/*
 * #%L
 * HAPI FHIR JPA Server
 * %%
 * Copyright (C) 2014 - 2023 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.term;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
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.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import ca.uhn.fhir.jpa.config.util.ConnectionPoolInfoProvider;
import ca.uhn.fhir.jpa.config.util.IConnectionPoolInfoProvider;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptViewDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptViewOracleDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
import ca.uhn.fhir.jpa.entity.ITermValueSetConceptView;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.entity.TermConceptPropertyTypeEnum;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.sched.HapiJob;
import ca.uhn.fhir.jpa.model.sched.IHasScheduledJobs;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.api.ReindexTerminologyResult;
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.sl.cache.Cache;
import ca.uhn.fhir.sl.cache.CacheFactory;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.FhirVersionIndependentConcept;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.ValidateUtil;
import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Stopwatch;
import com.google.common.collect.ArrayListMultimap;
import org.apache.commons.collections4.ListUtils;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.lucene.index.Term;
import org.apache.lucene.search.BooleanQuery;
import org.hibernate.CacheMode;
import org.hibernate.search.engine.search.predicate.dsl.BooleanPredicateClausesStep;
import org.hibernate.search.engine.search.predicate.dsl.PredicateFinalStep;
import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
import org.hibernate.search.engine.search.query.SearchQuery;
import org.hibernate.search.engine.search.query.SearchScroll;
import org.hibernate.search.engine.search.query.SearchScrollResult;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.common.EntityReference;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hibernate.search.mapper.pojo.massindexing.impl.PojoMassIndexingLoggingMonitor;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.context.ConversionContext40_50;
import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
import org.hl7.fhir.convertors.conv40_50.resources40_50.ValueSet40_50;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
import org.quartz.JobExecutionContext;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.interceptor.NoRollbackRuleAttribute;
import org.springframework.transaction.interceptor.RuleBasedTransactionAttribute;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;
import org.springframework.util.CollectionUtils;
import org.springframework.util.comparator.Comparators;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.UUID;
import java.util.concurrent.TimeUnit;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.persistence.NonUniqueResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;

import static ca.uhn.fhir.jpa.entity.TermConceptPropertyBinder.CONCEPT_PROPERTY_PREFIX_NAME;
import static ca.uhn.fhir.jpa.term.api.ITermLoaderSvc.LOINC_URI;
import static java.lang.String.join;
import static java.util.stream.Collectors.joining;
import static java.util.stream.Collectors.toList;
import static java.util.stream.Collectors.toSet;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isEmpty;
import static org.apache.commons.lang3.StringUtils.isNoneBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.lowerCase;
import static org.apache.commons.lang3.StringUtils.startsWithIgnoreCase;

public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
        public static final int DEFAULT_FETCH_SIZE = 250;
        public static final int DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS = 2;
        // doesn't seem to be much gain by using more threads than this value
        public static final int MAX_MASS_INDEXER_OBJECT_LOADING_THREADS = 6;
        private static final int SINGLE_FETCH_SIZE = 1;
        private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermReadSvcImpl.class);
        private static final ValueSetExpansionOptions DEFAULT_EXPANSION_OPTIONS = new ValueSetExpansionOptions();
        private static final TermCodeSystemVersionDetails NO_CURRENT_VERSION = new TermCodeSystemVersionDetails(-1L, null);
        private static final String IDX_PROPERTIES = "myProperties";
        private static final String IDX_PROP_KEY = IDX_PROPERTIES + ".myKey";
        private static final String IDX_PROP_VALUE_STRING = IDX_PROPERTIES + ".myValueString";
        private static final String IDX_PROP_DISPLAY_STRING = IDX_PROPERTIES + ".myDisplayString";
        private static final String OUR_PIPE_CHARACTER = "|";
        private static final int SECONDS_IN_MINUTE = 60;
        private static final int INDEXED_ROOTS_LOGGING_COUNT = 50_000;
        private static Runnable myInvokeOnNextCallForUnitTest;
        private static boolean ourForceDisableHibernateSearchForUnitTest;
        private final Cache<String, TermCodeSystemVersionDetails> myCodeSystemCurrentVersionCache =
                        CacheFactory.build(TimeUnit.MINUTES.toMillis(1));

        @Autowired
        protected DaoRegistry myDaoRegistry;

        @Autowired
        protected ITermCodeSystemDao myCodeSystemDao;

        @Autowired
        protected ITermConceptDao myConceptDao;

        @Autowired
        protected ITermConceptPropertyDao myConceptPropertyDao;

        @Autowired
        protected ITermConceptDesignationDao myConceptDesignationDao;

        @Autowired
        protected ITermValueSetDao myTermValueSetDao;

        @Autowired
        protected ITermValueSetConceptDao myValueSetConceptDao;

        @Autowired
        protected ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;

        @Autowired
        protected FhirContext myContext;

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

        private boolean myPreExpandingValueSets = false;

        @Autowired
        private ITermCodeSystemVersionDao myCodeSystemVersionDao;

        @Autowired
        private JpaStorageSettings myStorageSettings;

        private TransactionTemplate myTxTemplate;

        @Autowired
        private PlatformTransactionManager myTransactionManager;

        @Autowired(required = false)
        private IFulltextSearchSvc myFulltextSearchSvc;

        @Autowired
        private PlatformTransactionManager myTxManager;

        @Autowired
        private ITermConceptDao myTermConceptDao;

        @Autowired
        private ITermValueSetConceptViewDao myTermValueSetConceptViewDao;

        @Autowired
        private ITermValueSetConceptViewOracleDao myTermValueSetConceptViewOracleDao;

        @Autowired(required = false)
        private ITermDeferredStorageSvc myDeferredStorageSvc;

        @Autowired
        private IIdHelperService<JpaPid> myIdHelperService;

        @Autowired
        private ApplicationContext myApplicationContext;

        private volatile IValidationSupport myJpaValidationSupport;
        private volatile IValidationSupport myValidationSupport;
        // We need this bean so we can tell which mode hibernate search is running in.
        @Autowired
        private HibernatePropertiesProvider myHibernatePropertiesProvider;

        @Autowired
        private CachingValidationSupport myCachingValidationSupport;

        @Autowired
        private VersionCanonicalizer myVersionCanonicalizer;

        @Autowired
        private IJpaStorageResourceParser myJpaStorageResourceParser;

        @Override
        public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
                TermCodeSystemVersionDetails cs = getCurrentCodeSystemVersion(theSystem);
                return cs != null;
        }

        @Override
        public boolean isValueSetSupported(ValidationSupportContext theValidationSupportContext, String theValueSetUrl) {
                return fetchValueSet(theValueSetUrl) != null;
        }

        private boolean addCodeIfNotAlreadyAdded(
                        @Nullable ValueSetExpansionOptions theExpansionOptions,
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        Set<String> theAddedCodes,
                        TermConcept theConcept,
                        boolean theAdd,
                        String theValueSetIncludeVersion) {
                String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
                String codeSystemVersion = theConcept.getCodeSystemVersion().getCodeSystemVersionId();
                String code = theConcept.getCode();
                String display = theConcept.getDisplay();
                Long sourceConceptPid = theConcept.getId();
                String directParentPids = "";

                if (theExpansionOptions != null && theExpansionOptions.isIncludeHierarchy()) {
                        directParentPids = theConcept.getParents().stream()
                                        .map(t -> t.getParent().getId().toString())
                                        .collect(joining(" "));
                }

                Collection<TermConceptDesignation> designations = theConcept.getDesignations();
                if (StringUtils.isNotEmpty(theValueSetIncludeVersion)) {
                        return addCodeIfNotAlreadyAdded(
                                        theValueSetCodeAccumulator,
                                        theAddedCodes,
                                        designations,
                                        theAdd,
                                        codeSystem + OUR_PIPE_CHARACTER + theValueSetIncludeVersion,
                                        code,
                                        display,
                                        sourceConceptPid,
                                        directParentPids,
                                        codeSystemVersion);
                } else {
                        return addCodeIfNotAlreadyAdded(
                                        theValueSetCodeAccumulator,
                                        theAddedCodes,
                                        designations,
                                        theAdd,
                                        codeSystem,
                                        code,
                                        display,
                                        sourceConceptPid,
                                        directParentPids,
                                        codeSystemVersion);
                }
        }

        private boolean addCodeIfNotAlreadyAdded(
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        Set<String> theAddedCodes,
                        boolean theAdd,
                        String theCodeSystem,
                        String theCodeSystemVersion,
                        String theCode,
                        String theDisplay,
                        Long theSourceConceptPid,
                        String theSourceConceptDirectParentPids,
                        Collection<TermConceptDesignation> theDesignations) {
                if (StringUtils.isNotEmpty(theCodeSystemVersion)) {
                        if (isNoneBlank(theCodeSystem, theCode)) {
                                if (theAdd && theAddedCodes.add(theCodeSystem + OUR_PIPE_CHARACTER + theCode)) {
                                        theValueSetCodeAccumulator.includeConceptWithDesignations(
                                                        theCodeSystem + OUR_PIPE_CHARACTER + theCodeSystemVersion,
                                                        theCode,
                                                        theDisplay,
                                                        theDesignations,
                                                        theSourceConceptPid,
                                                        theSourceConceptDirectParentPids,
                                                        theCodeSystemVersion);
                                        return true;
                                }

                                if (!theAdd && theAddedCodes.remove(theCodeSystem + OUR_PIPE_CHARACTER + theCode)) {
                                        theValueSetCodeAccumulator.excludeConcept(
                                                        theCodeSystem + OUR_PIPE_CHARACTER + theCodeSystemVersion, theCode);
                                        return true;
                                }
                        }
                } else {
                        if (theAdd && theAddedCodes.add(theCodeSystem + OUR_PIPE_CHARACTER + theCode)) {
                                theValueSetCodeAccumulator.includeConceptWithDesignations(
                                                theCodeSystem,
                                                theCode,
                                                theDisplay,
                                                theDesignations,
                                                theSourceConceptPid,
                                                theSourceConceptDirectParentPids,
                                                theCodeSystemVersion);
                                return true;
                        }

                        if (!theAdd && theAddedCodes.remove(theCodeSystem + OUR_PIPE_CHARACTER + theCode)) {
                                theValueSetCodeAccumulator.excludeConcept(theCodeSystem, theCode);
                                return true;
                        }
                }

                return false;
        }

        private boolean addCodeIfNotAlreadyAdded(
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        Set<String> theAddedCodes,
                        Collection<TermConceptDesignation> theDesignations,
                        boolean theAdd,
                        String theCodeSystem,
                        String theCode,
                        String theDisplay,
                        Long theSourceConceptPid,
                        String theSourceConceptDirectParentPids,
                        String theSystemVersion) {
                if (isNoneBlank(theCodeSystem, theCode)) {
                        if (theAdd && theAddedCodes.add(theCodeSystem + OUR_PIPE_CHARACTER + theCode)) {
                                theValueSetCodeAccumulator.includeConceptWithDesignations(
                                                theCodeSystem,
                                                theCode,
                                                theDisplay,
                                                theDesignations,
                                                theSourceConceptPid,
                                                theSourceConceptDirectParentPids,
                                                theSystemVersion);
                                return true;
                        }

                        if (!theAdd && theAddedCodes.remove(theCodeSystem + OUR_PIPE_CHARACTER + theCode)) {
                                theValueSetCodeAccumulator.excludeConcept(theCodeSystem, theCode);
                                return true;
                        }
                }

                return false;
        }

        private boolean addToSet(Set<TermConcept> theSetToPopulate, TermConcept theConcept) {
                boolean retVal = theSetToPopulate.add(theConcept);
                if (retVal) {
                        if (theSetToPopulate.size() >= myStorageSettings.getMaximumExpansionSize()) {
                                String msg = myContext
                                                .getLocalizer()
                                                .getMessage(
                                                                TermReadSvcImpl.class,
                                                                "expansionTooLarge",
                                                                myStorageSettings.getMaximumExpansionSize());
                                throw new ExpansionTooCostlyException(Msg.code(885) + msg);
                        }
                }
                return retVal;
        }

        /**
         * This method is present only for unit tests, do not call from client code
         */
        @VisibleForTesting
        public void clearCaches() {
                myCodeSystemCurrentVersionCache.invalidateAll();
        }

        public void deleteValueSetForResource(ResourceTable theResourceTable) {
                // Get existing entity so it can be deleted.
                Optional<TermValueSet> optionalExistingTermValueSetById =
                                myTermValueSetDao.findByResourcePid(theResourceTable.getId());

                if (optionalExistingTermValueSetById.isPresent()) {
                        TermValueSet existingTermValueSet = optionalExistingTermValueSetById.get();

                        ourLog.info("Deleting existing TermValueSet[{}] and its children...", existingTermValueSet.getId());
                        deletePreCalculatedValueSetContents(existingTermValueSet);
                        myTermValueSetDao.deleteById(existingTermValueSet.getId());
                        ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
                }
        }

        private void deletePreCalculatedValueSetContents(TermValueSet theValueSet) {
                myValueSetConceptDesignationDao.deleteByTermValueSetId(theValueSet.getId());
                myValueSetConceptDao.deleteByTermValueSetId(theValueSet.getId());
        }

        @Override
        @Transactional
        public void deleteValueSetAndChildren(ResourceTable theResourceTable) {
                deleteValueSetForResource(theResourceTable);
        }

        @Override
        @Transactional
        public List<FhirVersionIndependentConcept> expandValueSetIntoConceptList(
                        @Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull String theValueSetCanonicalUrl) {
                // TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not be found
                // in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the expansion may
                // time-out.

