        paramName,
                                                                        () -> theSqlBuilder.addQuantityNormalizedPredicateBuilder(theSourceJoinColumn))
                                                        .getResult();
                                        quantityParams = normalizedQuantityParams;
                                }
                        }

                        if (join == null) {
                                join = createOrReusePredicateBuilder(
                                                                PredicateBuilderTypeEnum.QUANTITY,
                                                                theSourceJoinColumn,
                                                                paramName,
                                                                () -> theSqlBuilder.addQuantityPredicateBuilder(theSourceJoinColumn))
                                                .getResult();
                        }

                        List<Condition> codePredicates = new ArrayList<>();
                        for (QuantityParam nextOr : quantityParams) {
                                Condition singleCode = join.createPredicateQuantity(
                                                nextOr, theResourceName, paramName, null, join, theOperation, theRequestPartitionId);
                                codePredicates.add(singleCode);
                        }

                        return join.combineWithRequestPartitionIdPredicate(
                                        theRequestPartitionId, ComboCondition.or(codePredicates.toArray(new Condition[0])));
                }
        }

        public Condition createPredicateReference(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theParamName,
                        List<String> theQualifiers,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId) {
                return createPredicateReference(
                                theSourceJoinColumn,
                                theResourceName,
                                theParamName,
                                theQualifiers,
                                theList,
                                theOperation,
                                theRequestPartitionId,
                                mySqlBuilder);
        }

        public Condition createPredicateReference(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theParamName,
                        List<String> theQualifiers,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {

                if ((theOperation != null)
                                && (theOperation != SearchFilterParser.CompareOperation.eq)
                                && (theOperation != SearchFilterParser.CompareOperation.ne)) {
                        throw new InvalidRequestException(
                                        Msg.code(1212)
                                                        + "Invalid operator specified for reference predicate.  Supported operators for reference predicate are \"eq\" and \"ne\".");
                }

                Boolean isMissing = theList.get(0).getMissing();
                if (isMissing != null) {
                        return createMissingParameterQuery(new MissingParameterQueryParams(
                                        theSqlBuilder,
                                        RestSearchParameterTypeEnum.REFERENCE,
                                        theList,
                                        theParamName,
                                        theResourceName,
                                        theSourceJoinColumn,
                                        theRequestPartitionId));
                } else {
                        ResourceLinkPredicateBuilder predicateBuilder = createOrReusePredicateBuilder(
                                                        PredicateBuilderTypeEnum.REFERENCE,
                                                        theSourceJoinColumn,
                                                        theParamName,
                                                        () -> theSqlBuilder.addReferencePredicateBuilder(this, theSourceJoinColumn))
                                        .getResult();
                        return predicateBuilder.createPredicate(
                                        myRequestDetails,
                                        theResourceName,
                                        theParamName,
                                        theQualifiers,
                                        theList,
                                        theOperation,
                                        theRequestPartitionId);
                }
        }

        public void addGrouping() {
                if (!myGroupingAdded) {
                        BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();

                        /*
                         * Postgres and Oracle don't like it if we are doing a SELECT DISTINCT
                         * with multiple selected columns but no GROUP BY clause.
                         */
                        if (mySqlBuilder.isSelectPartitionId()) {
                                mySqlBuilder
                                                .getSelect()
                                                .addGroupings(
                                                                firstPredicateBuilder.getPartitionIdColumn(),
                                                                firstPredicateBuilder.getResourceIdColumn());
                        } else {
                                mySqlBuilder.getSelect().addGroupings(firstPredicateBuilder.getJoinColumns());
                        }
                        myGroupingAdded = true;
                }
        }

        public void addOrdering() {
                BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                mySqlBuilder.getSelect().addOrderings(firstPredicateBuilder.getJoinColumns());
        }

        public Condition createPredicateReferenceForEmbeddedChainedSearchResource(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId,
                        EmbeddedChainedSearchModeEnum theEmbeddedChainedSearchModeEnum) {

                boolean wantChainedAndNormal =
                                theEmbeddedChainedSearchModeEnum == EmbeddedChainedSearchModeEnum.UPLIFTED_AND_REF_JOIN;

                // A bit of a hack, but we need to turn off cache reuse while in this method so that we don't try to reuse
                // builders across different subselects
                EnumSet<PredicateBuilderTypeEnum> cachedReusePredicateBuilderTypes =
                                EnumSet.copyOf(myReusePredicateBuilderTypes);
                if (wantChainedAndNormal) {
                        myReusePredicateBuilderTypes.clear();
                }

                ReferenceChainExtractor chainExtractor = new ReferenceChainExtractor();
                chainExtractor.deriveChains(theResourceName, theSearchParam, theList);
                Map<List<ChainElement>, Set<LeafNodeDefinition>> chains = chainExtractor.getChains();

                Map<List<String>, Set<LeafNodeDefinition>> referenceLinks = Maps.newHashMap();
                for (List<ChainElement> nextChain : chains.keySet()) {
                        Set<LeafNodeDefinition> leafNodes = chains.get(nextChain);

                        collateChainedSearchOptions(referenceLinks, nextChain, leafNodes, theEmbeddedChainedSearchModeEnum);
                }

                UnionQuery union = null;
                if (wantChainedAndNormal) {
                        union = new UnionQuery(SetOperationQuery.Type.UNION_ALL);
                }

                List<Condition> predicates = new ArrayList<>();
                for (List<String> nextReferenceLink : referenceLinks.keySet()) {
                        for (LeafNodeDefinition leafNodeDefinition : referenceLinks.get(nextReferenceLink)) {
                                SearchQueryBuilder builder;
                                if (wantChainedAndNormal) {
                                        builder = mySqlBuilder.newChildSqlBuilder(mySqlBuilder.isIncludePartitionIdInJoins());
                                } else {
                                        builder = mySqlBuilder;
                                }

                                DbColumn[] previousJoinColumn = null;

                                // Create a reference link predicates to the subselect for every link but the last one
                                for (String nextLink : nextReferenceLink) {
                                        // We don't want to call createPredicateReference() here, because the whole point is to avoid the
                                        // recursion.
                                        // TODO: Are we missing any important business logic from that method? All tests are passing.
                                        ResourceLinkPredicateBuilder resourceLinkPredicateBuilder =
                                                        builder.addReferencePredicateBuilder(this, previousJoinColumn);
                                        builder.addPredicate(
                                                        resourceLinkPredicateBuilder.createPredicateSourcePaths(Lists.newArrayList(nextLink)));
                                        previousJoinColumn = resourceLinkPredicateBuilder.getJoinColumnsForTarget();
                                }

                                Condition containedCondition = createIndexPredicate(
                                                previousJoinColumn,
                                                leafNodeDefinition.getLeafTarget(),
                                                leafNodeDefinition.getLeafPathPrefix(),
                                                leafNodeDefinition.getLeafParamName(),
                                                leafNodeDefinition.getParamDefinition(),
                                                leafNodeDefinition.getOrValues(),
                                                theOperation,
                                                leafNodeDefinition.getQualifiers(),
                                                theRequestPartitionId,
                                                builder);

                                if (wantChainedAndNormal) {
                                        builder.addPredicate(containedCondition);
                                        union.addQueries(builder.getSelect());
                                } else {
                                        predicates.add(containedCondition);
                                }
                        }
                }

                Condition retVal;
                if (wantChainedAndNormal) {

                        if (theSourceJoinColumn == null) {
                                BaseJoiningPredicateBuilder root = mySqlBuilder.getOrCreateFirstPredicateBuilder(false, null);
                                DbColumn[] joinColumns = root.getJoinColumns();
                                Object joinColumnObject;
                                if (joinColumns.length == 1) {
                                        joinColumnObject = joinColumns[0];
                                } else {
                                        joinColumnObject = ColumnTupleObject.from(joinColumns);
                                }
                                retVal = new InCondition(joinColumnObject, union);
                        } else {
                                // -- for the resource link, need join with target_resource_id
                                retVal = new InCondition(theSourceJoinColumn, union);
                        }