                ValueSet expanded = expandValueSet(theExpansionOptions, theValueSetCanonicalUrl);

                ArrayList<FhirVersionIndependentConcept> retVal = new ArrayList<>();
                for (ValueSet.ValueSetExpansionContainsComponent nextContains :
                                expanded.getExpansion().getContains()) {
                        retVal.add(new FhirVersionIndependentConcept(
                                        nextContains.getSystem(),
                                        nextContains.getCode(),
                                        nextContains.getDisplay(),
                                        nextContains.getVersion()));
                }
                return retVal;
        }

        @Override
        public ValueSet expandValueSet(
                        @Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull String theValueSetCanonicalUrl) {
                ValueSet valueSet = fetchCanonicalValueSetFromCompleteContext(theValueSetCanonicalUrl);
                if (valueSet == null) {
                        throw new ResourceNotFoundException(
                                        Msg.code(886) + "Unknown ValueSet: " + UrlUtil.escapeUrlParam(theValueSetCanonicalUrl));
                }

                return expandValueSet(theExpansionOptions, valueSet);
        }

        @Override
        public ValueSet expandValueSet(
                        @Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull ValueSet theValueSetToExpand) {
                String filter = null;
                if (theExpansionOptions != null) {
                        filter = theExpansionOptions.getFilter();
                }
                return doExpandValueSet(theExpansionOptions, theValueSetToExpand, ExpansionFilter.fromFilterString(filter));
        }

        private ValueSet doExpandValueSet(
                        @Nullable ValueSetExpansionOptions theExpansionOptions,
                        ValueSet theValueSetToExpand,
                        ExpansionFilter theFilter) {
                ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSetToExpand, "ValueSet to expand can not be null");

                ValueSetExpansionOptions expansionOptions = provideExpansionOptions(theExpansionOptions);
                int offset = expansionOptions.getOffset();
                int count = expansionOptions.getCount();

                ValueSetExpansionComponentWithConceptAccumulator accumulator =
                                new ValueSetExpansionComponentWithConceptAccumulator(
                                                myContext, count, expansionOptions.isIncludeHierarchy());
                accumulator.setHardExpansionMaximumSize(myStorageSettings.getMaximumExpansionSize());
                accumulator.setSkipCountRemaining(offset);
                accumulator.setIdentifier(UUID.randomUUID().toString());
                accumulator.setTimestamp(new Date());
                accumulator.setOffset(offset);

                if (theExpansionOptions != null && isHibernateSearchEnabled()) {
                        accumulator.addParameter().setName("offset").setValue(new IntegerType(offset));
                        accumulator.addParameter().setName("count").setValue(new IntegerType(count));
                }

                myTxTemplate.executeWithoutResult(tx -> {
                        expandValueSetIntoAccumulator(theValueSetToExpand, theExpansionOptions, accumulator, theFilter, true);
                });

                if (accumulator.getTotalConcepts() != null) {
                        accumulator.setTotal(accumulator.getTotalConcepts());
                }

                ValueSet valueSet = new ValueSet();
                valueSet.setUrl(theValueSetToExpand.getUrl());
                valueSet.setId(theValueSetToExpand.getId());
                valueSet.setStatus(Enumerations.PublicationStatus.ACTIVE);
                valueSet.setCompose(theValueSetToExpand.getCompose());
                valueSet.setExpansion(accumulator);

                for (String next : accumulator.getMessages()) {
                        valueSet.getMeta()
                                        .addExtension()
                                        .setUrl(HapiExtensions.EXT_VALUESET_EXPANSION_MESSAGE)
                                        .setValue(new StringType(next));
                }

                if (expansionOptions.isIncludeHierarchy()) {
                        accumulator.applyHierarchy();
                }

                return valueSet;
        }

        private void expandValueSetIntoAccumulator(
                        ValueSet theValueSetToExpand,
                        ValueSetExpansionOptions theExpansionOptions,
                        IValueSetConceptAccumulator theAccumulator,
                        ExpansionFilter theFilter,
                        boolean theAdd) {
                Optional<TermValueSet> optionalTermValueSet;
                if (theValueSetToExpand.hasUrl()) {
                        if (theValueSetToExpand.hasVersion()) {
                                optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(
                                                theValueSetToExpand.getUrl(), theValueSetToExpand.getVersion());
                        } else {
                                optionalTermValueSet = findCurrentTermValueSet(theValueSetToExpand.getUrl());
                        }
                } else {
                        optionalTermValueSet = Optional.empty();
                }

                /*
                 * ValueSet doesn't exist in pre-expansion database, so perform in-memory expansion
                 */
                if (optionalTermValueSet.isEmpty()) {
                        ourLog.debug(
                                        "ValueSet is not present in terminology tables. Will perform in-memory expansion without parameters. {}",
                                        getValueSetInfo(theValueSetToExpand));
                        String msg = myContext
                                        .getLocalizer()
                                        .getMessage(
                                                        TermReadSvcImpl.class,
                                                        "valueSetExpandedUsingInMemoryExpansion",
                                                        getValueSetInfo(theValueSetToExpand));
                        theAccumulator.addMessage(msg);
                        doExpandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter);
                        return;
                }

                /*
                 * ValueSet exists in pre-expansion database, but pre-expansion is not yet complete so perform in-memory expansion
                 */
                TermValueSet termValueSet = optionalTermValueSet.get();
                if (termValueSet.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
                        String msg = myContext
                                        .getLocalizer()
                                        .getMessage(
                                                        TermReadSvcImpl.class,
                                                        "valueSetNotYetExpanded",
                                                        getValueSetInfo(theValueSetToExpand),
                                                        termValueSet.getExpansionStatus().name(),
                                                        termValueSet.getExpansionStatus().getDescription());
                        theAccumulator.addMessage(msg);
                        doExpandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter);
                        return;
                }

                /*
                 * ValueSet is pre-expanded in database so let's use that
                 */
                String expansionTimestamp = toHumanReadableExpansionTimestamp(termValueSet);
                String msg = myContext
                                .getLocalizer()
                                .getMessage(TermReadSvcImpl.class, "valueSetExpandedUsingPreExpansion", expansionTimestamp);
                theAccumulator.addMessage(msg);
                expandConcepts(theExpansionOptions, theAccumulator, termValueSet, theFilter, theAdd, isOracleDialect());
        }

        @Nonnull
        private String toHumanReadableExpansionTimestamp(TermValueSet termValueSet) {
                String expansionTimestamp = "(unknown)";
                if (termValueSet.getExpansionTimestamp() != null) {
                        String timeElapsed = StopWatch.formatMillis(System.currentTimeMillis()
                                        - termValueSet.getExpansionTimestamp().getTime());
                        expansionTimestamp = new InstantType(termValueSet.getExpansionTimestamp()).getValueAsString() + " ("
                                        + timeElapsed + " ago)";
                }
                return expansionTimestamp;
        }

        private boolean isOracleDialect() {
                return myHibernatePropertiesProvider.getDialect() instanceof org.hibernate.dialect.Oracle12cDialect;
        }

        private void expandConcepts(
                        ValueSetExpansionOptions theExpansionOptions,
                        IValueSetConceptAccumulator theAccumulator,
                        TermValueSet theTermValueSet,
                        ExpansionFilter theFilter,
                        boolean theAdd,
                        boolean theOracle) {
                // NOTE: if you modifiy the logic here, look to `expandConceptsOracle` and see if your new code applies to its
                // copy pasted sibling
                Integer offset = theAccumulator.getSkipCountRemaining();
                offset = ObjectUtils.defaultIfNull(offset, 0);
                offset = Math.min(offset, theTermValueSet.getTotalConcepts().intValue());

                Integer count = theAccumulator.getCapacityRemaining();
                count = defaultIfNull(count, myStorageSettings.getMaximumExpansionSize());

                int conceptsExpanded = 0;
                int designationsExpanded = 0;
                int toIndex = offset + count;

                Collection<? extends ITermValueSetConceptView> conceptViews;
                boolean wasFilteredResult = false;
                String filterDisplayValue = null;
                if (!theFilter.getFilters().isEmpty()
                                && JpaConstants.VALUESET_FILTER_DISPLAY.equals(
                                                theFilter.getFilters().get(0).getProperty())
                                && theFilter.getFilters().get(0).getOp() == ValueSet.FilterOperator.EQUAL) {
                        filterDisplayValue =
                                        lowerCase(theFilter.getFilters().get(0).getValue().replace("%", "[%]"));
                        String displayValue = "%" + lowerCase(filterDisplayValue) + "%";
                        if (theOracle) {
                                conceptViews =
                                                myTermValueSetConceptViewOracleDao.findByTermValueSetId(theTermValueSet.getId(), displayValue);
                        } else {
                                conceptViews = myTermValueSetConceptViewDao.findByTermValueSetId(theTermValueSet.getId(), displayValue);
                        }
                        wasFilteredResult = true;
                } else {
                        // TODO JA HS: I'm pretty sure we are overfetching here.  test says offset 3, count 4, but we are fetching
                        // index 3 -> 10 here, grabbing 7 concepts.
                        // Specifically this test
                        // testExpandInline_IncludePreExpandedValueSetByUri_FilterOnDisplay_LeftMatch_SelectRange
                        if (theOracle) {
                                conceptViews = myTermValueSetConceptViewOracleDao.findByTermValueSetId(
                                                offset, toIndex, theTermValueSet.getId());
                        } else {
                                conceptViews =
                                                myTermValueSetConceptViewDao.findByTermValueSetId(offset, toIndex, theTermValueSet.getId());
                        }
                        theAccumulator.consumeSkipCount(offset);
                        if (theAdd) {
                                theAccumulator.incrementOrDecrementTotalConcepts(
                                                true, theTermValueSet.getTotalConcepts().intValue());
                        }
                }

                if (conceptViews.isEmpty()) {
                        logConceptsExpanded("No concepts to expand. ", theTermValueSet, conceptsExpanded);
                        return;
                }

                Map<Long, FhirVersionIndependentConcept> pidToConcept = new LinkedHashMap<>();
                ArrayListMultimap<Long, TermConceptDesignation> pidToDesignations = ArrayListMultimap.create();
                Map<Long, Long> pidToSourcePid = new HashMap<>();
                Map<Long, String> pidToSourceDirectParentPids = new HashMap<>();

                for (ITermValueSetConceptView conceptView : conceptViews) {

                        String system = conceptView.getConceptSystemUrl();
                        String code = conceptView.getConceptCode();
                        String display = conceptView.getConceptDisplay();
                        String systemVersion = conceptView.getConceptSystemVersion();

                        // -- this is quick solution, may need to revisit
                        if (!applyFilter(display, filterDisplayValue)) {
                                continue;
                        }

                        Long conceptPid = conceptView.getConceptPid();
                        if (!pidToConcept.containsKey(conceptPid)) {
                                FhirVersionIndependentConcept concept =
                                                new FhirVersionIndependentConcept(system, code, display, systemVersion);
                                pidToConcept.put(conceptPid, concept);
                        }

                        // TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to designations
                        // optional.
                        if (conceptView.getDesignationPid() != null) {
                                TermConceptDesignation designation = new TermConceptDesignation();

                                if (isValueSetDisplayLanguageMatch(theExpansionOptions, conceptView.getDesignationLang())) {
                                        designation.setUseSystem(conceptView.getDesignationUseSystem());
                                        designation.setUseCode(conceptView.getDesignationUseCode());
                                        designation.setUseDisplay(conceptView.getDesignationUseDisplay());
                                        designation.setValue(conceptView.getDesignationVal());
                                        designation.setLanguage(conceptView.getDesignationLang());
                                        pidToDesignations.put(conceptPid, designation);
                                }

                                if (++designationsExpanded % 250 == 0) {
                                        logDesignationsExpanded(
                                                        "Expansion of designations in progress. ", theTermValueSet, designationsExpanded);
                                }
                        }

                        if (theAccumulator.isTrackingHierarchy()) {
                                pidToSourcePid.put(conceptPid, conceptView.getSourceConceptPid());
                                pidToSourceDirectParentPids.put(conceptPid, conceptView.getSourceConceptDirectParentPids());
                        }

                        if (++conceptsExpanded % 250 == 0) {
                                logConceptsExpanded("Expansion of concepts in progress. ", theTermValueSet, conceptsExpanded);
                        }
                }

                for (Long nextPid : pidToConcept.keySet()) {
                        FhirVersionIndependentConcept concept = pidToConcept.get(nextPid);
                        List<TermConceptDesignation> designations = pidToDesignations.get(nextPid);
                        String system = concept.getSystem();
                        String code = concept.getCode();
                        String display = concept.getDisplay();
                        String systemVersion = concept.getSystemVersion();

                        if (theAdd) {
                                if (theAccumulator.getCapacityRemaining() != null) {
                                        if (theAccumulator.getCapacityRemaining() == 0) {
                                                break;
                                        }
                                }

                                Long sourceConceptPid = pidToSourcePid.get(nextPid);
                                String sourceConceptDirectParentPids = pidToSourceDirectParentPids.get(nextPid);
                                theAccumulator.includeConceptWithDesignations(
                                                system,
                                                code,
                                                display,
                                                designations,
                                                sourceConceptPid,
                                                sourceConceptDirectParentPids,
                                                systemVersion);
                        } else {
                                boolean removed = theAccumulator.excludeConcept(system, code);
                                if (removed) {
                                        theAccumulator.incrementOrDecrementTotalConcepts(false, 1);
                                }
                        }
                }

                if (wasFilteredResult && theAdd) {
                        theAccumulator.incrementOrDecrementTotalConcepts(true, pidToConcept.size());
                }

                logDesignationsExpanded("Finished expanding designations. ", theTermValueSet, designationsExpanded);
                logConceptsExpanded("Finished expanding concepts. ", theTermValueSet, conceptsExpanded);
        }

        private void logConceptsExpanded(
                        String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theConceptsExpanded) {
                if (theConceptsExpanded > 0) {
                        ourLog.debug(
                                        "{}Have expanded {} concepts in ValueSet[{}]",
                                        theLogDescriptionPrefix,
                                        theConceptsExpanded,
                                        theTermValueSet.getUrl());
                }
        }

        private void logDesignationsExpanded(
                        String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theDesignationsExpanded) {
                if (theDesignationsExpanded > 0) {
                        ourLog.debug(
                                        "{}Have expanded {} designations in ValueSet[{}]",
                                        theLogDescriptionPrefix,
                                        theDesignationsExpanded,
                                        theTermValueSet.getUrl());
                }
        }

        public boolean applyFilter(final String theDisplay, final String theFilterDisplay) {

                // -- safety check only, no need to apply filter
                if (theDisplay == null || theFilterDisplay == null) return true;

                // -- sentence case
                if (startsWithIgnoreCase(theDisplay, theFilterDisplay)) return true;

                // -- token case
                return startsWithByWordBoundaries(theDisplay, theFilterDisplay);
        }

        private boolean startsWithByWordBoundaries(String theDisplay, String theFilterDisplay) {
                // return true only e.g. the input is 'Body height', theFilterDisplay is "he", or 'bo'
                StringTokenizer tok = new StringTokenizer(theDisplay);
                List<String> tokens = new ArrayList<>();
                while (tok.hasMoreTokens()) {
                        String token = tok.nextToken();
                        if (startsWithIgnoreCase(token, theFilterDisplay)) return true;
                        tokens.add(token);
                }

                // Allow to search by the end of the phrase.  E.g.  "working proficiency" will match "Limited working
                // proficiency"
                for (int start = 0; start <= tokens.size() - 1; ++start) {
                        for (int end = start + 1; end <= tokens.size(); ++end) {
                                String sublist = String.join(" ", tokens.subList(start, end));
                                if (startsWithIgnoreCase(sublist, theFilterDisplay)) return true;
                        }
                }
                return false;
        }

        @Override
        public void expandValueSet(
                        ValueSetExpansionOptions theExpansionOptions,
                        ValueSet theValueSetToExpand,
                        IValueSetConceptAccumulator theValueSetCodeAccumulator) {
                doExpandValueSet(
                                theExpansionOptions, theValueSetToExpand, theValueSetCodeAccumulator, ExpansionFilter.NO_FILTER);
        }

        /**
         * Note: Not transactional because specific calls within this method
         * get executed in a transaction
         */
        private void doExpandValueSet(
                        ValueSetExpansionOptions theExpansionOptions,
                        ValueSet theValueSetToExpand,
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        @Nonnull ExpansionFilter theExpansionFilter) {
                Set<String> addedCodes = new HashSet<>();

                StopWatch sw = new StopWatch();
                String valueSetInfo = getValueSetInfo(theValueSetToExpand);
                ourLog.debug("Working with {}", valueSetInfo);

                // Offset can't be combined with excludes
                Integer skipCountRemaining = theValueSetCodeAccumulator.getSkipCountRemaining();
                if (skipCountRemaining != null && skipCountRemaining > 0) {
                        if (theValueSetToExpand.getCompose().getExclude().size() > 0) {
                                String msg = myContext
                                                .getLocalizer()
                                                .getMessage(TermReadSvcImpl.class, "valueSetNotYetExpanded_OffsetNotAllowed", valueSetInfo);
                                throw new InvalidRequestException(Msg.code(887) + msg);
                        }
                }

                // Handle includes
                ourLog.debug("Handling includes");
                for (ValueSet.ConceptSetComponent include :
                                theValueSetToExpand.getCompose().getInclude()) {
                        myTxTemplate.executeWithoutResult(tx -> expandValueSetHandleIncludeOrExclude(
                                        theExpansionOptions, theValueSetCodeAccumulator, addedCodes, include, true, theExpansionFilter));
                }

                // Handle excludes
                ourLog.debug("Handling excludes");
                for (ValueSet.ConceptSetComponent exclude :
                                theValueSetToExpand.getCompose().getExclude()) {
                        myTxTemplate.executeWithoutResult(tx -> expandValueSetHandleIncludeOrExclude(
                                        theExpansionOptions,
                                        theValueSetCodeAccumulator,
                                        addedCodes,
                                        exclude,
                                        false,
                                        ExpansionFilter.NO_FILTER));
                }

                if (theValueSetCodeAccumulator instanceof ValueSetConceptAccumulator) {
                        myTxTemplate.execute(
                                        t -> ((ValueSetConceptAccumulator) theValueSetCodeAccumulator).removeGapsFromConceptOrder());
                }

                ourLog.debug("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
        }

        private String getValueSetInfo(ValueSet theValueSet) {
                StringBuilder sb = new StringBuilder();
                boolean isIdentified = false;
                if (theValueSet.hasUrl()) {
                        isIdentified = true;
                        sb.append("ValueSet.url[").append(theValueSet.getUrl()).append("]");
                } else if (theValueSet.hasId()) {
                        isIdentified = true;
                        sb.append("ValueSet.id[").append(theValueSet.getId()).append("]");
                }

                if (!isIdentified) {
                        sb.append("Unidentified ValueSet");
                }

                return sb.toString();
        }

        /**
         * Returns true if there are potentially more results to process.
         */
        private void expandValueSetHandleIncludeOrExclude(
                        @Nullable ValueSetExpansionOptions theExpansionOptions,
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        Set<String> theAddedCodes,
                        ValueSet.ConceptSetComponent theIncludeOrExclude,
                        boolean theAdd,
                        @Nonnull ExpansionFilter theExpansionFilter) {

                String system = theIncludeOrExclude.getSystem();
                boolean hasSystem = isNotBlank(system);
                boolean hasValueSet = theIncludeOrExclude.getValueSet().size() > 0;

                if (hasSystem) {

                        if (theExpansionFilter.hasCode()
                                        && theExpansionFilter.getSystem() != null
                                        && !system.equals(theExpansionFilter.getSystem())) {
                                return;
                        }

                        ourLog.debug("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), system);

                        Optional<TermCodeSystemVersion> termCodeSystemVersion =
                                        optionalFindTermCodeSystemVersion(theIncludeOrExclude);
                        if (termCodeSystemVersion.isPresent()) {

                                expandValueSetHandleIncludeOrExcludeUsingDatabase(
                                                theExpansionOptions,
                                                theValueSetCodeAccumulator,
                                                theAddedCodes,
                                                theIncludeOrExclude,
                                                theAdd,
                                                theExpansionFilter,
                                                system,
                                                termCodeSystemVersion.get());

                        } else {

                                if (theIncludeOrExclude.getConcept().size() > 0 && theExpansionFilter.hasCode()) {
                                        if (defaultString(theIncludeOrExclude.getSystem()).equals(theExpansionFilter.getSystem())) {
                                                if (theIncludeOrExclude.getConcept().stream()
                                                                .noneMatch(t -> t.getCode().equals(theExpansionFilter.getCode()))) {
                                                        return;
                                                }
                                        }
                                }

                                Consumer<FhirVersionIndependentConcept> consumer = c -> addOrRemoveCode(
                                                theValueSetCodeAccumulator,
                                                theAddedCodes,
                                                theAdd,
                                                system,
                                                c.getCode(),
                                                c.getDisplay(),
                                                c.getSystemVersion());

                                try {
                                        ConversionContext40_50.INSTANCE.init(
                                                        new VersionConvertor_40_50(new BaseAdvisor_40_50()), "ValueSet");
                                        org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent includeOrExclude =
                                                        ValueSet40_50.convertConceptSetComponent(theIncludeOrExclude);
                                        new InMemoryTerminologyServerValidationSupport(myContext)
                                                        .expandValueSetIncludeOrExclude(
                                                                        new ValidationSupportContext(provideValidationSupport()),
                                                                        consumer,
                                                                        includeOrExclude);
                                } catch (InMemoryTerminologyServerValidationSupport.ExpansionCouldNotBeCompletedInternallyException e) {
                                        if (theExpansionOptions != null
                                                        && !theExpansionOptions.isFailOnMissingCodeSystem()
                                                        && e.getFailureType()
                                                                        == InMemoryTerminologyServerValidationSupport.FailureType.UNKNOWN_CODE_SYSTEM) {
                                                return;
                                        }
                                        throw new InternalErrorException(Msg.code(888) + e);
                                } finally {
                                        ConversionContext40_50.INSTANCE.close("ValueSet");
                                }
                        }

                } else if (hasValueSet) {

                        for (CanonicalType nextValueSet : theIncludeOrExclude.getValueSet()) {
                                String valueSetUrl = nextValueSet.getValueAsString();
                                ourLog.debug(
                                                "Starting {} expansion around ValueSet: {}", (theAdd ? "inclusion" : "exclusion"), valueSetUrl);

                                ExpansionFilter subExpansionFilter = new ExpansionFilter(
                                                theExpansionFilter,
                                                theIncludeOrExclude.getFilter(),
                                                theValueSetCodeAccumulator.getCapacityRemaining());

                                // TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not
                                // be found in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the
                                // expansion may time-out.

                                ValueSet valueSet = fetchCanonicalValueSetFromCompleteContext(valueSetUrl);
                                if (valueSet == null) {
                                        throw new ResourceNotFoundException(
                                                        Msg.code(889) + "Unknown ValueSet: " + UrlUtil.escapeUrlParam(valueSetUrl));
                                }

                                expandValueSetIntoAccumulator(
                                                valueSet, theExpansionOptions, theValueSetCodeAccumulator, subExpansionFilter, theAdd);
                        }

                } else {
                        throw new InvalidRequestException(Msg.code(890) + "ValueSet contains " + (theAdd ? "include" : "exclude")
                                        + " criteria with no system defined");
                }
        }

        private Optional<TermCodeSystemVersion> optionalFindTermCodeSystemVersion(
                        ValueSet.ConceptSetComponent theIncludeOrExclude) {
                if (isEmpty(theIncludeOrExclude.getVersion())) {
                        return Optional.ofNullable(myCodeSystemDao.findByCodeSystemUri(theIncludeOrExclude.getSystem()))
                                        .map(TermCodeSystem::getCurrentVersion);
                } else {
                        return Optional.ofNullable(myCodeSystemVersionDao.findByCodeSystemUriAndVersion(
                                        theIncludeOrExclude.getSystem(), theIncludeOrExclude.getVersion()));
                }
        }

        private boolean isHibernateSearchEnabled() {
                return myFulltextSearchSvc != null && !ourForceDisableHibernateSearchForUnitTest;
        }

        private void expandValueSetHandleIncludeOrExcludeUsingDatabase(
                        ValueSetExpansionOptions theExpansionOptions,
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        Set<String> theAddedCodes,
                        ValueSet.ConceptSetComponent theIncludeOrExclude,
                        boolean theAdd,
                        @Nonnull ExpansionFilter theExpansionFilter,
                        String theSystem,
                        TermCodeSystemVersion theTermCodeSystemVersion) {

                StopWatch fullOperationSw = new StopWatch();
                String includeOrExcludeVersion = theIncludeOrExclude.getVersion();

                /*
                 * If FullText searching is not enabled, we can handle only basic expansions
                 * since we're going to do it without the database.
                 */
                if (!isHibernateSearchEnabled()) {
                        expandWithoutHibernateSearch(
                                        theValueSetCodeAccumulator,
                                        theTermCodeSystemVersion,
                                        theAddedCodes,
                                        theIncludeOrExclude,
                                        theSystem,
                                        theAdd);
                        return;
                }

                /*
                 * Ok, let's use hibernate search to build the expansion
                 */

                int count = 0;

                Optional<Integer> chunkSizeOpt = getScrollChunkSize(theAdd, theValueSetCodeAccumulator);
                if (chunkSizeOpt.isEmpty()) {
                        return;
                }
                int chunkSize = chunkSizeOpt.get();

                SearchProperties searchProps = buildSearchScroll(
                                theTermCodeSystemVersion,
                                theExpansionFilter,
                                theSystem,
                                theIncludeOrExclude,
                                chunkSize,
                                includeOrExcludeVersion);

                int accumulatedBatchesSoFar = 0;
                try (SearchScroll<EntityReference> scroll = searchProps.getSearchScroll()) {

                        ourLog.debug(
                                        "Beginning batch expansion for {} with max results per batch: {}",
                                        (theAdd ? "inclusion" : "exclusion"),
                                        chunkSize);
                        for (SearchScrollResult<EntityReference> chunk = scroll.next(); chunk.hasHits(); chunk = scroll.next()) {
                                int countForBatch = 0;

                                List<Long> pids = chunk.hits().stream().map(t -> (Long) t.id()).collect(Collectors.toList());

                                List<TermConcept> termConcepts = myTermConceptDao.fetchConceptsAndDesignationsByPid(pids);

                                // If the include section had multiple codes, return the codes in the same order
                                termConcepts = sortTermConcepts(searchProps, termConcepts);

                                //       int firstResult = theQueryIndex * maxResultsPerBatch;// TODO GGG HS we lose the ability to check the
                                // index of the first result, so just best-guessing it here.
                                Optional<PredicateFinalStep> expansionStepOpt = searchProps.getExpansionStepOpt();
                                int delta = 0;
                                for (TermConcept concept : termConcepts) {
                                        count++;
                                        countForBatch++;
                                        if (theAdd && expansionStepOpt.isPresent()) {
                                                ValueSet.ConceptReferenceComponent theIncludeConcept =
                                                                getMatchedConceptIncludedInValueSet(theIncludeOrExclude, concept);
                                                if (theIncludeConcept != null && isNotBlank(theIncludeConcept.getDisplay())) {
                                                        concept.setDisplay(theIncludeConcept.getDisplay());
                                                }
                                        }
                                        boolean added = addCodeIfNotAlreadyAdded(
                                                        theExpansionOptions,
                                                        theValueSetCodeAccumulator,
                                                        theAddedCodes,
                                                        concept,
                                                        theAdd,
                                                        includeOrExcludeVersion);
                                        if (added) {
                                                delta++;
                                        }
                                }

                                ourLog.debug(
                                                "Batch expansion scroll for {} with offset {} produced {} results in {}ms",
                                                (theAdd ? "inclusion" : "exclusion"),
                                                accumulatedBatchesSoFar,
                                                chunk.hits().size(),
                                                chunk.took().toMillis());

                                theValueSetCodeAccumulator.incrementOrDecrementTotalConcepts(theAdd, delta);
                                accumulatedBatchesSoFar += countForBatch;

                                // keep session bounded
                                myEntityManager.flush();
                                myEntityManager.clear();
                        }

                        ourLog.debug(
                                        "Expansion for {} produced {} results in {}ms",
                                        (theAdd ? "inclusion" : "exclusion"),
                                        count,
                                        fullOperationSw.getMillis());
                }
        }

        private List<TermConcept> sortTermConcepts(SearchProperties searchProps, List<TermConcept> termConcepts) {
                List<String> codes = searchProps.getIncludeOrExcludeCodes();
                if (codes.size() > 1) {
                        termConcepts = new ArrayList<>(termConcepts);
                        Map<String, Integer> codeToIndex = new HashMap<>(codes.size());
                        for (int i = 0; i < codes.size(); i++) {
                                codeToIndex.put(codes.get(i), i);
                        }
                        termConcepts.sort(((o1, o2) -> {
                                Integer idx1 = codeToIndex.get(o1.getCode());
                                Integer idx2 = codeToIndex.get(o2.getCode());
                                return Comparators.nullsHigh().compare(idx1, idx2);
                        }));
                }
                return termConcepts;
        }

        private Optional<Integer> getScrollChunkSize(
                        boolean theAdd, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
                int maxResultsPerBatch = SearchBuilder.getMaximumPageSize();

                /*
                 * If the accumulator is bounded, we may reduce the size of the query to
                 * Lucene in order to be more efficient.
                 */
                if (theAdd) {
                        Integer accumulatorCapacityRemaining = theValueSetCodeAccumulator.getCapacityRemaining();
                        if (accumulatorCapacityRemaining != null) {
                                maxResultsPerBatch = Math.min(maxResultsPerBatch, accumulatorCapacityRemaining + 1);
                        }
                }
                return maxResultsPerBatch > 0 ? Optional.of(maxResultsPerBatch) : Optional.empty();
        }

        private SearchProperties buildSearchScroll(
                        TermCodeSystemVersion theTermCodeSystemVersion,
                        ExpansionFilter theExpansionFilter,
                        String theSystem,
                        ValueSet.ConceptSetComponent theIncludeOrExclude,
                        Integer theScrollChunkSize,
                        String theIncludeOrExcludeVersion) {
                SearchSession searchSession = Search.session(myEntityManager);
                // Manually building a predicate since we need to throw it around.
                SearchPredicateFactory predicate =
                                searchSession.scope(TermConcept.class).predicate();