                } else {

                        retVal = toOrPredicate(predicates);
                }

                // restore the state of this collection to turn caching back on before we exit
                myReusePredicateBuilderTypes.addAll(cachedReusePredicateBuilderTypes);
                return retVal;
        }

        private void collateChainedSearchOptions(
                        Map<List<String>, Set<LeafNodeDefinition>> referenceLinks,
                        List<ChainElement> nextChain,
                        Set<LeafNodeDefinition> leafNodes,
                        EmbeddedChainedSearchModeEnum theEmbeddedChainedSearchModeEnum) {
                // Manually collapse the chain using all possible variants of contained resource patterns.
                // This is a bit excruciating to extend beyond three references. Do we want to find a way to automate this
                // someday?
                // Note: the first element in each chain is assumed to be discrete. This may need to change when we add proper
                // support for `_contained`
                if (nextChain.size() == 1) {
                        // discrete -> discrete
                        if (theEmbeddedChainedSearchModeEnum == EmbeddedChainedSearchModeEnum.UPLIFTED_AND_REF_JOIN) {
                                // If !theWantChainedAndNormal that means we're only processing refchains
                                // so the discrete -> contained case is the only one that applies
                                updateMapOfReferenceLinks(
                                                referenceLinks, Lists.newArrayList(nextChain.get(0).getPath()), leafNodes);
                        }

                        // discrete -> contained
                        RuntimeSearchParam firstParamDefinition =
                                        leafNodes.iterator().next().getParamDefinition();
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(),
                                        leafNodes.stream()
                                                        .map(t -> t.withPathPrefix(
                                                                        nextChain.get(0).getResourceType(),
                                                                        nextChain.get(0).getSearchParameterName()))
                                                        // When we're handling discrete->contained the differences between search
                                                        // parameters don't matter. E.g. if we're processing "subject.name=foo"
                                                        // the name could be Patient:name or Group:name but it doesn't actually
                                                        // matter that these are different since in this case both of these end
                                                        // up being an identical search in the string table for "subject.name".
                                                        .map(t -> t.withParam(firstParamDefinition))
                                                        .collect(Collectors.toSet()));
                } else if (nextChain.size() == 2) {
                        // discrete -> discrete -> discrete
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(
                                                        nextChain.get(0).getPath(), nextChain.get(1).getPath()),
                                        leafNodes);
                        // discrete -> discrete -> contained
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(nextChain.get(0).getPath()),
                                        leafNodes.stream()
                                                        .map(t -> t.withPathPrefix(
                                                                        nextChain.get(1).getResourceType(),
                                                                        nextChain.get(1).getSearchParameterName()))
                                                        .collect(Collectors.toSet()));
                        // discrete -> contained -> discrete
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(mergePaths(
                                                        nextChain.get(0).getPath(), nextChain.get(1).getPath())),
                                        leafNodes);
                        if (myStorageSettings.isIndexOnContainedResourcesRecursively()) {
                                // discrete -> contained -> contained
                                updateMapOfReferenceLinks(
                                                referenceLinks,
                                                Lists.newArrayList(),
                                                leafNodes.stream()
                                                                .map(t -> t.withPathPrefix(
                                                                                nextChain.get(0).getResourceType(),
                                                                                nextChain.get(0).getSearchParameterName() + "."
                                                                                                + nextChain.get(1).getSearchParameterName()))
                                                                .collect(Collectors.toSet()));
                        }
                } else if (nextChain.size() == 3) {
                        // discrete -> discrete -> discrete -> discrete
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(
                                                        nextChain.get(0).getPath(),
                                                        nextChain.get(1).getPath(),
                                                        nextChain.get(2).getPath()),
                                        leafNodes);
                        // discrete -> discrete -> discrete -> contained
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(
                                                        nextChain.get(0).getPath(), nextChain.get(1).getPath()),
                                        leafNodes.stream()
                                                        .map(t -> t.withPathPrefix(
                                                                        nextChain.get(2).getResourceType(),
                                                                        nextChain.get(2).getSearchParameterName()))
                                                        .collect(Collectors.toSet()));
                        // discrete -> discrete -> contained -> discrete
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(
                                                        nextChain.get(0).getPath(),
                                                        mergePaths(
                                                                        nextChain.get(1).getPath(), nextChain.get(2).getPath())),
                                        leafNodes);
                        // discrete -> contained -> discrete -> discrete
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(
                                                        mergePaths(
                                                                        nextChain.get(0).getPath(), nextChain.get(1).getPath()),
                                                        nextChain.get(2).getPath()),
                                        leafNodes);
                        // discrete -> contained -> discrete -> contained
                        updateMapOfReferenceLinks(
                                        referenceLinks,
                                        Lists.newArrayList(mergePaths(
                                                        nextChain.get(0).getPath(), nextChain.get(1).getPath())),
                                        leafNodes.stream()
                                                        .map(t -> t.withPathPrefix(
                                                                        nextChain.get(2).getResourceType(),
                                                                        nextChain.get(2).getSearchParameterName()))
                                                        .collect(Collectors.toSet()));
                        if (myStorageSettings.isIndexOnContainedResourcesRecursively()) {
                                // discrete -> contained -> contained -> discrete
                                updateMapOfReferenceLinks(
                                                referenceLinks,
                                                Lists.newArrayList(mergePaths(
                                                                nextChain.get(0).getPath(),
                                                                nextChain.get(1).getPath(),
                                                                nextChain.get(2).getPath())),
                                                leafNodes);
                                // discrete -> discrete -> contained -> contained
                                updateMapOfReferenceLinks(
                                                referenceLinks,
                                                Lists.newArrayList(nextChain.get(0).getPath()),
                                                leafNodes.stream()
                                                                .map(t -> t.withPathPrefix(
                                                                                nextChain.get(1).getResourceType(),
                                                                                nextChain.get(1).getSearchParameterName() + "."
                                                                                                + nextChain.get(2).getSearchParameterName()))
                                                                .collect(Collectors.toSet()));
                                // discrete -> contained -> contained -> contained
                                updateMapOfReferenceLinks(
                                                referenceLinks,
                                                Lists.newArrayList(),
                                                leafNodes.stream()
                                                                .map(t -> t.withPathPrefix(
                                                                                nextChain.get(0).getResourceType(),
                                                                                nextChain.get(0).getSearchParameterName() + "."
                                                                                                + nextChain.get(1).getSearchParameterName() + "."
                                                                                                + nextChain.get(2).getSearchParameterName()))
                                                                .collect(Collectors.toSet()));
                        }
                } else {
                        // TODO: the chain is too long, it isn't practical to hard-code all the possible patterns. If anyone ever
                        // needs this, we should revisit the approach
                        throw new InvalidRequestException(Msg.code(2011)
                                        + "The search chain is too long. Only chains of up to three references are supported.");
                }
        }

        private void updateMapOfReferenceLinks(
                        Map<List<String>, Set<LeafNodeDefinition>> theReferenceLinksMap,
                        ArrayList<String> thePath,
                        Set<LeafNodeDefinition> theLeafNodesToAdd) {
                Set<LeafNodeDefinition> leafNodes = theReferenceLinksMap.computeIfAbsent(thePath, k -> Sets.newHashSet());
                leafNodes.addAll(theLeafNodesToAdd);
        }

        private String mergePaths(String... paths) {
                String result = "";
                for (String nextPath : paths) {
                        int separatorIndex = nextPath.indexOf('.');
                        if (StringUtils.isEmpty(result)) {
                                result = nextPath;
                        } else {
                                result = result + nextPath.substring(separatorIndex);
                        }
                }
                return result;
        }

        private Condition createIndexPredicate(
                        DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        String theParamName,
                        RuntimeSearchParam theParamDefinition,
                        ArrayList<IQueryParameterType> theOrValues,
                        SearchFilterParser.CompareOperation theOperation,
                        List<String> theQualifiers,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {
                Condition containedCondition;

                switch (theParamDefinition.getParamType()) {
                        case DATE:
                                containedCondition = createPredicateDate(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParamDefinition,
                                                theOrValues,
                                                theOperation,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                                break;
                        case NUMBER:
                                containedCondition = createPredicateNumber(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParamDefinition,
                                                theOrValues,
                                                theOperation,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                                break;
                        case QUANTITY:
                                containedCondition = createPredicateQuantity(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParamDefinition,
                                                theOrValues,
                                                theOperation,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                                break;
                        case STRING:
                                containedCondition = createPredicateString(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParamDefinition,
                                                theOrValues,
                                                theOperation,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                                break;
                        case TOKEN:
                                containedCondition = createPredicateToken(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParamDefinition,
                                                theOrValues,
                                                theOperation,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                                break;
                        case COMPOSITE:
                                containedCondition = createPredicateComposite(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParamDefinition,
                                                theOrValues,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                                break;
                        case URI:
                                containedCondition = createPredicateUri(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                theSpnamePrefix,
                                                theParamDefinition,
                                                theOrValues,
                                                theOperation,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                                break;
                        case REFERENCE:
                                containedCondition = createPredicateReference(
                                                theSourceJoinColumn,
                                                theResourceName,
                                                isBlank(theSpnamePrefix) ? theParamName : theSpnamePrefix + "." + theParamName,
                                                theQualifiers,
                                                theOrValues,
                                                theOperation,
                                                theRequestPartitionId,
                                                theSqlBuilder);
                                break;
                        case HAS:
                        case SPECIAL:
                        default:
                                throw new InvalidRequestException(
                                                Msg.code(1215) + "The search type:" + theParamDefinition.getParamType() + " is not supported.");
                }
                return containedCondition;
        }