                // Build the top-level expansion on filters.
                PredicateFinalStep step = predicate.bool(b -> {
                        b.must(predicate.match().field("myCodeSystemVersionPid").matching(theTermCodeSystemVersion.getPid()));

                        if (theExpansionFilter.hasCode()) {
                                b.must(predicate.match().field("myCode").matching(theExpansionFilter.getCode()));
                        }

                        String codeSystemUrlAndVersion = buildCodeSystemUrlAndVersion(theSystem, theIncludeOrExcludeVersion);
                        for (ValueSet.ConceptSetFilterComponent nextFilter : theIncludeOrExclude.getFilter()) {
                                handleFilter(codeSystemUrlAndVersion, predicate, b, nextFilter);
                        }
                        for (ValueSet.ConceptSetFilterComponent nextFilter : theExpansionFilter.getFilters()) {
                                handleFilter(codeSystemUrlAndVersion, predicate, b, nextFilter);
                        }
                });

                SearchProperties returnProps = new SearchProperties();

                List<String> codes = theIncludeOrExclude.getConcept().stream()
                                .filter(Objects::nonNull)
                                .map(ValueSet.ConceptReferenceComponent::getCode)
                                .filter(StringUtils::isNotBlank)
                                .collect(Collectors.toList());
                returnProps.setIncludeOrExcludeCodes(codes);

                Optional<PredicateFinalStep> expansionStepOpt = buildExpansionPredicate(codes, predicate);
                final PredicateFinalStep finishedQuery =
                                expansionStepOpt.isPresent() ? predicate.bool().must(step).must(expansionStepOpt.get()) : step;
                returnProps.setExpansionStepOpt(expansionStepOpt);

                /*
                 * DM 2019-08-21 - Processing slows after any ValueSets with many codes explicitly identified. This might
                 * be due to the dark arts that is memory management. Will monitor but not do anything about this right now.
                 */

                // BooleanQuery.setMaxClauseCount(SearchBuilder.getMaximumPageSize());
                // TODO GGG HS looks like we can't set max clause count, but it can be set server side.
                // BooleanQuery.setMaxClauseCount(10000);
                // JM 22-02-15 - Hopefully increasing maxClauseCount should be not needed anymore

                SearchQuery<EntityReference> termConceptsQuery = searchSession
                                .search(TermConcept.class)
                                .selectEntityReference()
                                .where(f -> finishedQuery)
                                .toQuery();

                returnProps.setSearchScroll(termConceptsQuery.scroll(theScrollChunkSize));
                return returnProps;
        }

        private ValueSet.ConceptReferenceComponent getMatchedConceptIncludedInValueSet(
                        ValueSet.ConceptSetComponent theIncludeOrExclude, TermConcept concept) {
                return theIncludeOrExclude.getConcept().stream()
                                .filter(includedConcept -> includedConcept.getCode().equalsIgnoreCase(concept.getCode()))
                                .findFirst()
                                .orElse(null);
        }

        /**
         * Helper method which builds a predicate for the expansion
         */
        private Optional<PredicateFinalStep> buildExpansionPredicate(
                        List<String> theCodes, SearchPredicateFactory thePredicate) {
                if (CollectionUtils.isEmpty(theCodes)) {
                        return Optional.empty();
                }

                if (theCodes.size() < BooleanQuery.getMaxClauseCount()) {
                        return Optional.of(thePredicate.simpleQueryString().field("myCode").matching(String.join(" | ", theCodes)));
                }

                // Number of codes is larger than maxClauseCount, so we split the query in several clauses

                // partition codes in lists of BooleanQuery.getMaxClauseCount() size
                List<List<String>> listOfLists = ListUtils.partition(theCodes, BooleanQuery.getMaxClauseCount());

                PredicateFinalStep step = thePredicate.bool(b -> {
                        b.minimumShouldMatchNumber(1);
                        for (List<String> codeList : listOfLists) {
                                b.should(p -> p.simpleQueryString().field("myCode").matching(String.join(" | ", codeList)));
                        }
                });

                return Optional.of(step);
        }

        private String buildCodeSystemUrlAndVersion(String theSystem, String theIncludeOrExcludeVersion) {
                String codeSystemUrlAndVersion;
                if (theIncludeOrExcludeVersion != null) {
                        codeSystemUrlAndVersion = theSystem + OUR_PIPE_CHARACTER + theIncludeOrExcludeVersion;
                } else {
                        codeSystemUrlAndVersion = theSystem;
                }
                return codeSystemUrlAndVersion;
        }

        private @Nonnull ValueSetExpansionOptions provideExpansionOptions(
                        @Nullable ValueSetExpansionOptions theExpansionOptions) {
                return Objects.requireNonNullElse(theExpansionOptions, DEFAULT_EXPANSION_OPTIONS);
        }

        private void addOrRemoveCode(
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        Set<String> theAddedCodes,
                        boolean theAdd,
                        String theSystem,
                        String theCode,
                        String theDisplay,
                        String theSystemVersion) {
                if (theAdd && theAddedCodes.add(theSystem + OUR_PIPE_CHARACTER + theCode)) {
                        theValueSetCodeAccumulator.includeConcept(theSystem, theCode, theDisplay, null, null, theSystemVersion);
                }
                if (!theAdd && theAddedCodes.remove(theSystem + OUR_PIPE_CHARACTER + theCode)) {
                        theValueSetCodeAccumulator.excludeConcept(theSystem, theCode);
                }
        }

        private void handleFilter(
                        String theCodeSystemIdentifier,
                        SearchPredicateFactory theF,
                        BooleanPredicateClausesStep<?> theB,
                        ValueSet.ConceptSetFilterComponent theFilter) {
                if (isBlank(theFilter.getValue()) && theFilter.getOp() == null && isBlank(theFilter.getProperty())) {
                        return;
                }

                if (isBlank(theFilter.getValue()) || theFilter.getOp() == null || isBlank(theFilter.getProperty())) {
                        throw new InvalidRequestException(
                                        Msg.code(891) + "Invalid filter, must have fields populated: property op value");
                }

                switch (theFilter.getProperty()) {
                        case "display:exact":
                        case "display":
                                handleFilterDisplay(theF, theB, theFilter);
                                break;
                        case "concept":
                        case "code":
                                handleFilterConceptAndCode(theCodeSystemIdentifier, theF, theB, theFilter);
                                break;
                        case "parent":
                        case "child":
                                isCodeSystemLoincOrThrowInvalidRequestException(theCodeSystemIdentifier, theFilter.getProperty());
                                handleFilterLoincParentChild(theF, theB, theFilter);
                                break;
                        case "ancestor":
                                isCodeSystemLoincOrThrowInvalidRequestException(theCodeSystemIdentifier, theFilter.getProperty());
                                handleFilterLoincAncestor(theCodeSystemIdentifier, theF, theB, theFilter);
                                break;
                        case "descendant":
                                isCodeSystemLoincOrThrowInvalidRequestException(theCodeSystemIdentifier, theFilter.getProperty());
                                handleFilterLoincDescendant(theCodeSystemIdentifier, theF, theB, theFilter);
                                break;
                        case "copyright":
                                isCodeSystemLoincOrThrowInvalidRequestException(theCodeSystemIdentifier, theFilter.getProperty());
                                handleFilterLoincCopyright(theF, theB, theFilter);
                                break;
                        default:
                                if (theFilter.getOp() == ValueSet.FilterOperator.REGEX) {
                                        handleFilterRegex(theF, theB, theFilter);
                                } else {
                                        handleFilterPropertyDefault(theF, theB, theFilter);
                                }
                                break;
                }
        }

        private void handleFilterPropertyDefault(
                        SearchPredicateFactory theF,
                        BooleanPredicateClausesStep<?> theB,
                        ValueSet.ConceptSetFilterComponent theFilter) {

                String value = theFilter.getValue();
                Term term = new Term(CONCEPT_PROPERTY_PREFIX_NAME + theFilter.getProperty(), value);
                theB.must(theF.match().field(term.field()).matching(term.text()));
        }

        private void handleFilterRegex(
                        SearchPredicateFactory theF,
                        BooleanPredicateClausesStep<?> theB,
                        ValueSet.ConceptSetFilterComponent theFilter) {
                /*
                 * We treat the regex filter as a match on the regex
                 * anywhere in the property string. The spec does not
                 * say whether this is the right behaviour or not, but
                 * there are examples that seem to suggest that it is.
                 */
                String value = theFilter.getValue();
                if (value.endsWith("$")) {
                        value = value.substring(0, value.length() - 1);
                } else if (!value.endsWith(".*")) {
                        value = value + ".*";
                }
                if (!value.startsWith("^") && !value.startsWith(".*")) {
                        value = ".*" + value;
                } else if (value.startsWith("^")) {
                        value = value.substring(1);
                }

                theB.must(theF.regexp()
                                .field(CONCEPT_PROPERTY_PREFIX_NAME + theFilter.getProperty())
                                .matching(value));
        }

        private void handleFilterLoincCopyright(
                        SearchPredicateFactory theF,
                        BooleanPredicateClausesStep<?> theB,
                        ValueSet.ConceptSetFilterComponent theFilter) {

                if (theFilter.getOp() == ValueSet.FilterOperator.EQUAL) {

                        String copyrightFilterValue = defaultString(theFilter.getValue()).toLowerCase();
                        switch (copyrightFilterValue) {
                                case "3rdparty":
                                        logFilteringValueOnProperty(theFilter.getValue(), theFilter.getProperty());
                                        addFilterLoincCopyright3rdParty(theF, theB);
                                        break;
                                case "loinc":
                                        logFilteringValueOnProperty(theFilter.getValue(), theFilter.getProperty());
                                        addFilterLoincCopyrightLoinc(theF, theB);
                                        break;
                                default:
                                        throwInvalidRequestForValueOnProperty(theFilter.getValue(), theFilter.getProperty());
                        }

                } else {
                        throwInvalidRequestForOpOnProperty(theFilter.getOp(), theFilter.getProperty());
                }
        }

        private void addFilterLoincCopyrightLoinc(SearchPredicateFactory theF, BooleanPredicateClausesStep<?> theB) {
                theB.mustNot(theF.exists().field(CONCEPT_PROPERTY_PREFIX_NAME + "EXTERNAL_COPYRIGHT_NOTICE"));
        }

        private void addFilterLoincCopyright3rdParty(SearchPredicateFactory theF, BooleanPredicateClausesStep<?> theB) {
                theB.must(theF.exists().field(CONCEPT_PROPERTY_PREFIX_NAME + "EXTERNAL_COPYRIGHT_NOTICE"));
        }

        @SuppressWarnings("EnumSwitchStatementWhichMissesCases")
        private void handleFilterLoincAncestor(
                        String theSystem,
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> b,
                        ValueSet.ConceptSetFilterComponent theFilter) {
                switch (theFilter.getOp()) {
                        case EQUAL:
                                addLoincFilterAncestorEqual(theSystem, f, b, theFilter);
                                break;
                        case IN:
                                addLoincFilterAncestorIn(theSystem, f, b, theFilter);
                                break;
                        default:
                                throw new InvalidRequestException(Msg.code(892) + "Don't know how to handle op=" + theFilter.getOp()
                                                + " on property " + theFilter.getProperty());
                }
        }

        private void addLoincFilterAncestorEqual(
                        String theSystem,
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> b,
                        ValueSet.ConceptSetFilterComponent theFilter) {
                addLoincFilterAncestorEqual(theSystem, f, b, theFilter.getProperty(), theFilter.getValue());
        }

        private void addLoincFilterAncestorEqual(
                        String theSystem,
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> b,
                        String theProperty,
                        String theValue) {
                List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue);
                b.must(f.bool(innerB -> terms.forEach(
                                term -> innerB.should(f.match().field(term.field()).matching(term.text())))));
        }

        private void addLoincFilterAncestorIn(
                        String theSystem,
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> b,
                        ValueSet.ConceptSetFilterComponent theFilter) {
                String[] values = theFilter.getValue().split(",");
                List<Term> terms = new ArrayList<>();
                for (String value : values) {
                        terms.addAll(getAncestorTerms(theSystem, theFilter.getProperty(), value));
                }
                b.must(f.bool(innerB -> terms.forEach(
                                term -> innerB.should(f.match().field(term.field()).matching(term.text())))));
        }

        @SuppressWarnings("EnumSwitchStatementWhichMissesCases")
        private void handleFilterLoincParentChild(
                        SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
                switch (theFilter.getOp()) {
                        case EQUAL:
                                addLoincFilterParentChildEqual(f, b, theFilter.getProperty(), theFilter.getValue());
                                break;
                        case IN:
                                addLoincFilterParentChildIn(f, b, theFilter);
                                break;
                        default:
                                throw new InvalidRequestException(Msg.code(893) + "Don't know how to handle op=" + theFilter.getOp()
                                                + " on property " + theFilter.getProperty());
                }
        }

        private void addLoincFilterParentChildIn(
                        SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
                String[] values = theFilter.getValue().split(",");
                List<Term> terms = new ArrayList<>();
                for (String value : values) {
                        logFilteringValueOnProperty(value, theFilter.getProperty());
                        terms.add(getPropertyTerm(theFilter.getProperty(), value));
                }

                b.must(f.bool(innerB -> terms.forEach(
                                term -> innerB.should(f.match().field(term.field()).matching(term.text())))));
        }

        private void addLoincFilterParentChildEqual(
                        SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, String theProperty, String theValue) {
                logFilteringValueOnProperty(theValue, theProperty);
                b.must(f.match().field(CONCEPT_PROPERTY_PREFIX_NAME + theProperty).matching(theValue));
        }

        private void handleFilterConceptAndCode(
                        String theSystem,
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> b,
                        ValueSet.ConceptSetFilterComponent theFilter) {
                TermConcept code = findCodeForFilterCriteria(theSystem, theFilter);

                if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
                        ourLog.debug(
                                        " * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());

                        b.must(f.match().field("myParentPids").matching("" + code.getId()));
                } else {
                        throwInvalidFilter(theFilter, "");
                }
        }

        @Nonnull
        private TermConcept findCodeForFilterCriteria(String theSystem, ValueSet.ConceptSetFilterComponent theFilter) {
                return findCode(theSystem, theFilter.getValue())
                                .orElseThrow(() ->
                                                new InvalidRequestException(Msg.code(2071) + "Invalid filter criteria - code does not exist: {"
                                                                + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theFilter.getValue()));
        }

        private void throwInvalidFilter(ValueSet.ConceptSetFilterComponent theFilter, String theErrorSuffix) {
                throw new InvalidRequestException(Msg.code(894) + "Don't know how to handle op=" + theFilter.getOp()
                                + " on property " + theFilter.getProperty() + theErrorSuffix);
        }

        private void isCodeSystemLoincOrThrowInvalidRequestException(String theSystemIdentifier, String theProperty) {
                String systemUrl = getUrlFromIdentifier(theSystemIdentifier);
                if (!isCodeSystemLoinc(systemUrl)) {
                        throw new InvalidRequestException(Msg.code(895) + "Invalid filter, property " + theProperty
                                        + " is LOINC-specific and cannot be used with system: " + systemUrl);
                }
        }

        private boolean isCodeSystemLoinc(String theSystem) {
                return LOINC_URI.equals(theSystem);
        }

        private void handleFilterDisplay(
                        SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
                if (theFilter.getProperty().equals("display:exact") && theFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
                        addDisplayFilterExact(f, b, theFilter);
                } else if (theFilter.getProperty().equals("display") && theFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
                        if (theFilter.getValue().trim().contains(" ")) {
                                addDisplayFilterExact(f, b, theFilter);
                        } else {
                                addDisplayFilterInexact(f, b, theFilter);
                        }
                }
        }

        private void addDisplayFilterExact(
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> bool,
                        ValueSet.ConceptSetFilterComponent nextFilter) {
                bool.must(f.phrase().field("myDisplay").matching(nextFilter.getValue()));
        }

        private void addDisplayFilterInexact(
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> bool,
                        ValueSet.ConceptSetFilterComponent nextFilter) {
                bool.must(f.phrase()
                                .field("myDisplay")
                                .boost(4.0f)
                                .field("myDisplayWordEdgeNGram")
                                .boost(1.0f)
                                .field("myDisplayEdgeNGram")
                                .boost(1.0f)
                                .matching(nextFilter.getValue().toLowerCase())
                                .slop(2));
        }

        private Term getPropertyTerm(String theProperty, String theValue) {
                return new Term(CONCEPT_PROPERTY_PREFIX_NAME + theProperty, theValue);
        }

        private List<Term> getAncestorTerms(String theSystem, String theProperty, String theValue) {
                List<Term> retVal = new ArrayList<>();

                TermConcept code = findCode(theSystem, theValue)
                                .orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {"
                                                + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));

                retVal.add(new Term("myParentPids", "" + code.getId()));
                logFilteringValueOnProperty(theValue, theProperty);

                return retVal;
        }

        @SuppressWarnings("EnumSwitchStatementWhichMissesCases")
        private void handleFilterLoincDescendant(
                        String theSystem,
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> b,
                        ValueSet.ConceptSetFilterComponent theFilter) {
                switch (theFilter.getOp()) {
                        case EQUAL:
                                addLoincFilterDescendantEqual(theSystem, f, b, theFilter);
                                break;
                        case IN:
                                addLoincFilterDescendantIn(theSystem, f, b, theFilter);
                                break;
                        default:
                                throw new InvalidRequestException(Msg.code(896) + "Don't know how to handle op=" + theFilter.getOp()
                                                + " on property " + theFilter.getProperty());
                }
        }

        private void addLoincFilterDescendantEqual(
                        String theSystem,
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> b,
                        ValueSet.ConceptSetFilterComponent theFilter) {

                List<Long> parentPids = getCodeParentPids(theSystem, theFilter.getProperty(), theFilter.getValue());
                if (parentPids.isEmpty()) {
                        // Can't return empty must, because it wil match according to other predicates.
                        // Some day there will be a 'matchNone' predicate
                        // (https://discourse.hibernate.org/t/fail-fast-predicate/6062)
                        b.mustNot(f.matchAll());
                        return;
                }

                b.must(f.bool(innerB -> {
                        innerB.minimumShouldMatchNumber(1);
                        parentPids.forEach(pid -> innerB.should(f.match().field("myId").matching(pid)));
                }));
        }

        /**
         * We are looking for codes which have codes indicated in theFilter.getValue() as descendants.
         * Strategy is to find codes which have their pId(s) in the list of the parentId(s) of all the TermConcept(s)
         * representing the codes in theFilter.getValue()
         */
        private void addLoincFilterDescendantIn(
                        String theSystem,
                        SearchPredicateFactory f,
                        BooleanPredicateClausesStep<?> b,
                        ValueSet.ConceptSetFilterComponent theFilter) {

                String[] values = theFilter.getValue().split(",");
                if (values.length == 0) {
                        throw new InvalidRequestException(Msg.code(2062) + "Invalid filter criteria - no codes specified");
                }

                List<Long> descendantCodePidList = getMultipleCodeParentPids(theSystem, theFilter.getProperty(), values);

                b.must(f.bool(innerB -> descendantCodePidList.forEach(
                                pId -> innerB.should(f.match().field("myId").matching(pId)))));
        }

        /**
         * Returns the list of parentId(s) of the TermConcept representing theValue as a code
         */
        private List<Long> getCodeParentPids(String theSystem, String theProperty, String theValue) {
                TermConcept code = findCode(theSystem, theValue)
                                .orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {"
                                                + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));

                String[] parentPids = code.getParentPidsAsString().split(" ");
                List<Long> retVal = Arrays.stream(parentPids)
                                .filter(pid -> !StringUtils.equals(pid, "NONE"))
                                .map(Long::parseLong)
                                .collect(Collectors.toList());
                logFilteringValueOnProperty(theValue, theProperty);
                return retVal;
        }

        /**
         * Returns the list of parentId(s) of the TermConcept representing theValue as a code
         */
        private List<Long> getMultipleCodeParentPids(String theSystem, String theProperty, String[] theValues) {
                List<String> valuesList = Arrays.asList(theValues);
                List<TermConcept> termConcepts = findCodes(theSystem, valuesList);
                if (valuesList.size() != termConcepts.size()) {
                        String exMsg = getTermConceptsFetchExceptionMsg(termConcepts, valuesList);
                        throw new InvalidRequestException(Msg.code(2064) + "Invalid filter criteria - {"
                                        + Constants.codeSystemWithDefaultDescription(theSystem) + "}: " + exMsg);
                }

                List<Long> retVal = termConcepts.stream()
                                .flatMap(tc -> Arrays.stream(tc.getParentPidsAsString().split(" ")))
                                .filter(pid -> !StringUtils.equals(pid, "NONE"))
                                .map(Long::parseLong)
                                .collect(Collectors.toList());

                logFilteringValueOnProperties(valuesList, theProperty);

                return retVal;
        }

        /**
         * Generate message indicating for which of theValues a TermConcept was not found
         */
        private String getTermConceptsFetchExceptionMsg(List<TermConcept> theTermConcepts, List<String> theValues) {
                // case: more TermConcept(s) retrieved than codes queried
                if (theTermConcepts.size() > theValues.size()) {
                        return "Invalid filter criteria - More TermConcepts were found than indicated codes. Queried codes: ["
                                        + join(
                                                        ",",
                                                        theValues + "]; Obtained TermConcept IDs, codes: ["
                                                                        + theTermConcepts.stream()
                                                                                        .map(tc -> tc.getId() + ", " + tc.getCode())
                                                                                        .collect(joining("; "))
                                                                        + "]");
                }

                // case: less TermConcept(s) retrieved than codes queried
                Set<String> matchedCodes =
                                theTermConcepts.stream().map(TermConcept::getCode).collect(toSet());
                List<String> notMatchedValues =
                                theValues.stream().filter(v -> !matchedCodes.contains(v)).collect(toList());

                return "Invalid filter criteria - No TermConcept(s) were found for the requested codes: ["
                                + join(",", notMatchedValues + "]");
        }

        private void logFilteringValueOnProperty(String theValue, String theProperty) {
                ourLog.debug(" * Filtering with value={} on property {}", theValue, theProperty);
        }

        private void logFilteringValueOnProperties(List<String> theValues, String theProperty) {
                ourLog.debug(" * Filtering with values={} on property {}", String.join(", ", theValues), theProperty);
        }

        private void throwInvalidRequestForOpOnProperty(ValueSet.FilterOperator theOp, String theProperty) {
                throw new InvalidRequestException(
                                Msg.code(897) + "Don't know how to handle op=" + theOp + " on property " + theProperty);
        }

        private void throwInvalidRequestForValueOnProperty(String theValue, String theProperty) {
                throw new InvalidRequestException(
                                Msg.code(898) + "Don't know how to handle value=" + theValue + " on property " + theProperty);
        }

        private void expandWithoutHibernateSearch(
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        TermCodeSystemVersion theVersion,
                        Set<String> theAddedCodes,
                        ValueSet.ConceptSetComponent theInclude,
                        String theSystem,
                        boolean theAdd) {
                ourLog.trace("Hibernate search is not enabled");

                if (theValueSetCodeAccumulator instanceof ValueSetExpansionComponentWithConceptAccumulator) {
                        Validate.isTrue(
                                        ((ValueSetExpansionComponentWithConceptAccumulator) theValueSetCodeAccumulator)
                                                        .getParameter()
                                                        .isEmpty(),
                                        "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
                }

                Validate.isTrue(
                                isNotBlank(theSystem),
                                "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");

                for (ValueSet.ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
                        boolean handled = false;
                        switch (nextFilter.getProperty()) {
                                case "concept":
                                case "code":
                                        if (nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
                                                theValueSetCodeAccumulator.addMessage(
                                                                "Processing IS-A filter in database - Note that Hibernate Search is not enabled on this server, so this operation can be inefficient.");
                                                TermConcept code = findCodeForFilterCriteria(theSystem, nextFilter);
                                                addConceptAndChildren(
                                                                theValueSetCodeAccumulator, theAddedCodes, theInclude, theSystem, theAdd, code);
                                                handled = true;
                                        }
                                        break;
                        }

                        if (!handled) {
                                throwInvalidFilter(
                                                nextFilter,
                                                " - Note that Hibernate Search is disabled on this server so not all ValueSet expansion funtionality is available.");
                        }
                }

                if (theInclude.getConcept().isEmpty()) {

                        Collection<TermConcept> concepts =
                                        myConceptDao.fetchConceptsAndDesignationsByVersionPid(theVersion.getPid());
                        for (TermConcept next : concepts) {
                                addCodeIfNotAlreadyAdded(
                                                theValueSetCodeAccumulator,
                                                theAddedCodes,
                                                theAdd,
                                                theSystem,
                                                theInclude.getVersion(),
                                                next.getCode(),
                                                next.getDisplay(),
                                                next.getId(),
                                                next.getParentPidsAsString(),
                                                next.getDesignations());
                        }
                }

                for (ValueSet.ConceptReferenceComponent next : theInclude.getConcept()) {
                        if (!theSystem.equals(theInclude.getSystem()) && isNotBlank(theSystem)) {
                                continue;
                        }
                        Collection<TermConceptDesignation> designations = next.getDesignation().stream()
                                        .map(t -> new TermConceptDesignation()
                                                        .setValue(t.getValue())
                                                        .setLanguage(t.getLanguage())
                                                        .setUseCode(t.getUse().getCode())
                                                        .setUseSystem(t.getUse().getSystem())
                                                        .setUseDisplay(t.getUse().getDisplay()))
                                        .collect(Collectors.toList());
                        addCodeIfNotAlreadyAdded(
                                        theValueSetCodeAccumulator,
                                        theAddedCodes,
                                        theAdd,
                                        theSystem,
                                        theInclude.getVersion(),
                                        next.getCode(),
                                        next.getDisplay(),
                                        null,
                                        null,
                                        designations);
                }
        }

        private void addConceptAndChildren(
                        IValueSetConceptAccumulator theValueSetCodeAccumulator,
                        Set<String> theAddedCodes,
                        ValueSet.ConceptSetComponent theInclude,
                        String theSystem,
                        boolean theAdd,
                        TermConcept theConcept) {
                for (TermConcept nextChild : theConcept.getChildCodes()) {
                        boolean added = addCodeIfNotAlreadyAdded(
                                        theValueSetCodeAccumulator,
                                        theAddedCodes,
                                        theAdd,
                                        theSystem,
                                        theInclude.getVersion(),
                                        nextChild.getCode(),
                                        nextChild.getDisplay(),
                                        nextChild.getId(),
                                        nextChild.getParentPidsAsString(),
                                        nextChild.getDesignations());
                        if (added) {
                                addConceptAndChildren(
                                                theValueSetCodeAccumulator, theAddedCodes, theInclude, theSystem, theAdd, nextChild);
                        }
                }
        }

        @Override
        @Transactional
        public String invalidatePreCalculatedExpansion(IIdType theValueSetId, RequestDetails theRequestDetails) {
                IBaseResource valueSet = myDaoRegistry.getResourceDao("ValueSet").read(theValueSetId, theRequestDetails);
                ValueSet canonicalValueSet = myVersionCanonicalizer.valueSetToCanonical(valueSet);
                Optional<TermValueSet> optionalTermValueSet = fetchValueSetEntity(canonicalValueSet);
                if (optionalTermValueSet.isEmpty()) {
                        return myContext
                                        .getLocalizer()
                                        .getMessage(TermReadSvcImpl.class, "valueSetNotFoundInTerminologyDatabase", theValueSetId);
                }

                ourLog.info(
                                "Invalidating pre-calculated expansion on ValueSet {} / {}", theValueSetId, canonicalValueSet.getUrl());

                TermValueSet termValueSet = optionalTermValueSet.get();
                if (termValueSet.getExpansionStatus() == TermValueSetPreExpansionStatusEnum.NOT_EXPANDED) {
                        return myContext
                                        .getLocalizer()
                                        .getMessage(
                                                        TermReadSvcImpl.class,
                                                        "valueSetCantInvalidateNotYetPrecalculated",
                                                        termValueSet.getUrl(),
                                                        termValueSet.getExpansionStatus());
                }

                Long totalConcepts = termValueSet.getTotalConcepts();

                deletePreCalculatedValueSetContents(termValueSet);

                termValueSet.setExpansionStatus(TermValueSetPreExpansionStatusEnum.NOT_EXPANDED);
                termValueSet.setExpansionTimestamp(null);
                myTermValueSetDao.save(termValueSet);

                afterValueSetExpansionStatusChange();

                return myContext
                                .getLocalizer()
                                .getMessage(
                                                TermReadSvcImpl.class, "valueSetPreExpansionInvalidated", termValueSet.getUrl(), totalConcepts);
        }