        @Nullable
        public Condition createPredicateResourceId(SearchForIdsParams theSearchForIdsParams) {
                ResourceIdPredicateBuilder builder = mySqlBuilder.newResourceIdBuilder();
                return builder.createPredicateResourceId(theSearchForIdsParams);
        }

        private Condition createPredicateSourceForAndList(
                        @Nullable DbColumn[] theSourceJoinColumn, List<List<IQueryParameterType>> theAndOrParams) {
                mySqlBuilder.getOrCreateFirstPredicateBuilder();

                List<Condition> andPredicates = new ArrayList<>(theAndOrParams.size());
                for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                        andPredicates.add(createPredicateSource(theSourceJoinColumn, nextAnd));
                }
                return toAndPredicate(andPredicates);
        }

        private Condition createPredicateSource(
                        @Nullable DbColumn[] theSourceJoinColumn, List<? extends IQueryParameterType> theList) {
                if (myStorageSettings.getStoreMetaSourceInformation()
                                == JpaStorageSettings.StoreMetaSourceInformationEnum.NONE) {
                        String msg = myFhirContext.getLocalizer().getMessage(QueryStack.class, "sourceParamDisabled");
                        throw new InvalidRequestException(Msg.code(1216) + msg);
                }

                List<Condition> orPredicates = new ArrayList<>();

                // :missing=true modifier processing requires "LEFT JOIN" with HFJ_RESOURCE table to return correct results
                // if both sourceUri and requestId are not populated for the resource
                Optional<? extends IQueryParameterType> isMissingSourceOptional = theList.stream()
                                .filter(nextParameter -> nextParameter.getMissing() != null && nextParameter.getMissing())
                                .findFirst();

                if (isMissingSourceOptional.isPresent()) {
                        ISourcePredicateBuilder join =
                                        getSourcePredicateBuilder(theSourceJoinColumn, SelectQuery.JoinType.LEFT_OUTER);
                        orPredicates.add(join.createPredicateMissingSourceUri());
                        return toOrPredicate(orPredicates);
                }
                // for all other cases we use "INNER JOIN" to match search parameters
                ISourcePredicateBuilder join = getSourcePredicateBuilder(theSourceJoinColumn, SelectQuery.JoinType.INNER);

                for (IQueryParameterType nextParameter : theList) {
                        SourceParam sourceParameter = new SourceParam(nextParameter.getValueAsQueryToken(myFhirContext));
                        String sourceUri = sourceParameter.getSourceUri();
                        String requestId = sourceParameter.getRequestId();
                        if (isNotBlank(sourceUri) && isNotBlank(requestId)) {
                                orPredicates.add(toAndPredicate(
                                                join.createPredicateSourceUri(sourceUri), join.createPredicateRequestId(requestId)));
                        } else if (isNotBlank(sourceUri)) {
                                orPredicates.add(
                                                join.createPredicateSourceUriWithModifiers(nextParameter, myStorageSettings, sourceUri));
                        } else if (isNotBlank(requestId)) {
                                orPredicates.add(join.createPredicateRequestId(requestId));
                        }
                }

                return toOrPredicate(orPredicates);
        }

        private ISourcePredicateBuilder getSourcePredicateBuilder(
                        @Nullable DbColumn[] theSourceJoinColumn, SelectQuery.JoinType theJoinType) {
                if (myStorageSettings.isAccessMetaSourceInformationFromProvenanceTable()) {
                        return createOrReusePredicateBuilder(
                                                        PredicateBuilderTypeEnum.SOURCE,
                                                        theSourceJoinColumn,
                                                        Constants.PARAM_SOURCE,
                                                        () -> mySqlBuilder.addResourceHistoryProvenancePredicateBuilder(
                                                                        theSourceJoinColumn, theJoinType))
                                        .getResult();
                }
                return createOrReusePredicateBuilder(
                                                PredicateBuilderTypeEnum.SOURCE,
                                                theSourceJoinColumn,
                                                Constants.PARAM_SOURCE,
                                                () -> mySqlBuilder.addResourceHistoryPredicateBuilder(theSourceJoinColumn, theJoinType))
                                .getResult();
        }

        public Condition createPredicateString(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId) {
                return createPredicateString(
                                theSourceJoinColumn,
                                theResourceName,
                                theSpnamePrefix,
                                theSearchParam,
                                theList,
                                theOperation,
                                theRequestPartitionId,
                                mySqlBuilder);
        }

        public Condition createPredicateString(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {
                Boolean isMissing = theList.get(0).getMissing();
                String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());

                if (isMissing != null) {
                        return createMissingParameterQuery(new MissingParameterQueryParams(
                                        theSqlBuilder,
                                        theSearchParam.getParamType(),
                                        theList,
                                        paramName,
                                        theResourceName,
                                        theSourceJoinColumn,
                                        theRequestPartitionId));
                }

                StringPredicateBuilder join = createOrReusePredicateBuilder(
                                                PredicateBuilderTypeEnum.STRING,
                                                theSourceJoinColumn,
                                                paramName,
                                                () -> theSqlBuilder.addStringPredicateBuilder(theSourceJoinColumn))
                                .getResult();

                List<Condition> codePredicates = new ArrayList<>();
                for (IQueryParameterType nextOr : theList) {
                        Condition singleCode = join.createPredicateString(
                                        nextOr, theResourceName, theSpnamePrefix, theSearchParam, join, theOperation);
                        codePredicates.add(singleCode);
                }

                return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, toOrPredicate(codePredicates));
        }

        public Condition createPredicateTag(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        List<List<IQueryParameterType>> theList,
                        String theParamName,
                        RequestPartitionId theRequestPartitionId) {
                TagTypeEnum tagType;
                if (Constants.PARAM_TAG.equals(theParamName)) {
                        tagType = TagTypeEnum.TAG;
                } else if (Constants.PARAM_PROFILE.equals(theParamName)) {
                        tagType = TagTypeEnum.PROFILE;
                } else if (Constants.PARAM_SECURITY.equals(theParamName)) {
                        tagType = TagTypeEnum.SECURITY_LABEL;
                } else {
                        throw new IllegalArgumentException(Msg.code(1217) + "Param name: " + theParamName); // shouldn't happen
                }

                List<Condition> andPredicates = new ArrayList<>();
                for (List<? extends IQueryParameterType> nextAndParams : theList) {
                        if (!checkHaveTags(nextAndParams, theParamName)) {
                                continue;
                        }

                        List<Triple<String, String, String>> tokens = Lists.newArrayList();
                        boolean paramInverted = populateTokens(tokens, nextAndParams);
                        if (tokens.isEmpty()) {
                                continue;
                        }

                        Condition tagPredicate;
                        BaseJoiningPredicateBuilder join;
                        if (paramInverted) {

                                boolean selectPartitionId = myPartitionSettings.isDatabasePartitionMode();
                                SearchQueryBuilder sqlBuilder = mySqlBuilder.newChildSqlBuilder(selectPartitionId);
                                TagPredicateBuilder tagSelector = sqlBuilder.addTagPredicateBuilder(null);
                                sqlBuilder.addPredicate(
                                                tagSelector.createPredicateTag(tagType, tokens, theParamName, theRequestPartitionId));
                                SelectQuery sql = sqlBuilder.getSelect();

                                join = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                                Expression subSelect = new Subquery(sql);

                                Object left;
                                if (selectPartitionId) {
                                        left = new ColumnTupleObject(join.getJoinColumns());
                                } else {
                                        left = join.getResourceIdColumn();
                                }
                                tagPredicate = new InCondition(left, subSelect).setNegate(true);

                        } else {
                                // Tag table can't be a query root because it will include deleted resources, and can't select by
                                // resource type
                                mySqlBuilder.getOrCreateFirstPredicateBuilder();

                                TagPredicateBuilder tagJoin = createOrReusePredicateBuilder(
                                                                PredicateBuilderTypeEnum.TAG,
                                                                theSourceJoinColumn,
                                                                theParamName,
                                                                () -> mySqlBuilder.addTagPredicateBuilder(theSourceJoinColumn))
                                                .getResult();
                                tagPredicate = tagJoin.createPredicateTag(tagType, tokens, theParamName, theRequestPartitionId);
                                join = tagJoin;
                        }