        @Override
        @Transactional
        public boolean isValueSetPreExpandedForCodeValidation(ValueSet theValueSet) {
                Optional<TermValueSet> optionalTermValueSet = fetchValueSetEntity(theValueSet);

                if (optionalTermValueSet.isEmpty()) {
                        ourLog.warn(
                                        "ValueSet is not present in terminology tables. Will perform in-memory code validation. {}",
                                        getValueSetInfo(theValueSet));
                        return false;
                }

                TermValueSet termValueSet = optionalTermValueSet.get();

                if (termValueSet.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
                        ourLog.warn(
                                        "{} is present in terminology tables but not ready for persistence-backed invocation of operation $validation-code. Will perform in-memory code validation. Current status: {} | {}",
                                        getValueSetInfo(theValueSet),
                                        termValueSet.getExpansionStatus().name(),
                                        termValueSet.getExpansionStatus().getDescription());
                        return false;
                }

                return true;
        }

        private Optional<TermValueSet> fetchValueSetEntity(ValueSet theValueSet) {
                JpaPid valueSetResourcePid = getValueSetResourcePersistentId(theValueSet);
                return myTermValueSetDao.findByResourcePid(valueSetResourcePid.getId());
        }

        private JpaPid getValueSetResourcePersistentId(ValueSet theValueSet) {
                return myIdHelperService.resolveResourcePersistentIds(
                                RequestPartitionId.allPartitions(),
                                theValueSet.getIdElement().getResourceType(),
                                theValueSet.getIdElement().getIdPart());
        }

        protected IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(
                        ConceptValidationOptions theValidationOptions,
                        ValueSet theValueSet,
                        String theSystem,
                        String theCode,
                        String theDisplay,
                        Coding theCoding,
                        CodeableConcept theCodeableConcept) {
                assert TransactionSynchronizationManager.isSynchronizationActive();

                ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
                JpaPid valueSetResourcePid = getValueSetResourcePersistentId(theValueSet);

                List<TermValueSetConcept> concepts = new ArrayList<>();
                if (isNotBlank(theCode)) {
                        if (theValidationOptions.isInferSystem()) {
                                concepts.addAll(
                                                myValueSetConceptDao.findByValueSetResourcePidAndCode(valueSetResourcePid.getId(), theCode));
                        } else if (isNotBlank(theSystem)) {
                                concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, theSystem, theCode));
                        }
                } else if (theCoding != null) {
                        if (theCoding.hasSystem() && theCoding.hasCode()) {
                                concepts.addAll(findByValueSetResourcePidSystemAndCode(
                                                valueSetResourcePid, theCoding.getSystem(), theCoding.getCode()));
                        }
                } else if (theCodeableConcept != null) {
                        for (Coding coding : theCodeableConcept.getCoding()) {
                                if (coding.hasSystem() && coding.hasCode()) {
                                        concepts.addAll(findByValueSetResourcePidSystemAndCode(
                                                        valueSetResourcePid, coding.getSystem(), coding.getCode()));
                                        if (!concepts.isEmpty()) {
                                                break;
                                        }
                                }
                        }
                } else {
                        return null;
                }

                TermValueSet valueSetEntity = myTermValueSetDao
                                .findByResourcePid(valueSetResourcePid.getId())
                                .orElseThrow(IllegalStateException::new);
                String timingDescription = toHumanReadableExpansionTimestamp(valueSetEntity);
                String msg = myContext
                                .getLocalizer()
                                .getMessage(TermReadSvcImpl.class, "validationPerformedAgainstPreExpansion", timingDescription);

                if (theValidationOptions.isValidateDisplay() && concepts.size() > 0) {
                        String systemVersion = null;
                        for (TermValueSetConcept concept : concepts) {
                                systemVersion = concept.getSystemVersion();
                                if (isBlank(theDisplay) || isBlank(concept.getDisplay()) || theDisplay.equals(concept.getDisplay())) {
                                        return new IValidationSupport.CodeValidationResult()
                                                        .setCode(concept.getCode())
                                                        .setDisplay(concept.getDisplay())
                                                        .setCodeSystemVersion(concept.getSystemVersion())
                                                        .setMessage(msg);
                                }
                        }

                        String expectedDisplay = concepts.get(0).getDisplay();
                        String append = createMessageAppendForDisplayMismatch(theSystem, theDisplay, expectedDisplay) + " - " + msg;
                        return createFailureCodeValidationResult(theSystem, theCode, systemVersion, append)
                                        .setDisplay(expectedDisplay);
                }

                if (!concepts.isEmpty()) {
                        return new IValidationSupport.CodeValidationResult()
                                        .setCode(concepts.get(0).getCode())
                                        .setDisplay(concepts.get(0).getDisplay())
                                        .setCodeSystemVersion(concepts.get(0).getSystemVersion())
                                        .setMessage(msg);
                }

                // Ok, we failed
                List<TermValueSetConcept> outcome = myValueSetConceptDao.findByTermValueSetIdSystemOnly(
                                Pageable.ofSize(1), valueSetEntity.getId(), theSystem);
                String append;
                if (outcome.size() == 0) {
                        append = " - No codes in ValueSet belong to CodeSystem with URL " + theSystem;
                } else {
                        append = " - Unknown code " + theSystem + "#" + theCode + ". " + msg;
                }

                return createFailureCodeValidationResult(theSystem, theCode, null, append);
        }

        private CodeValidationResult createFailureCodeValidationResult(
                        String theSystem, String theCode, String theCodeSystemVersion, String theAppend) {
                return new CodeValidationResult()
                                .setSeverity(IssueSeverity.ERROR)
                                .setCodeSystemVersion(theCodeSystemVersion)
                                .setMessage("Unable to validate code " + theSystem + "#" + theCode + theAppend);
        }

        private List<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(
                        JpaPid theResourcePid, String theSystem, String theCode) {
                assert TransactionSynchronizationManager.isSynchronizationActive();

                List<TermValueSetConcept> retVal = new ArrayList<>();
                Optional<TermValueSetConcept> optionalTermValueSetConcept;
                int versionIndex = theSystem.indexOf(OUR_PIPE_CHARACTER);
                if (versionIndex >= 0) {
                        String systemUrl = theSystem.substring(0, versionIndex);
                        String systemVersion = theSystem.substring(versionIndex + 1);
                        optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCodeWithVersion(
                                        theResourcePid.getId(), systemUrl, systemVersion, theCode);
                } else {
                        optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCode(
                                        theResourcePid.getId(), theSystem, theCode);
                }
                optionalTermValueSetConcept.ifPresent(retVal::add);
                return retVal;
        }

        private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
                for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
                        TermConcept nextChild = nextChildLink.getChild();
                        if (addToSet(theSetToPopulate, nextChild)) {
                                fetchChildren(nextChild, theSetToPopulate);
                        }
                }
        }

        private Optional<TermConcept> fetchLoadedCode(Long theCodeSystemResourcePid, String theCode) {
                TermCodeSystemVersion codeSystem =
                                myCodeSystemVersionDao.findCurrentVersionForCodeSystemResourcePid(theCodeSystemResourcePid);
                return myConceptDao.findByCodeSystemAndCode(codeSystem.getPid(), theCode);
        }

        private void fetchParents(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
                for (TermConceptParentChildLink nextChildLink : theConcept.getParents()) {
                        TermConcept nextChild = nextChildLink.getParent();
                        if (addToSet(theSetToPopulate, nextChild)) {
                                fetchParents(nextChild, theSetToPopulate);
                        }
                }
        }

        @Override
        public Optional<TermConcept> findCode(String theCodeSystem, String theCode) {
                /*
                 * Loading concepts without a transaction causes issues later on some
                 * platforms (e.g. PSQL) so this transactiontemplate is here to make
                 * sure that we always call this with an open transaction
                 */
                TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
                txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_MANDATORY);
                txTemplate.setReadOnly(true);

                return txTemplate.execute(t -> {
                        TermCodeSystemVersionDetails csv = getCurrentCodeSystemVersion(theCodeSystem);
                        if (csv == null) {
                                return Optional.empty();
                        }
                        return myConceptDao.findByCodeSystemAndCode(csv.myPid, theCode);
                });
        }

        @Override
        @Transactional(propagation = Propagation.MANDATORY)
        public List<TermConcept> findCodes(String theCodeSystem, List<String> theCodeList) {
                TermCodeSystemVersionDetails csv = getCurrentCodeSystemVersion(theCodeSystem);
                if (csv == null) {
                        return Collections.emptyList();
                }

                return myConceptDao.findByCodeSystemAndCodeList(csv.myPid, theCodeList);
        }

        @Nullable
        private TermCodeSystemVersionDetails getCurrentCodeSystemVersion(String theCodeSystemIdentifier) {
                String version = getVersionFromIdentifier(theCodeSystemIdentifier);
                TermCodeSystemVersionDetails retVal = myCodeSystemCurrentVersionCache.get(
                                theCodeSystemIdentifier,
                                t -> myTxTemplate.execute(tx -> {
                                        TermCodeSystemVersion csv = null;
                                        TermCodeSystem cs =
                                                        myCodeSystemDao.findByCodeSystemUri(getUrlFromIdentifier(theCodeSystemIdentifier));
                                        if (cs != null) {
                                                if (version != null) {
                                                        csv = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(cs.getPid(), version);
                                                } else if (cs.getCurrentVersion() != null) {
                                                        csv = cs.getCurrentVersion();
                                                }
                                        }
                                        if (csv != null) {
                                                return new TermCodeSystemVersionDetails(csv.getPid(), csv.getCodeSystemVersionId());
                                        } else {
                                                return NO_CURRENT_VERSION;
                                        }
                                }));
                if (retVal == NO_CURRENT_VERSION) {
                        return null;
                }
                return retVal;
        }

        private String getVersionFromIdentifier(String theUri) {
                String retVal = null;
                if (StringUtils.isNotEmpty((theUri))) {
                        int versionSeparator = theUri.lastIndexOf('|');
                        if (versionSeparator != -1) {
                                retVal = theUri.substring(versionSeparator + 1);
                        }
                }
                return retVal;
        }

        private String getUrlFromIdentifier(String theUri) {
                String retVal = theUri;
                if (StringUtils.isNotEmpty((theUri))) {
                        int versionSeparator = theUri.lastIndexOf('|');
                        if (versionSeparator != -1) {
                                retVal = theUri.substring(0, versionSeparator);
                        }
                }
                return retVal;
        }

        @Transactional(propagation = Propagation.REQUIRED)
        @Override
        public Set<TermConcept> findCodesAbove(
                        Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
                StopWatch stopwatch = new StopWatch();

                Optional<TermConcept> concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
                if (concept.isEmpty()) {
                        return Collections.emptySet();
                }

                Set<TermConcept> retVal = new HashSet<>();
                retVal.add(concept.get());

                fetchParents(concept.get(), retVal);

                ourLog.debug("Fetched {} codes above code {} in {}ms", retVal.size(), theCode, stopwatch.getMillis());
                return retVal;
        }

        @Transactional
        @Override
        public List<FhirVersionIndependentConcept> findCodesAbove(String theSystem, String theCode) {
                TermCodeSystem cs = getCodeSystem(theSystem);
                if (cs == null) {
                        return findCodesAboveUsingBuiltInSystems(theSystem, theCode);
                }
                TermCodeSystemVersion csv = cs.getCurrentVersion();

                Set<TermConcept> codes = findCodesAbove(cs.getResource().getId(), csv.getPid(), theCode);
                return toVersionIndependentConcepts(theSystem, codes);
        }

        @Transactional(propagation = Propagation.REQUIRED)
        @Override
        public Set<TermConcept> findCodesBelow(
                        Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
                Stopwatch stopwatch = Stopwatch.createStarted();

                Optional<TermConcept> concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
                if (concept.isEmpty()) {
                        return Collections.emptySet();
                }

                Set<TermConcept> retVal = new HashSet<>();
                retVal.add(concept.get());

                fetchChildren(concept.get(), retVal);

                ourLog.debug(
                                "Fetched {} codes below code {} in {}ms",
                                retVal.size(),
                                theCode,
                                stopwatch.elapsed(TimeUnit.MILLISECONDS));
                return retVal;
        }

        @Transactional
        @Override
        public List<FhirVersionIndependentConcept> findCodesBelow(String theSystem, String theCode) {
                TermCodeSystem cs = getCodeSystem(theSystem);
                if (cs == null) {
                        return findCodesBelowUsingBuiltInSystems(theSystem, theCode);
                }
                TermCodeSystemVersion csv = cs.getCurrentVersion();

                Set<TermConcept> codes = findCodesBelow(cs.getResource().getId(), csv.getPid(), theCode);
                return toVersionIndependentConcepts(theSystem, codes);
        }

        private TermCodeSystem getCodeSystem(String theSystem) {
                return myCodeSystemDao.findByCodeSystemUri(theSystem);
        }

        @PostConstruct
        public void start() {
                RuleBasedTransactionAttribute rules = new RuleBasedTransactionAttribute();
                rules.getRollbackRules().add(new NoRollbackRuleAttribute(ExpansionTooCostlyException.class));
                myTxTemplate = new TransactionTemplate(myTransactionManager, rules);
        }

        @Override
        public void scheduleJobs(ISchedulerService theSchedulerService) {
                // Register scheduled job to pre-expand ValueSets
                // In the future it would be great to make this a cluster-aware task somehow
                ScheduledJobDefinition vsJobDefinition = new ScheduledJobDefinition();
                vsJobDefinition.setId(getClass().getName());
                vsJobDefinition.setJobClass(Job.class);
                theSchedulerService.scheduleClusteredJob(10 * DateUtils.MILLIS_PER_MINUTE, vsJobDefinition);
        }

        @Override
        public synchronized void preExpandDeferredValueSetsToTerminologyTables() {
                if (!myStorageSettings.isEnableTaskPreExpandValueSets()) {
                        return;
                }
                if (isNotSafeToPreExpandValueSets()) {
                        ourLog.info("Skipping scheduled pre-expansion of ValueSets while deferred entities are being loaded.");
                        return;
                }
                TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);

                while (true) {
                        StopWatch sw = new StopWatch();
                        TermValueSet valueSetToExpand = txTemplate.execute(t -> {
                                Optional<TermValueSet> optionalTermValueSet = getNextTermValueSetNotExpanded();
                                if (optionalTermValueSet.isEmpty()) {
                                        return null;
                                }