                        andPredicates.add(join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, tagPredicate));
                }

                return toAndPredicate(andPredicates);
        }

        private boolean populateTokens(
                        List<Triple<String, String, String>> theTokens, List<? extends IQueryParameterType> theAndParams) {
                boolean paramInverted = false;

                for (IQueryParameterType nextOrParam : theAndParams) {
                        String code;
                        String system;
                        if (nextOrParam instanceof TokenParam) {
                                TokenParam nextParam = (TokenParam) nextOrParam;
                                code = nextParam.getValue();
                                system = nextParam.getSystem();
                                if (nextParam.getModifier() == TokenParamModifier.NOT) {
                                        paramInverted = true;
                                }
                        } else if (nextOrParam instanceof ReferenceParam) {
                                ReferenceParam nextParam = (ReferenceParam) nextOrParam;
                                code = nextParam.getValue();
                                system = null;
                        } else {
                                UriParam nextParam = (UriParam) nextOrParam;
                                code = nextParam.getValue();
                                system = null;
                        }

                        if (isNotBlank(code)) {
                                theTokens.add(Triple.of(system, nextOrParam.getQueryParameterQualifier(), code));
                        }
                }
                return paramInverted;
        }

        private boolean checkHaveTags(List<? extends IQueryParameterType> theParams, String theParamName) {
                for (IQueryParameterType nextParamUncasted : theParams) {
                        if (nextParamUncasted instanceof TokenParam) {
                                TokenParam nextParam = (TokenParam) nextParamUncasted;
                                if (isNotBlank(nextParam.getValue())) {
                                        return true;
                                }
                                if (isNotBlank(nextParam.getSystem())) {
                                        throw new TokenParamFormatInvalidRequestException(
                                                        Msg.code(1218), theParamName, nextParam.getValueAsQueryToken(myFhirContext));
                                }
                        }

                        if (nextParamUncasted instanceof ReferenceParam
                                        && isNotBlank(((ReferenceParam) nextParamUncasted).getValue())) {
                                return true;
                        } else if (nextParamUncasted instanceof UriParam && isNotBlank(((UriParam) nextParamUncasted).getValue())) {
                                return true;
                        }
                }

                return false;
        }

        public Condition createPredicateToken(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId) {
                return createPredicateToken(
                                theSourceJoinColumn,
                                theResourceName,
                                theSpnamePrefix,
                                theSearchParam,
                                theList,
                                theOperation,
                                theRequestPartitionId,
                                mySqlBuilder);
        }

        public Condition createPredicateToken(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {

                List<IQueryParameterType> tokens = new ArrayList<>();

                boolean paramInverted = false;
                TokenParamModifier modifier;

                for (IQueryParameterType nextOr : theList) {
                        if (nextOr instanceof TokenParam) {
                                if (!((TokenParam) nextOr).isEmpty()) {
                                        TokenParam id = (TokenParam) nextOr;
                                        if (id.isText()) {

                                                // Check whether the :text modifier is actually enabled here
                                                boolean tokenTextIndexingEnabled =
                                                                BaseSearchParamExtractor.tokenTextIndexingEnabledForSearchParam(
                                                                                myStorageSettings, theSearchParam);
                                                if (!tokenTextIndexingEnabled) {
                                                        String msg;
                                                        if (myStorageSettings.isSuppressStringIndexingInTokens()) {
                                                                msg = myFhirContext
                                                                                .getLocalizer()
                                                                                .getMessage(QueryStack.class, "textModifierDisabledForServer");
                                                        } else {
                                                                msg = myFhirContext
                                                                                .getLocalizer()
                                                                                .getMessage(QueryStack.class, "textModifierDisabledForSearchParam");
                                                        }
                                                        throw new MethodNotAllowedException(Msg.code(1219) + msg);
                                                }
                                                return createPredicateString(
                                                                theSourceJoinColumn,
                                                                theResourceName,
                                                                theSpnamePrefix,
                                                                theSearchParam,
                                                                theList,
                                                                null,
                                                                theRequestPartitionId,
                                                                theSqlBuilder);
                                        }

                                        modifier = id.getModifier();
                                        // for :not modifier, create a token and remove the :not modifier
                                        if (modifier == TokenParamModifier.NOT) {
                                                tokens.add(new TokenParam(((TokenParam) nextOr).getSystem(), ((TokenParam) nextOr).getValue()));
                                                paramInverted = true;
                                        } else {
                                                tokens.add(nextOr);
                                        }
                                }
                        } else {
                                tokens.add(nextOr);
                        }
                }

                if (tokens.isEmpty()) {
                        return null;
                }

                String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
                Condition predicate;
                BaseJoiningPredicateBuilder join;

                if (paramInverted) {
                        boolean selectPartitionId = myPartitionSettings.isDatabasePartitionMode();
                        SearchQueryBuilder sqlBuilder = theSqlBuilder.newChildSqlBuilder(selectPartitionId);
                        TokenPredicateBuilder tokenSelector = sqlBuilder.addTokenPredicateBuilder(null);
                        sqlBuilder.addPredicate(tokenSelector.createPredicateToken(
                                        tokens, theResourceName, theSpnamePrefix, theSearchParam, theRequestPartitionId));
                        SelectQuery sql = sqlBuilder.getSelect();
                        Expression subSelect = new Subquery(sql);

                        join = theSqlBuilder.getOrCreateFirstPredicateBuilder();

                        DbColumn[] leftColumns;
                        if (theSourceJoinColumn == null) {
                                leftColumns = join.getJoinColumns();
                        } else {
                                leftColumns = theSourceJoinColumn;
                        }

                        Object left = new ColumnTupleObject(leftColumns);
                        predicate = new InCondition(left, subSelect).setNegate(true);

                } else {
                        Boolean isMissing = theList.get(0).getMissing();
                        if (isMissing != null) {
                                return createMissingParameterQuery(new MissingParameterQueryParams(
                                                theSqlBuilder,
                                                theSearchParam.getParamType(),
                                                theList,
                                                paramName,
                                                theResourceName,
                                                theSourceJoinColumn,
                                                theRequestPartitionId));
                        }

                        TokenPredicateBuilder tokenJoin = createOrReusePredicateBuilder(
                                                        PredicateBuilderTypeEnum.TOKEN,
                                                        theSourceJoinColumn,
                                                        paramName,
                                                        () -> theSqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn))
                                        .getResult();

                        predicate = tokenJoin.createPredicateToken(
                                        tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
                        join = tokenJoin;
                }

                return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
        }

        public Condition createPredicateUri(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId) {
                return createPredicateUri(
                                theSourceJoinColumn,
                                theResourceName,
                                theSpnamePrefix,
                                theSearchParam,
                                theList,
                                theOperation,
                                theRequestPartitionId,
                                mySqlBuilder);
        }

        public Condition createPredicateUri(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theSpnamePrefix,
                        RuntimeSearchParam theSearchParam,
                        List<? extends IQueryParameterType> theList,
                        SearchFilterParser.CompareOperation theOperation,
                        RequestPartitionId theRequestPartitionId,
                        SearchQueryBuilder theSqlBuilder) {

                String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());

                Boolean isMissing = theList.get(0).getMissing();
                if (isMissing != null) {
                        return createMissingParameterQuery(new MissingParameterQueryParams(
                                        theSqlBuilder,
                                        theSearchParam.getParamType(),
                                        theList,
                                        paramName,
                                        theResourceName,
                                        theSourceJoinColumn,
                                        theRequestPartitionId));
                } else {
                        UriPredicateBuilder join = theSqlBuilder.addUriPredicateBuilder(theSourceJoinColumn);

                        Condition predicate = join.addPredicate(theList, paramName, theOperation, myRequestDetails);
                        return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
                }
        }

        public QueryStack newChildQueryFactoryWithFullBuilderReuse() {
                return new QueryStack(
                                myRequestDetails,
                                mySearchParameters,
                                myStorageSettings,
                                myFhirContext,
                                mySqlBuilder,
                                mySearchParamRegistry,
                                myPartitionSettings,
                                EnumSet.allOf(PredicateBuilderTypeEnum.class));
        }

        @Nullable
        public Condition searchForIdsWithAndOr(SearchForIdsParams theSearchForIdsParams) {

                if (theSearchForIdsParams.myAndOrParams.isEmpty()) {
                        return null;
                }

                switch (theSearchForIdsParams.myParamName) {
                        case IAnyResource.SP_RES_ID:
                                return createPredicateResourceId(theSearchForIdsParams);

                        case Constants.PARAM_PID:
                                return createPredicateResourcePID(
                                                theSearchForIdsParams.mySourceJoinColumn, theSearchForIdsParams.myAndOrParams);

                        case PARAM_HAS:
                                return createPredicateHas(
                                                theSearchForIdsParams.mySourceJoinColumn,
                                                theSearchForIdsParams.myResourceName,
                                                theSearchForIdsParams.myAndOrParams,
                                                theSearchForIdsParams.myRequest,
                                                theSearchForIdsParams.myRequestPartitionId);

                        case Constants.PARAM_TAG:
                        case Constants.PARAM_PROFILE:
                        case Constants.PARAM_SECURITY:
                                if (myStorageSettings.getTagStorageMode() == JpaStorageSettings.TagStorageModeEnum.INLINE) {
                                        return createPredicateSearchParameter(
                                                        theSearchForIdsParams.mySourceJoinColumn,
                                                        theSearchForIdsParams.myResourceName,
                                                        theSearchForIdsParams.myParamName,
                                                        theSearchForIdsParams.myAndOrParams,
                                                        theSearchForIdsParams.myRequestPartitionId);
                                } else {
                                        return createPredicateTag(
                                                        theSearchForIdsParams.mySourceJoinColumn,
                                                        theSearchForIdsParams.myAndOrParams,
                                                        theSearchForIdsParams.myParamName,
                                                        theSearchForIdsParams.myRequestPartitionId);
                                }

                        case Constants.PARAM_SOURCE:
                                return createPredicateSourceForAndList(
                                                theSearchForIdsParams.mySourceJoinColumn, theSearchForIdsParams.myAndOrParams);

                        case Constants.PARAM_LASTUPDATED:
                                // this case statement handles a _lastUpdated query as part of a reverse search
                                // only (/Patient?_has:Encounter:patient:_lastUpdated=ge2023-10-24).
                                // performing a _lastUpdated query on a resource (/Patient?_lastUpdated=eq2023-10-24)
                                // is handled in {@link SearchBuilder#createChunkedQuery}.
                                return createReverseSearchPredicateLastUpdated(
                                                theSearchForIdsParams.myAndOrParams, theSearchForIdsParams.mySourceJoinColumn);

                        default:
                                return createPredicateSearchParameter(
                                                theSearchForIdsParams.mySourceJoinColumn,
                                                theSearchForIdsParams.myResourceName,
                                                theSearchForIdsParams.myParamName,
                                                theSearchForIdsParams.myAndOrParams,
                                                theSearchForIdsParams.myRequestPartitionId);
                }
        }

        /**
         * Raw match on RES_ID
         */
        private Condition createPredicateResourcePID(
                        DbColumn[] theSourceJoinColumn, List<List<IQueryParameterType>> theAndOrParams) {
                DbColumn pidColumn = getResourceIdColumn(theSourceJoinColumn);

                if (pidColumn == null) {
                        BaseJoiningPredicateBuilder predicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
                        pidColumn = predicateBuilder.getResourceIdColumn();
                }

                // we don't support any modifiers for now
                Set<Long> pids = theAndOrParams.stream()
                                .map(orList -> orList.stream()
                                                .map(v -> v.getValueAsQueryToken(myFhirContext))
                                                .map(Long::valueOf)
                                                .collect(Collectors.toSet()))
                                .reduce(Sets::intersection)
                                .orElse(Set.of());

                if (pids.isEmpty()) {
                        mySqlBuilder.setMatchNothing();
                        return null;
                }

                return toEqualToOrInPredicate(pidColumn, mySqlBuilder.generatePlaceholders(pids));
        }

        private Condition createReverseSearchPredicateLastUpdated(
                        List<List<IQueryParameterType>> theAndOrParams, DbColumn[] theSourceColumn) {

                ResourceTablePredicateBuilder resourceTableJoin =
                                mySqlBuilder.addResourceTablePredicateBuilder(theSourceColumn);

                List<Condition> andPredicates = new ArrayList<>(theAndOrParams.size());

                for (List<IQueryParameterType> aList : theAndOrParams) {
                        if (!aList.isEmpty()) {
                                DateParam dateParam = (DateParam) aList.get(0);
                                DateRangeParam dateRangeParam = new DateRangeParam(dateParam);
                                Condition aCondition = mySqlBuilder.addPredicateLastUpdated(dateRangeParam, resourceTableJoin);
                                andPredicates.add(aCondition);
                        }
                }

                return toAndPredicate(andPredicates);
        }

        @Nullable
        private Condition createPredicateSearchParameter(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theParamName,
                        List<List<IQueryParameterType>> theAndOrParams,
                        RequestPartitionId theRequestPartitionId) {
                List<Condition> andPredicates = new ArrayList<>();
                RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(
                                theResourceName, theParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                if (nextParamDef != null) {

                        if (myPartitionSettings.isPartitioningEnabled() && myPartitionSettings.isIncludePartitionInSearchHashes()) {
                                if (theRequestPartitionId.isAllPartitions()) {
                                        throw new PreconditionFailedException(
                                                        Msg.code(1220) + "This server is not configured to support search against all partitions");
                                }
                        }

                        switch (nextParamDef.getParamType()) {
                                case DATE:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                                                // FT: 2021-01-18 use operation 'gt', 'ge', 'le' or 'lt'
                                                // to create the predicateDate instead of generic one with operation = null
                                                SearchFilterParser.CompareOperation operation = null;
                                                if (!nextAnd.isEmpty()) {
                                                        DateParam param = (DateParam) nextAnd.get(0);
                                                        operation = toOperation(param.getPrefix());
                                                }
                                                andPredicates.add(createPredicateDate(
                                                                theSourceJoinColumn,
                                                                theResourceName,
                                                                null,
                                                                nextParamDef,
                                                                nextAnd,
                                                                operation,
                                                                theRequestPartitionId));
                                        }
                                        break;
                                case QUANTITY:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                                                SearchFilterParser.CompareOperation operation = null;
                                                if (!nextAnd.isEmpty()) {
                                                        QuantityParam param = (QuantityParam) nextAnd.get(0);
                                                        operation = toOperation(param.getPrefix());
                                                }
                                                andPredicates.add(createPredicateQuantity(
                                                                theSourceJoinColumn,
                                                                theResourceName,
                                                                null,
                                                                nextParamDef,
                                                                nextAnd,
                                                                operation,
                                                                theRequestPartitionId));
                                        }
                                        break;
                                case REFERENCE:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {

                                                // Handle Search Parameters where the name is a full chain
                                                // (e.g. SearchParameter with name=composition.patient.identifier)
                                                if (handleFullyChainedParameter(
                                                                theSourceJoinColumn,
                                                                theResourceName,
                                                                theParamName,
                                                                theRequestPartitionId,
                                                                andPredicates,
                                                                nextAnd)) {
                                                        continue;
                                                }

                                                EmbeddedChainedSearchModeEnum embeddedChainedSearchModeEnum =
                                                                isEligibleForEmbeddedChainedResourceSearch(theResourceName, theParamName, nextAnd);
                                                if (embeddedChainedSearchModeEnum == EmbeddedChainedSearchModeEnum.REF_JOIN_ONLY) {
                                                        andPredicates.add(createPredicateReference(
                                                                        theSourceJoinColumn,
                                                                        theResourceName,
                                                                        theParamName,
                                                                        new ArrayList<>(),
                                                                        nextAnd,
                                                                        null,
                                                                        theRequestPartitionId));
                                                } else {
                                                        andPredicates.add(createPredicateReferenceForEmbeddedChainedSearchResource(
                                                                        theSourceJoinColumn,
                                                                        theResourceName,
                                                                        nextParamDef,
                                                                        nextAnd,
                                                                        null,
                                                                        theRequestPartitionId,
                                                                        embeddedChainedSearchModeEnum));
                                                }
                                        }
                                        break;
                                case STRING:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                                                andPredicates.add(createPredicateString(
                                                                theSourceJoinColumn,
                                                                theResourceName,
                                                                null,
                                                                nextParamDef,
                                                                nextAnd,
                                                                SearchFilterParser.CompareOperation.sw,
                                                                theRequestPartitionId));
                                        }
                                        break;
                                case TOKEN:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                                                if (LOCATION_POSITION.equals(nextParamDef.getPath())) {
                                                        andPredicates.add(createPredicateCoords(
                                                                        theSourceJoinColumn,
                                                                        theResourceName,
                                                                        null,
                                                                        nextParamDef,
                                                                        nextAnd,
                                                                        theRequestPartitionId,
                                                                        mySqlBuilder));
                                                } else {
                                                        andPredicates.add(createPredicateToken(
                                                                        theSourceJoinColumn,
                                                                        theResourceName,
                                                                        null,
                                                                        nextParamDef,
                                                                        nextAnd,
                                                                        null,
                                                                        theRequestPartitionId));
                                                }
                                        }
                                        break;
                                case NUMBER:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                                                andPredicates.add(createPredicateNumber(
                                                                theSourceJoinColumn,
                                                                theResourceName,
                                                                null,
                                                                nextParamDef,
                                                                nextAnd,
                                                                null,
                                                                theRequestPartitionId));
                                        }
                                        break;
                                case COMPOSITE:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                                                andPredicates.add(createPredicateComposite(
                                                                theSourceJoinColumn,
                                                                theResourceName,
                                                                null,
                                                                nextParamDef,
                                                                nextAnd,
                                                                theRequestPartitionId));
                                        }
                                        break;
                                case URI:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                                                andPredicates.add(createPredicateUri(
                                                                theSourceJoinColumn,
                                                                theResourceName,
                                                                null,
                                                                nextParamDef,
                                                                nextAnd,
                                                                SearchFilterParser.CompareOperation.eq,
                                                                theRequestPartitionId));
                                        }
                                        break;
                                case HAS:
                                case SPECIAL:
                                        for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
                                                if (LOCATION_POSITION.equals(nextParamDef.getPath())) {
                                                        andPredicates.add(createPredicateCoords(
                                                                        theSourceJoinColumn,
                                                                        theResourceName,
                                                                        null,
                                                                        nextParamDef,
                                                                        nextAnd,
                                                                        theRequestPartitionId,
                                                                        mySqlBuilder));
                                                }
                                        }
                                        break;
                        }
                } else {
                        // These are handled later
                        if (!Constants.PARAM_CONTENT.equals(theParamName) && !Constants.PARAM_TEXT.equals(theParamName)) {
                                if (Constants.PARAM_FILTER.equals(theParamName)) {