                                TermValueSet termValueSet = optionalTermValueSet.get();
                                termValueSet.setTotalConcepts(0L);
                                termValueSet.setTotalConceptDesignations(0L);
                                termValueSet.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
                                return myTermValueSetDao.saveAndFlush(termValueSet);
                        });
                        if (valueSetToExpand == null) {
                                return;
                        }

                        // We have a ValueSet to pre-expand.
                        setPreExpandingValueSets(true);
                        try {
                                ValueSet valueSet = txTemplate.execute(t -> {
                                        TermValueSet refreshedValueSetToExpand = myTermValueSetDao
                                                        .findById(valueSetToExpand.getId())
                                                        .orElseThrow(() -> new IllegalStateException("Unknown VS ID: " + valueSetToExpand.getId()));
                                        return getValueSetFromResourceTable(refreshedValueSetToExpand.getResource());
                                });
                                assert valueSet != null;

                                ValueSetConceptAccumulator accumulator = new ValueSetConceptAccumulator(
                                                valueSetToExpand, myTermValueSetDao, myValueSetConceptDao, myValueSetConceptDesignationDao);
                                ValueSetExpansionOptions options = new ValueSetExpansionOptions();
                                options.setIncludeHierarchy(true);
                                expandValueSet(options, valueSet, accumulator);

                                // We are done with this ValueSet.
                                txTemplate.executeWithoutResult(t -> {
                                        valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANDED);
                                        valueSetToExpand.setExpansionTimestamp(new Date());
                                        myTermValueSetDao.saveAndFlush(valueSetToExpand);
                                });

                                afterValueSetExpansionStatusChange();

                                ourLog.info(
                                                "Pre-expanded ValueSet[{}] with URL[{}] - Saved {} concepts in {}",
                                                valueSet.getId(),
                                                valueSet.getUrl(),
                                                accumulator.getConceptsSaved(),
                                                sw);

                        } catch (Exception e) {
                                ourLog.error("Failed to pre-expand ValueSet: " + e.getMessage(), e);
                                txTemplate.executeWithoutResult(t -> {
                                        valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.FAILED_TO_EXPAND);
                                        myTermValueSetDao.saveAndFlush(valueSetToExpand);
                                });

                        } finally {
                                setPreExpandingValueSets(false);
                        }
                }
        }

        /*
         * If a ValueSet has just finished pre-expanding, let's flush the caches. This is
         * kind of a blunt tool, but it should ensure that users don't get unpredictable
         * results while they test changes, which is probably a worthwhile sacrifice
         */
        private void afterValueSetExpansionStatusChange() {
                // TODO: JA2 - Move this caching into the memorycacheservice, and only purge the
                // relevant individual cache
                myCachingValidationSupport.invalidateCaches();
        }

        private synchronized boolean isPreExpandingValueSets() {
                return myPreExpandingValueSets;
        }

        private synchronized void setPreExpandingValueSets(boolean thePreExpandingValueSets) {
                myPreExpandingValueSets = thePreExpandingValueSets;
        }

        private boolean isNotSafeToPreExpandValueSets() {
                return myDeferredStorageSvc != null && !myDeferredStorageSvc.isStorageQueueEmpty(true);
        }

        private Optional<TermValueSet> getNextTermValueSetNotExpanded() {
                Optional<TermValueSet> retVal = Optional.empty();
                Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(
                                PageRequest.of(0, 1), TermValueSetPreExpansionStatusEnum.NOT_EXPANDED);

                if (!page.getContent().isEmpty()) {
                        retVal = Optional.of(page.getContent().get(0));
                }

                return retVal;
        }

        @Override
        @Transactional
        public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {

                ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
                if (isPlaceholder(theValueSet)) {
                        ourLog.info(
                                        "Not storing TermValueSet for placeholder {}",
                                        theValueSet.getIdElement().toVersionless().getValueAsString());
                        return;
                }

                ValidateUtil.isNotBlankOrThrowUnprocessableEntity(
                                theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
                ourLog.info(
                                "Storing TermValueSet for {}",
                                theValueSet.getIdElement().toVersionless().getValueAsString());

                /*
                 * Get CodeSystem and validate CodeSystemVersion
                 */
                TermValueSet termValueSet = new TermValueSet();
                termValueSet.setResource(theResourceTable);
                termValueSet.setUrl(theValueSet.getUrl());
                termValueSet.setVersion(theValueSet.getVersion());
                termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);

                // Delete version being replaced
                deleteValueSetForResource(theResourceTable);

                /*
                 * Do the upload.
                 */
                String url = termValueSet.getUrl();
                String version = termValueSet.getVersion();
                Optional<TermValueSet> optionalExistingTermValueSetByUrl;
                if (version != null) {
                        optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndVersion(url, version);
                } else {
                        optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(url);
                }
                if (optionalExistingTermValueSetByUrl.isEmpty()) {

                        myTermValueSetDao.save(termValueSet);

                } else {
                        TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();
                        String msg;
                        if (version != null) {
                                msg = myContext
                                                .getLocalizer()
                                                .getMessage(
                                                                TermReadSvcImpl.class,
                                                                "cannotCreateDuplicateValueSetUrlAndVersion",
                                                                url,
                                                                version,
                                                                existingTermValueSet
                                                                                .getResource()
                                                                                .getIdDt()
                                                                                .toUnqualifiedVersionless()
                                                                                .getValue());
                        } else {
                                msg = myContext
                                                .getLocalizer()
                                                .getMessage(
                                                                TermReadSvcImpl.class,
                                                                "cannotCreateDuplicateValueSetUrl",
                                                                url,
                                                                existingTermValueSet
                                                                                .getResource()
                                                                                .getIdDt()
                                                                                .toUnqualifiedVersionless()
                                                                                .getValue());
                        }
                        throw new UnprocessableEntityException(Msg.code(902) + msg);
                }
        }

        @Override
        @Transactional
        public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(
                        IPrimitiveType<String> theCodeA,
                        IPrimitiveType<String> theCodeB,
                        IPrimitiveType<String> theSystem,
                        IBaseCoding theCodingA,
                        IBaseCoding theCodingB) {
                FhirVersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA);
                FhirVersionIndependentConcept conceptB = toConcept(theCodeB, theSystem, theCodingB);

                if (!StringUtils.equals(conceptA.getSystem(), conceptB.getSystem())) {
                        throw new InvalidRequestException(
                                        Msg.code(903) + "Unable to test subsumption across different code systems");
                }

                if (!StringUtils.equals(conceptA.getSystemVersion(), conceptB.getSystemVersion())) {
                        throw new InvalidRequestException(
                                        Msg.code(904) + "Unable to test subsumption across different code system versions");
                }

                String codeASystemIdentifier;
                if (StringUtils.isNotEmpty(conceptA.getSystemVersion())) {
                        codeASystemIdentifier = conceptA.getSystem() + OUR_PIPE_CHARACTER + conceptA.getSystemVersion();
                } else {
                        codeASystemIdentifier = conceptA.getSystem();
                }
                TermConcept codeA = findCode(codeASystemIdentifier, conceptA.getCode())
                                .orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptA));

                String codeBSystemIdentifier;
                if (StringUtils.isNotEmpty(conceptB.getSystemVersion())) {
                        codeBSystemIdentifier = conceptB.getSystem() + OUR_PIPE_CHARACTER + conceptB.getSystemVersion();
                } else {
                        codeBSystemIdentifier = conceptB.getSystem();
                }
                TermConcept codeB = findCode(codeBSystemIdentifier, conceptB.getCode())
                                .orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptB));

                SearchSession searchSession = Search.session(myEntityManager);

                ConceptSubsumptionOutcome subsumes;
                subsumes = testForSubsumption(searchSession, codeA, codeB, ConceptSubsumptionOutcome.SUBSUMES);
                if (subsumes == null) {
                        subsumes = testForSubsumption(searchSession, codeB, codeA, ConceptSubsumptionOutcome.SUBSUMEDBY);
                }
                if (subsumes == null) {
                        subsumes = ConceptSubsumptionOutcome.NOTSUBSUMED;
                }

                return new IFhirResourceDaoCodeSystem.SubsumesResult(subsumes);
        }

        protected IValidationSupport.LookupCodeResult lookupCode(
                        String theSystem, String theCode, String theDisplayLanguage) {
                TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
                return txTemplate.execute(t -> {
                        Optional<TermConcept> codeOpt = findCode(theSystem, theCode);
                        if (codeOpt.isPresent()) {
                                TermConcept code = codeOpt.get();

                                IValidationSupport.LookupCodeResult result = new IValidationSupport.LookupCodeResult();
                                result.setCodeSystemDisplayName(code.getCodeSystemVersion().getCodeSystemDisplayName());
                                result.setCodeSystemVersion(code.getCodeSystemVersion().getCodeSystemVersionId());
                                result.setSearchedForSystem(theSystem);
                                result.setSearchedForCode(theCode);
                                result.setFound(true);
                                result.setCodeDisplay(code.getDisplay());

                                for (TermConceptDesignation next : code.getDesignations()) {
                                        // filter out the designation based on displayLanguage if any
                                        if (isDisplayLanguageMatch(theDisplayLanguage, next.getLanguage())) {
                                                IValidationSupport.ConceptDesignation designation = new IValidationSupport.ConceptDesignation();
                                                designation.setLanguage(next.getLanguage());
                                                designation.setUseSystem(next.getUseSystem());
                                                designation.setUseCode(next.getUseCode());
                                                designation.setUseDisplay(next.getUseDisplay());
                                                designation.setValue(next.getValue());
                                                result.getDesignations().add(designation);
                                        }
                                }

                                for (TermConceptProperty next : code.getProperties()) {
                                        if (next.getType() == TermConceptPropertyTypeEnum.CODING) {
                                                IValidationSupport.CodingConceptProperty property =
                                                                new IValidationSupport.CodingConceptProperty(
                                                                                next.getKey(), next.getCodeSystem(), next.getValue(), next.getDisplay());
                                                result.getProperties().add(property);
                                        } else if (next.getType() == TermConceptPropertyTypeEnum.STRING) {
                                                IValidationSupport.StringConceptProperty property =
                                                                new IValidationSupport.StringConceptProperty(next.getKey(), next.getValue());
                                                result.getProperties().add(property);
                                        } else {
                                                throw new InternalErrorException(Msg.code(905) + "Unknown type: " + next.getType());
                                        }
                                }

                                return result;

                        } else {
                                return new LookupCodeResult().setFound(false);
                        }
                });
        }

        @Nullable
        private ConceptSubsumptionOutcome testForSubsumption(
                        SearchSession theSearchSession,
                        TermConcept theLeft,
                        TermConcept theRight,
                        ConceptSubsumptionOutcome theOutput) {
                List<TermConcept> fetch = theSearchSession
                                .search(TermConcept.class)
                                .where(f -> f.bool()
                                                .must(f.match().field("myId").matching(theRight.getId()))
                                                .must(f.match().field("myParentPids").matching(Long.toString(theLeft.getId()))))
                                .fetchHits(1);

                if (fetch.size() > 0) {
                        return theOutput;
                } else {
                        return null;
                }
        }

        private ArrayList<FhirVersionIndependentConcept> toVersionIndependentConcepts(
                        String theSystem, Set<TermConcept> codes) {
                ArrayList<FhirVersionIndependentConcept> retVal = new ArrayList<>(codes.size());
                for (TermConcept next : codes) {
                        retVal.add(new FhirVersionIndependentConcept(theSystem, next.getCode()));
                }
                return retVal;
        }

        @Override
        @Transactional
        public CodeValidationResult validateCodeInValueSet(
                        ValidationSupportContext theValidationSupportContext,
                        ConceptValidationOptions theOptions,
                        String theCodeSystem,
                        String theCode,
                        String theDisplay,
                        @Nonnull IBaseResource theValueSet) {
                invokeRunnableForUnitTest();

                IPrimitiveType<?> urlPrimitive;
                if (theValueSet instanceof org.hl7.fhir.dstu2.model.ValueSet) {
                        urlPrimitive = FhirContext.forDstu2Hl7OrgCached()
                                        .newTerser()
                                        .getSingleValueOrNull(theValueSet, "url", IPrimitiveType.class);
                } else {
                        urlPrimitive = myContext.newTerser().getSingleValueOrNull(theValueSet, "url", IPrimitiveType.class);
                }
                String url = urlPrimitive.getValueAsString();
                if (isNotBlank(url)) {
                        return validateCode(theValidationSupportContext, theOptions, theCodeSystem, theCode, theDisplay, url);
                }
                return null;
        }

        @CoverageIgnore
        @Override
        public IValidationSupport.CodeValidationResult validateCode(
                        @Nonnull ValidationSupportContext theValidationSupportContext,
                        @Nonnull ConceptValidationOptions theOptions,
                        String theCodeSystemUrl,
                        String theCode,
                        String theDisplay,
                        String theValueSetUrl) {
                // TODO GGG TRY TO JUST AUTO_PASS HERE AND SEE WHAT HAPPENS.
                invokeRunnableForUnitTest();
                theOptions.setValidateDisplay(isNotBlank(theDisplay));

                if (isNotBlank(theValueSetUrl)) {
                        return validateCodeInValueSet(
                                        theValidationSupportContext, theOptions, theValueSetUrl, theCodeSystemUrl, theCode, theDisplay);
                }

                TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
                txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
                txTemplate.setReadOnly(true);
                Optional<FhirVersionIndependentConcept> codeOpt =
                                txTemplate.execute(tx -> findCode(theCodeSystemUrl, theCode).map(c -> {
                                        String codeSystemVersionId = getCurrentCodeSystemVersion(theCodeSystemUrl).myCodeSystemVersionId;
                                        return new FhirVersionIndependentConcept(
                                                        theCodeSystemUrl, c.getCode(), c.getDisplay(), codeSystemVersionId);
                                }));

                if (codeOpt != null && codeOpt.isPresent()) {
                        FhirVersionIndependentConcept code = codeOpt.get();
                        if (!theOptions.isValidateDisplay()
                                        || isBlank(code.getDisplay())
                                        || isBlank(theDisplay)
                                        || code.getDisplay().equals(theDisplay)) {
                                return new CodeValidationResult().setCode(code.getCode()).setDisplay(code.getDisplay());
                        } else {
                                String messageAppend =
                                                createMessageAppendForDisplayMismatch(theCodeSystemUrl, theDisplay, code.getDisplay());
                                return createFailureCodeValidationResult(
                                                                theCodeSystemUrl, theCode, code.getSystemVersion(), messageAppend)
                                                .setDisplay(code.getDisplay());
                        }
                }

                return createFailureCodeValidationResult(
                                theCodeSystemUrl, theCode, null, createMessageAppendForCodeNotFoundInCodeSystem(theCodeSystemUrl));
        }