                                        // Parse the predicates enumerated in the _filter separated by AND or OR...
                                        if (theAndOrParams.get(0).get(0) instanceof StringParam) {
                                                String filterString =
                                                                ((StringParam) theAndOrParams.get(0).get(0)).getValue();
                                                SearchFilterParser.BaseFilter filter;
                                                try {
                                                        filter = SearchFilterParser.parse(filterString);
                                                } catch (SearchFilterParser.FilterSyntaxException theE) {
                                                        throw new InvalidRequestException(
                                                                        Msg.code(1221) + "Error parsing _filter syntax: " + theE.getMessage());
                                                }
                                                if (filter != null) {

                                                        if (!myStorageSettings.isFilterParameterEnabled()) {
                                                                throw new InvalidRequestException(Msg.code(1222) + Constants.PARAM_FILTER
                                                                                + " parameter is disabled on this server");
                                                        }

                                                        Condition predicate =
                                                                        createPredicateFilter(this, filter, theResourceName, theRequestPartitionId);
                                                        if (predicate != null) {
                                                                mySqlBuilder.addPredicate(predicate);
                                                        }
                                                }
                                        }

                                } else {
                                        RuntimeSearchParam notEnabledForSearchParam = mySearchParamRegistry.getActiveSearchParam(
                                                        theResourceName, theParamName, ISearchParamRegistry.SearchParamLookupContextEnum.ALL);
                                        if (notEnabledForSearchParam == null) {
                                                String msg = myFhirContext
                                                                .getLocalizer()
                                                                .getMessageSanitized(
                                                                                BaseStorageDao.class,
                                                                                "invalidSearchParameter",
                                                                                theParamName,
                                                                                theResourceName,
                                                                                mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(
                                                                                                theResourceName,
                                                                                                ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH));
                                                throw new InvalidRequestException(Msg.code(1223) + msg);
                                        } else {
                                                String msg = myFhirContext
                                                                .getLocalizer()
                                                                .getMessageSanitized(
                                                                                BaseStorageDao.class,
                                                                                "invalidSearchParameterNotEnabledForSearch",
                                                                                theParamName,
                                                                                theResourceName,
                                                                                mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(
                                                                                                theResourceName,
                                                                                                ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH));
                                                throw new InvalidRequestException(Msg.code(2540) + msg);
                                        }
                                }
                        }
                }

                return toAndPredicate(andPredicates);
        }

        /**
         * This method handles the case of Search Parameters where the name/code
         * in the SP is a full chain expression. Normally to handle an expression
         * like <code>Observation?subject.name=foo</code> are handled by a SP
         * with a type of REFERENCE where the name is "subject". That is not
         * handled here. On the other hand, if the SP has a name value containing
         * the full chain (e.g. "subject.name") we handle that here.
         *
         * @return Returns {@literal true} if the search parameter was handled
         * by this method
         */
        private boolean handleFullyChainedParameter(
                        @Nullable DbColumn[] theSourceJoinColumn,
                        String theResourceName,
                        String theParamName,
                        RequestPartitionId theRequestPartitionId,
                        List<Condition> andPredicates,
                        List<? extends IQueryParameterType> nextAnd) {
                if (!nextAnd.isEmpty() && nextAnd.get(0) instanceof ReferenceParam) {
                        ReferenceParam param = (ReferenceParam) nextAnd.get(0);
                        if (isNotBlank(param.getChain())) {
                                String fullName = theParamName + "." + param.getChain();
                                RuntimeSearchParam fullChainParam = mySearchParamRegistry.getActiveSearchParam(
                                                theResourceName, fullName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                                if (fullChainParam != null) {
                                        List<IQueryParameterType> swappedParamTypes = nextAnd.stream()
                                                        .map(t -> newParameterInstance(fullChainParam, null, t.getValueAsQueryToken(myFhirContext)))
                                                        .collect(Collectors.toList());
                                        List<List<IQueryParameterType>> params = List.of(swappedParamTypes);
                                        Condition predicate = createPredicateSearchParameter(
                                                        theSourceJoinColumn, theResourceName, fullName, params, theRequestPartitionId);
                                        andPredicates.add(predicate);
                                        return true;
                                }
                        }
                }
                return false;
        }

        /**
         * When searching using a chained search expression (e.g. "Patient?organization.name=foo")
         * we have a few options:
         * <ul>
         * <li>
         *    A. If we want to match only {@link ca.uhn.fhir.jpa.model.entity.ResourceLink} for
         *    paramName="organization" with a join on {@link ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString}
         *    with paramName="name", that's {@link EmbeddedChainedSearchModeEnum#REF_JOIN_ONLY}
         *    which is the standard searching case. Let's guess that 99.9% of all searches work
         *    this way.
         * </ul>
         * <li>
         *    B. If we want to match only {@link ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString}
         *    with paramName="organization.name", that's {@link EmbeddedChainedSearchModeEnum#UPLIFTED_ONLY}.
         *    We only do this if there is an uplifted refchain declared on the "organization"
         *    search parameter for the "name" search parameter, and contained indexing is disabled.
         *    This kind of index can come from indexing normal references where the search parameter
         *      has an uplifted refchain declared, and it can also come from indexing contained resources.
         *      For both of these cases, the actual index in the database is identical. But the important
         *    difference is that when you're searching for contained resources you also want to
         *    search for normal references. When you're searching for explicit refchains, no normal
         *    indexes matter because they'd be a duplicate of the uplifted refchain.
         * </li>
         * <li>
         *    C. We can also do both and return a union of the two, using
         *    {@link EmbeddedChainedSearchModeEnum#UPLIFTED_AND_REF_JOIN}. We do that if contained
         *    resource indexing is enabled since we have to assume there may be indexes
         *    on "organization" for both contained and non-contained Organization.
         *    resources.
         * </li>
         */
        private EmbeddedChainedSearchModeEnum isEligibleForEmbeddedChainedResourceSearch(
                        String theResourceType, String theParameterName, List<? extends IQueryParameterType> theParameter) {
                boolean indexOnContainedResources = myStorageSettings.isIndexOnContainedResources();
                boolean indexOnUpliftedRefchains = myStorageSettings.isIndexOnUpliftedRefchains();

                if (!indexOnContainedResources && !indexOnUpliftedRefchains) {
                        return EmbeddedChainedSearchModeEnum.REF_JOIN_ONLY;
                }

                boolean haveUpliftCandidates = theParameter.stream()
                                .filter(t -> t instanceof ReferenceParam)
                                .map(t -> ((ReferenceParam) t).getChain())
                                .filter(StringUtils::isNotBlank)
                                // Chains on _has can't be indexed for contained searches - At least not yet. It's not clear to me if we
                                // ever want to support this, it would be really hard to do.
                                .filter(t -> !t.startsWith(PARAM_HAS + ":"))
                                .anyMatch(t -> {
                                        if (indexOnContainedResources) {
                                                return true;
                                        }
                                        RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
                                                        theResourceType,
                                                        theParameterName,
                                                        ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                                        return param != null && param.hasUpliftRefchain(t);
                                });

                if (haveUpliftCandidates) {
                        if (indexOnContainedResources) {
                                return EmbeddedChainedSearchModeEnum.UPLIFTED_AND_REF_JOIN;
                        }
                        ourLog.debug("Search on {}.{} uses an uplifted refchain.", theResourceType, theParameterName);
                        return EmbeddedChainedSearchModeEnum.UPLIFTED_ONLY;
                } else {
                        return EmbeddedChainedSearchModeEnum.REF_JOIN_ONLY;
                }
        }

        public void addPredicateCompositeUnique(List<String> theIndexStrings, RequestPartitionId theRequestPartitionId) {
                ComboUniqueSearchParameterPredicateBuilder predicateBuilder = mySqlBuilder.addComboUniquePredicateBuilder();
                Condition predicate = predicateBuilder.createPredicateIndexString(theRequestPartitionId, theIndexStrings);
                mySqlBuilder.addPredicate(predicate);
        }

        public void addPredicateCompositeNonUnique(List<String> theIndexStrings, RequestPartitionId theRequestPartitionId) {
                ComboNonUniqueSearchParameterPredicateBuilder predicateBuilder =
                                mySqlBuilder.addComboNonUniquePredicateBuilder();
                Condition predicate = predicateBuilder.createPredicateHashComplete(theRequestPartitionId, theIndexStrings);
                mySqlBuilder.addPredicate(predicate);
        }

        // expand out the pids
        public void addPredicateEverythingOperation(
                        String theResourceName, List<String> theTypeSourceResourceNames, JpaPid... theTargetPids) {
                ResourceLinkPredicateBuilder table = mySqlBuilder.addReferencePredicateBuilder(this, null);
                Condition predicate =
                                table.createEverythingPredicate(theResourceName, theTypeSourceResourceNames, theTargetPids);
                mySqlBuilder.addPredicate(predicate);
                mySqlBuilder.getSelect().setIsDistinct(true);
                addGrouping();
        }

        public IQueryParameterType newParameterInstance(
                        RuntimeSearchParam theParam, String theQualifier, String theValueAsQueryToken) {
                IQueryParameterType qp = newParameterInstance(theParam);

                qp.setValueAsQueryToken(myFhirContext, theParam.getName(), theQualifier, theValueAsQueryToken);
                return qp;
        }

        private IQueryParameterType newParameterInstance(RuntimeSearchParam theParam) {

                IQueryParameterType qp;
                switch (theParam.getParamType()) {
                        case DATE:
                                qp = new DateParam();
                                break;
                        case NUMBER:
                                qp = new NumberParam();
                                break;
                        case QUANTITY:
                                qp = new QuantityParam();
                                break;
                        case STRING:
                                qp = new StringParam();
                                break;
                        case TOKEN:
                                qp = new TokenParam();
                                break;
                        case COMPOSITE:
                                List<RuntimeSearchParam> compositeOf =
                                                JpaParamUtil.resolveComponentParameters(mySearchParamRegistry, theParam);
                                if (compositeOf.size() != 2) {
                                        throw new InternalErrorException(Msg.code(1224) + "Parameter " + theParam.getName() + " has "
                                                        + compositeOf.size() + " composite parts. Don't know how handlt this.");
                                }
                                IQueryParameterType leftParam = newParameterInstance(compositeOf.get(0));
                                IQueryParameterType rightParam = newParameterInstance(compositeOf.get(1));
                                qp = new CompositeParam<>(leftParam, rightParam);
                                break;
                        case URI:
                                qp = new UriParam();
                                break;
                        case REFERENCE:
                                qp = new ReferenceParam();
                                break;
                        case SPECIAL:
                                qp = new SpecialParam();
                                break;
                        case HAS:
                        default:
                                throw new InvalidRequestException(
                                                Msg.code(1225) + "The search type: " + theParam.getParamType() + " is not supported.");
                }
                return qp;
        }

        /**
         * @see #isEligibleForEmbeddedChainedResourceSearch(String, String, List) for an explanation of the values in this enum
         */
        public enum EmbeddedChainedSearchModeEnum {
                UPLIFTED_ONLY(true),
                UPLIFTED_AND_REF_JOIN(true),
                REF_JOIN_ONLY(false);

                private final boolean mySupportsUplifted;

                EmbeddedChainedSearchModeEnum(boolean theSupportsUplifted) {
                        mySupportsUplifted = theSupportsUplifted;
                }

                public boolean supportsUplifted() {
                        return mySupportsUplifted;
                }
        }

        private static final class ChainElement {
                private final String myResourceType;
                private final String mySearchParameterName;
                private final String myPath;

                public ChainElement(String theResourceType, String theSearchParameterName, String thePath) {
                        this.myResourceType = theResourceType;
                        this.mySearchParameterName = theSearchParameterName;
                        this.myPath = thePath;
                }

                public String getResourceType() {
                        return myResourceType;
                }

                public String getPath() {
                        return myPath;
                }

                public String getSearchParameterName() {
                        return mySearchParameterName;
                }

                @Override
                public boolean equals(Object o) {
                        if (this == o) return true;
                        if (o == null || getClass() != o.getClass()) return false;
                        ChainElement that = (ChainElement) o;
                        return myResourceType.equals(that.myResourceType)
                                        && mySearchParameterName.equals(that.mySearchParameterName)
                                        && myPath.equals(that.myPath);
                }

                @Override
                public int hashCode() {
                        return Objects.hash(myResourceType, mySearchParameterName, myPath);
                }
        }

        private class ReferenceChainExtractor {
                private final Map<List<ChainElement>, Set<LeafNodeDefinition>> myChains = Maps.newHashMap();

                public Map<List<ChainElement>, Set<LeafNodeDefinition>> getChains() {
                        return myChains;
                }

                private boolean isReferenceParamValid(ReferenceParam theReferenceParam) {
                        return split(theReferenceParam.getChain(), '.').length <= 3;
                }

                private List<String> extractPaths(String theResourceType, RuntimeSearchParam theSearchParam) {
                        List<String> pathsForType = theSearchParam.getPathsSplit().stream()
                                        .map(String::trim)
                                        .filter(t -> (t.startsWith(theResourceType) || t.startsWith("(" + theResourceType)))
                                        .collect(Collectors.toList());
                        if (pathsForType.isEmpty()) {
                                ourLog.warn(
                                                "Search parameter {} does not have a path for resource type {}.",
                                                theSearchParam.getName(),
                                                theResourceType);
                        }

                        return pathsForType;
                }

                public void deriveChains(
                                String theResourceType,
                                RuntimeSearchParam theSearchParam,
                                List<? extends IQueryParameterType> theList) {
                        List<String> paths = extractPaths(theResourceType, theSearchParam);
                        for (String path : paths) {
                                List<ChainElement> searchParams = Lists.newArrayList();
                                searchParams.add(new ChainElement(theResourceType, theSearchParam.getName(), path));
                                for (IQueryParameterType nextOr : theList) {
                                        String targetValue = nextOr.getValueAsQueryToken(myFhirContext);
                                        if (nextOr instanceof ReferenceParam) {
                                                ReferenceParam referenceParam = (ReferenceParam) nextOr;
                                                if (!isReferenceParamValid(referenceParam)) {
                                                        throw new InvalidRequestException(Msg.code(2007) + "The search chain "
                                                                        + theSearchParam.getName() + "." + referenceParam.getChain()
                                                                        + " is too long. Only chains up to three references are supported.");
                                                }

                                                String targetChain = referenceParam.getChain();
                                                List<String> qualifiers = Lists.newArrayList(referenceParam.getResourceType());

                                                processNextLinkInChain(
                                                                searchParams,
                                                                theSearchParam,
                                                                targetChain,
                                                                targetValue,
                                                                qualifiers,
                                                                referenceParam.getResourceType());
                                        }
                                }
                        }
                }

                private void processNextLinkInChain(
                                List<ChainElement> theSearchParams,
                                RuntimeSearchParam thePreviousSearchParam,
                                String theChain,
                                String theTargetValue,
                                List<String> theQualifiers,
                                String theResourceType) {

                        String nextParamName = theChain;
                        String nextChain = null;
                        String nextQualifier = null;
                        int linkIndex = theChain.indexOf('.');
                        if (linkIndex != -1) {
                                nextParamName = theChain.substring(0, linkIndex);
                                nextChain = theChain.substring(linkIndex + 1);
                        }

                        int qualifierIndex = nextParamName.indexOf(':');
                        if (qualifierIndex != -1) {
                                if (StringUtils.isEmpty(nextChain)) {
                                        nextQualifier = nextParamName.substring(qualifierIndex);
                                        nextParamName = nextParamName.substring(0, qualifierIndex);
                                } else {
                                        nextParamName = nextParamName.substring(0, qualifierIndex);
                                        nextQualifier = nextParamName.substring(qualifierIndex);
                                }
                        }

                        List<String> qualifiersBranch = Lists.newArrayList();
                        qualifiersBranch.addAll(theQualifiers);
                        qualifiersBranch.add(nextQualifier);

                        boolean searchParamFound = false;
                        for (String nextTarget : thePreviousSearchParam.getTargets()) {
                                RuntimeSearchParam nextSearchParam = null;
                                if (isBlank(theResourceType) || theResourceType.equals(nextTarget)) {
                                        nextSearchParam = mySearchParamRegistry.getActiveSearchParam(
                                                        nextTarget, nextParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
                                }
                                if (nextSearchParam != null) {
                                        searchParamFound = true;
                                        // If we find a search param on this resource type for this parameter name, keep iterating
                                        //  Otherwise, abandon this branch and carry on to the next one
                                        if (StringUtils.isEmpty(nextChain)) {
                                                // We've reached the end of the chain
                                                ArrayList<IQueryParameterType> orValues = Lists.newArrayList();

                                                if (RestSearchParameterTypeEnum.REFERENCE.equals(nextSearchParam.getParamType())) {
                                                        orValues.add(new ReferenceParam(nextQualifier, "", theTargetValue));
                                                } else {
                                                        IQueryParameterType qp = newParameterInstance(nextSearchParam);
                                                        qp.setValueAsQueryToken(
                                                                        myFhirContext, nextSearchParam.getName(), nextQualifier, theTargetValue);
                                                        orValues.add(qp);
                                                }

                                                Set<LeafNodeDefinition> leafNodes =
                                                                myChains.computeIfAbsent(theSearchParams, k -> Sets.newHashSet());
                                                leafNodes.add(new LeafNodeDefinition(
                                                                nextSearchParam, orValues, nextTarget, nextParamName, "", qualifiersBranch));
                                        } else {
                                                List<String> nextPaths = extractPaths(nextTarget, nextSearchParam);
                                                for (String nextPath : nextPaths) {
                                                        List<ChainElement> searchParamBranch = Lists.newArrayList();
                                                        searchParamBranch.addAll(theSearchParams);

                                                        searchParamBranch.add(new ChainElement(nextTarget, nextSearchParam.getName(), nextPath));
                                                        processNextLinkInChain(
                                                                        searchParamBranch,
                                                                        nextSearchParam,
                                                                        nextChain,
                                                                        theTargetValue,
                                                                        qualifiersBranch,
                                                                        nextQualifier);
                                                }
                                        }
                                }
                        }
                        if (!searchParamFound) {
                                throw new InvalidRequestException(Msg.code(1214)
                                                + myFhirContext
                                                                .getLocalizer()
                                                                .getMessage(
                                                                                BaseStorageDao.class,
                                                                                "invalidParameterChain",
                                                                                thePreviousSearchParam.getName() + '.' + theChain));
                        }
                }
        }

        private static class LeafNodeDefinition {
                private final RuntimeSearchParam myParamDefinition;
                private final ArrayList<IQueryParameterType> myOrValues;
                private final String myLeafTarget;
                private final String myLeafParamName;
                private final String myLeafPathPrefix;
                private final List<String> myQualifiers;

                public LeafNodeDefinition(
                                RuntimeSearchParam theParamDefinition,
                                ArrayList<IQueryParameterType> theOrValues,
                                String theLeafTarget,
                                String theLeafParamName,
                                String theLeafPathPrefix,
                                List<String> theQualifiers) {
                        myParamDefinition = theParamDefinition;
                        myOrValues = theOrValues;
                        myLeafTarget = theLeafTarget;
                        myLeafParamName = theLeafParamName;
                        myLeafPathPrefix = theLeafPathPrefix;
                        myQualifiers = theQualifiers;
                }

                public RuntimeSearchParam getParamDefinition() {
                        return myParamDefinition;
                }

                public ArrayList<IQueryParameterType> getOrValues() {
                        return myOrValues;
                }

                public String getLeafTarget() {
                        return myLeafTarget;
                }

                public String getLeafParamName() {
                        return myLeafParamName;
                }

                public String getLeafPathPrefix() {
                        return myLeafPathPrefix;
                }

                public List<String> getQualifiers() {
                        return myQualifiers;
                }

                public LeafNodeDefinition withPathPrefix(String theResourceType, String theName) {
                        return new LeafNodeDefinition(
                                        myParamDefinition, myOrValues, theResourceType, myLeafParamName, theName, myQualifiers);
                }

                @Override
                public boolean equals(Object o) {
                        if (this == o) return true;
                        if (o == null || getClass() != o.getClass()) return false;
                        LeafNodeDefinition that = (LeafNodeDefinition) o;
                        return Objects.equals(myParamDefinition, that.myParamDefinition)
                                        && Objects.equals(myOrValues, that.myOrValues)
                                        && Objects.equals(myLeafTarget, that.myLeafTarget)
                                        && Objects.equals(myLeafParamName, that.myLeafParamName)
                                        && Objects.equals(myLeafPathPrefix, that.myLeafPathPrefix)
                                        && Objects.equals(myQualifiers, that.myQualifiers);
                }

                @Override
                public int hashCode() {
                        return Objects.hash(
                                        myParamDefinition, myOrValues, myLeafTarget, myLeafParamName, myLeafPathPrefix, myQualifiers);
                }

                /**
                 * Return a copy of this object with the given {@link RuntimeSearchParam}
                 * but all other values unchanged.
                 */
                public LeafNodeDefinition withParam(RuntimeSearchParam theParamDefinition) {
                        return new LeafNodeDefinition(
                                        theParamDefinition, myOrValues, myLeafTarget, myLeafParamName, myLeafPathPrefix, myQualifiers);
                }
        }

        public static class SearchForIdsParams {
                DbColumn[] mySourceJoinColumn;
                String myResourceName;
                String myParamName;
                List<List<IQueryParameterType>> myAndOrParams;
                RequestDetails myRequest;
                RequestPartitionId myRequestPartitionId;
                SearchIncludeDeletedEnum myIncludeDeleted;
                SearchFilterParser.CompareOperation myOperation;

                public static SearchForIdsParams with() {
                        return new SearchForIdsParams();
                }

                public SearchForIdsParams setSourceJoinColumn(DbColumn[] theSourceJoinColumn) {
                        mySourceJoinColumn = theSourceJoinColumn;
                        return this;
                }

                public DbColumn[] getSourceJoinColumn() {
                        return mySourceJoinColumn;
                }

                public String getResourceName() {
                        return myResourceName;
                }

                public SearchForIdsParams setResourceName(String theResourceName) {
                        myResourceName = theResourceName;
                        return this;
                }

                public String getParamName() {
                        return myParamName;
                }

                public SearchForIdsParams setParamName(String theParamName) {
                        myParamName = theParamName;
                        return this;
                }

                public SearchForIdsParams setAndOrParams(List<List<IQueryParameterType>> theAndOrParams) {
                        myAndOrParams = theAndOrParams;
                        return this;
                }

                public List<List<IQueryParameterType>> getAndOrParams() {
                        return myAndOrParams;
                }

                public RequestDetails getRequest() {
                        return myRequest;
                }

                public SearchForIdsParams setRequest(RequestDetails theRequest) {
                        myRequest = theRequest;
                        return this;
                }

                public RequestPartitionId getRequestPartitionId() {
                        return myRequestPartitionId;
                }

                public SearchForIdsParams setRequestPartitionId(RequestPartitionId theRequestPartitionId) {
                        myRequestPartitionId = theRequestPartitionId;
                        return this;
                }

                @Nonnull
                public SearchIncludeDeletedEnum getIncludeDeleted() {
                        if (myIncludeDeleted == null) {
                                return SearchIncludeDeletedEnum.NEVER;
                        }
                        return myIncludeDeleted;
                }

                public SearchForIdsParams setIncludeDeleted(SearchIncludeDeletedEnum myIncludeDeleted) {
                        this.myIncludeDeleted = myIncludeDeleted;
                        return this;
                }

                public SearchFilterParser.CompareOperation getOperation() {
                        return myOperation;
                }

                public SearchForIdsParams setOperation(SearchFilterParser.CompareOperation myOperation) {
                        this.myOperation = myOperation;
                        return this;
                }
        }
}