        IValidationSupport.CodeValidationResult validateCodeInValueSet(
                        ValidationSupportContext theValidationSupportContext,
                        ConceptValidationOptions theValidationOptions,
                        String theValueSetUrl,
                        String theCodeSystem,
                        String theCode,
                        String theDisplay) {
                IBaseResource valueSet =
                                theValidationSupportContext.getRootValidationSupport().fetchValueSet(theValueSetUrl);
                CodeValidationResult retVal = null;

                // If we don't have a PID, this came from some source other than the JPA
                // database, so we don't need to check if it's pre-expanded or not
                if (valueSet instanceof IAnyResource) {
                        Long pid = IDao.RESOURCE_PID.get((IAnyResource) valueSet);
                        if (pid != null) {
                                TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
                                retVal = txTemplate.execute(tx -> {
                                        if (isValueSetPreExpandedForCodeValidation(valueSet)) {
                                                return validateCodeIsInPreExpandedValueSet(
                                                                theValidationOptions, valueSet, theCodeSystem, theCode, theDisplay, null, null);
                                        } else {
                                                return null;
                                        }
                                });
                        }
                }

                if (retVal == null) {
                        if (valueSet != null) {
                                retVal = new InMemoryTerminologyServerValidationSupport(myContext)
                                                .validateCodeInValueSet(
                                                                theValidationSupportContext,
                                                                theValidationOptions,
                                                                theCodeSystem,
                                                                theCode,
                                                                theDisplay,
                                                                valueSet);
                        } else {
                                String append = " - Unable to locate ValueSet[" + theValueSetUrl + "]";
                                retVal = createFailureCodeValidationResult(theCodeSystem, theCode, null, append);
                        }
                }

                // Check if someone is accidentally using a VS url where it should be a CS URL
                if (retVal != null
                                && retVal.getCode() == null
                                && theCodeSystem != null
                                && myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU2)) {
                        if (isValueSetSupported(theValidationSupportContext, theCodeSystem)) {
                                if (!isCodeSystemSupported(theValidationSupportContext, theCodeSystem)) {
                                        String newMessage = "Unable to validate code " + theCodeSystem + "#" + theCode
                                                        + " - Supplied system URL is a ValueSet URL and not a CodeSystem URL, check if it is correct: "
                                                        + theCodeSystem;
                                        retVal.setMessage(newMessage);
                                }
                        }
                }

                return retVal;
        }

        @Override
        public CodeSystem fetchCanonicalCodeSystemFromCompleteContext(String theSystem) {
                IValidationSupport validationSupport = provideValidationSupport();
                IBaseResource codeSystem = validationSupport.fetchCodeSystem(theSystem);
                if (codeSystem != null) {
                        codeSystem = myVersionCanonicalizer.codeSystemToCanonical(codeSystem);
                }
                return (CodeSystem) codeSystem;
        }

        @Nonnull
        private IValidationSupport provideJpaValidationSupport() {
                IValidationSupport jpaValidationSupport = myJpaValidationSupport;
                if (jpaValidationSupport == null) {
                        jpaValidationSupport = myApplicationContext.getBean("myJpaValidationSupport", IValidationSupport.class);
                        myJpaValidationSupport = jpaValidationSupport;
                }
                return jpaValidationSupport;
        }

        @Nonnull
        protected IValidationSupport provideValidationSupport() {
                IValidationSupport validationSupport = myValidationSupport;
                if (validationSupport == null) {
                        validationSupport = myApplicationContext.getBean(IValidationSupport.class);
                        myValidationSupport = validationSupport;
                }
                return validationSupport;
        }

        public ValueSet fetchCanonicalValueSetFromCompleteContext(String theSystem) {
                IValidationSupport validationSupport = provideValidationSupport();
                IBaseResource valueSet = validationSupport.fetchValueSet(theSystem);
                if (valueSet != null) {
                        valueSet = myVersionCanonicalizer.valueSetToCanonical(valueSet);
                }
                return (ValueSet) valueSet;
        }

        @Override
        public IBaseResource fetchValueSet(String theValueSetUrl) {
                return provideJpaValidationSupport().fetchValueSet(theValueSetUrl);
        }

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

        private void findCodesAbove(
                        CodeSystem theSystem,
                        String theSystemString,
                        String theCode,
                        List<FhirVersionIndependentConcept> theListToPopulate) {
                List<CodeSystem.ConceptDefinitionComponent> conceptList = theSystem.getConcept();
                for (CodeSystem.ConceptDefinitionComponent next : conceptList) {
                        addTreeIfItContainsCode(theSystemString, next, theCode, theListToPopulate);
                }
        }

        @Override
        public List<FhirVersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
                ArrayList<FhirVersionIndependentConcept> retVal = new ArrayList<>();
                CodeSystem system = fetchCanonicalCodeSystemFromCompleteContext(theSystem);
                if (system != null) {
                        findCodesAbove(system, theSystem, theCode, retVal);
                }
                return retVal;
        }

        private void findCodesBelow(
                        CodeSystem theSystem,
                        String theSystemString,
                        String theCode,
                        List<FhirVersionIndependentConcept> theListToPopulate) {
                List<CodeSystem.ConceptDefinitionComponent> conceptList = theSystem.getConcept();
                findCodesBelow(theSystemString, theCode, theListToPopulate, conceptList);
        }

        private void findCodesBelow(
                        String theSystemString,
                        String theCode,
                        List<FhirVersionIndependentConcept> theListToPopulate,
                        List<CodeSystem.ConceptDefinitionComponent> conceptList) {
                for (CodeSystem.ConceptDefinitionComponent next : conceptList) {
                        if (theCode.equals(next.getCode())) {
                                addAllChildren(theSystemString, next, theListToPopulate);
                        } else {
                                findCodesBelow(theSystemString, theCode, theListToPopulate, next.getConcept());
                        }
                }
        }

        @Override
        public List<FhirVersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
                ArrayList<FhirVersionIndependentConcept> retVal = new ArrayList<>();
                CodeSystem system = fetchCanonicalCodeSystemFromCompleteContext(theSystem);
                if (system != null) {
                        findCodesBelow(system, theSystem, theCode, retVal);
                }
                return retVal;
        }

        private void addAllChildren(
                        String theSystemString,
                        CodeSystem.ConceptDefinitionComponent theCode,
                        List<FhirVersionIndependentConcept> theListToPopulate) {
                if (isNotBlank(theCode.getCode())) {
                        theListToPopulate.add(new FhirVersionIndependentConcept(theSystemString, theCode.getCode()));
                }
                for (CodeSystem.ConceptDefinitionComponent nextChild : theCode.getConcept()) {
                        addAllChildren(theSystemString, nextChild, theListToPopulate);
                }
        }

        private boolean addTreeIfItContainsCode(
                        String theSystemString,
                        CodeSystem.ConceptDefinitionComponent theNext,
                        String theCode,
                        List<FhirVersionIndependentConcept> theListToPopulate) {
                boolean foundCodeInChild = false;
                for (CodeSystem.ConceptDefinitionComponent nextChild : theNext.getConcept()) {
                        foundCodeInChild |= addTreeIfItContainsCode(theSystemString, nextChild, theCode, theListToPopulate);
                }

                if (theCode.equals(theNext.getCode()) || foundCodeInChild) {
                        theListToPopulate.add(new FhirVersionIndependentConcept(theSystemString, theNext.getCode()));
                        return true;
                }

                return false;
        }

        @Nonnull
        private FhirVersionIndependentConcept toConcept(
                        IPrimitiveType<String> theCodeType,
                        IPrimitiveType<String> theCodeSystemIdentifierType,
                        IBaseCoding theCodingType) {
                String code = theCodeType != null ? theCodeType.getValueAsString() : null;
                String system = theCodeSystemIdentifierType != null
                                ? getUrlFromIdentifier(theCodeSystemIdentifierType.getValueAsString())
                                : null;
                String systemVersion = theCodeSystemIdentifierType != null
                                ? getVersionFromIdentifier(theCodeSystemIdentifierType.getValueAsString())
                                : null;
                if (theCodingType != null) {
                        Coding canonicalizedCoding = myVersionCanonicalizer.codingToCanonical(theCodingType);
                        assert canonicalizedCoding != null; // Shouldn't be null, since theCodingType isn't
                        code = canonicalizedCoding.getCode();
                        system = canonicalizedCoding.getSystem();
                        systemVersion = canonicalizedCoding.getVersion();
                }
                return new FhirVersionIndependentConcept(system, code, null, systemVersion);
        }

        /**
         * When the search is for unversioned loinc system it uses the forcedId to obtain the current
         * version, as it is not necessarily the last  one anymore.
         * For other cases it keeps on considering the last uploaded as the current
         */
        @Override
        public Optional<TermValueSet> findCurrentTermValueSet(String theUrl) {
                if (TermReadSvcUtil.isLoincUnversionedValueSet(theUrl)) {
                        Optional<String> vsIdOpt = TermReadSvcUtil.getValueSetId(theUrl);
                        if (vsIdOpt.isEmpty()) {
                                return Optional.empty();
                        }

                        return myTermValueSetDao.findTermValueSetByForcedId(vsIdOpt.get());
                }

                List<TermValueSet> termValueSetList = myTermValueSetDao.findTermValueSetByUrl(Pageable.ofSize(1), theUrl);
                if (termValueSetList.isEmpty()) {
                        return Optional.empty();
                }

                return Optional.of(termValueSetList.get(0));
        }

        @Override
        public Optional<IBaseResource> readCodeSystemByForcedId(String theForcedId) {
                @SuppressWarnings("unchecked")
                List<ResourceTable> resultList = (List<ResourceTable>) myEntityManager
                                .createQuery("select f.myResource from ForcedId f "
                                                + "where f.myResourceType = 'CodeSystem' and f.myForcedId = '" + theForcedId + "'")
                                .getResultList();
                if (resultList.isEmpty()) return Optional.empty();

                if (resultList.size() > 1)
                        throw new NonUniqueResultException(Msg.code(911) + "More than one CodeSystem is pointed by forcedId: "
                                        + theForcedId + ". Was constraint " + ForcedId.IDX_FORCEDID_TYPE_FID + " removed?");

                IFhirResourceDao<CodeSystem> csDao = myDaoRegistry.getResourceDao("CodeSystem");
                IBaseResource cs = myJpaStorageResourceParser.toResource(resultList.get(0), false);
                return Optional.of(cs);
        }

        @Transactional
        @Override
        public ReindexTerminologyResult reindexTerminology() throws InterruptedException {
                if (myFulltextSearchSvc == null) {
                        return ReindexTerminologyResult.SEARCH_SVC_DISABLED;
                }

                if (isBatchTerminologyTasksRunning()) {
                        return ReindexTerminologyResult.OTHER_BATCH_TERMINOLOGY_TASKS_RUNNING;
                }

                // disallow pre-expanding ValueSets while reindexing
                myDeferredStorageSvc.setProcessDeferred(false);

                int objectLoadingThreadNumber = calculateObjectLoadingThreadNumber();
                ourLog.info("Using {} threads to load objects", objectLoadingThreadNumber);

                try {
                        SearchSession searchSession = getSearchSession();
                        searchSession
                                        .massIndexer(TermConcept.class)
                                        .dropAndCreateSchemaOnStart(true)
                                        .purgeAllOnStart(false)
                                        .batchSizeToLoadObjects(100)
                                        .cacheMode(CacheMode.IGNORE)
                                        .threadsToLoadObjects(6)
                                        .transactionTimeout(60 * SECONDS_IN_MINUTE)
                                        .monitor(new PojoMassIndexingLoggingMonitor(INDEXED_ROOTS_LOGGING_COUNT))
                                        .startAndWait();
                } finally {
                        myDeferredStorageSvc.setProcessDeferred(true);
                }

                return ReindexTerminologyResult.SUCCESS;
        }

        @VisibleForTesting
        boolean isBatchTerminologyTasksRunning() {
                return isNotSafeToPreExpandValueSets() || isPreExpandingValueSets();
        }

        @VisibleForTesting
        int calculateObjectLoadingThreadNumber() {
                IConnectionPoolInfoProvider connectionPoolInfoProvider =
                                new ConnectionPoolInfoProvider(myHibernatePropertiesProvider.getDataSource());
                Optional<Integer> maxConnectionsOpt = connectionPoolInfoProvider.getTotalConnectionSize();
                if (maxConnectionsOpt.isEmpty()) {
                        return DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS;
                }

                int maxConnections = maxConnectionsOpt.get();
                int usableThreads = maxConnections < 6 ? 1 : maxConnections - 5;
                int objectThreads = Math.min(usableThreads, MAX_MASS_INDEXER_OBJECT_LOADING_THREADS);
                ourLog.debug(
                                "Data source connection pool has {} connections allocated, so reindexing will use {} object "
                                                + "loading threads (each using a connection)",
                                maxConnections,
                                objectThreads);
                return objectThreads;
        }

        @VisibleForTesting
        SearchSession getSearchSession() {
                return Search.session(myEntityManager);
        }

        @Override
        public ValueSetExpansionOutcome expandValueSet(
                        ValidationSupportContext theValidationSupportContext,
                        ValueSetExpansionOptions theExpansionOptions,
                        @Nonnull IBaseResource theValueSetToExpand) {
                ValueSet canonicalInput = myVersionCanonicalizer.valueSetToCanonical(theValueSetToExpand);
                org.hl7.fhir.r4.model.ValueSet expandedR4 = expandValueSet(theExpansionOptions, canonicalInput);
                return new ValueSetExpansionOutcome(myVersionCanonicalizer.valueSetFromCanonical(expandedR4));
        }

        @Override
        public IBaseResource expandValueSet(ValueSetExpansionOptions theExpansionOptions, IBaseResource theInput) {
                org.hl7.fhir.r4.model.ValueSet valueSetToExpand = myVersionCanonicalizer.valueSetToCanonical(theInput);
                org.hl7.fhir.r4.model.ValueSet valueSetR4 = expandValueSet(theExpansionOptions, valueSetToExpand);
                return myVersionCanonicalizer.valueSetFromCanonical(valueSetR4);
        }

        @Override
        public void expandValueSet(
                        ValueSetExpansionOptions theExpansionOptions,
                        IBaseResource theValueSetToExpand,
                        IValueSetConceptAccumulator theValueSetCodeAccumulator) {
                org.hl7.fhir.r4.model.ValueSet valueSetToExpand =
                                myVersionCanonicalizer.valueSetToCanonical(theValueSetToExpand);
                expandValueSet(theExpansionOptions, valueSetToExpand, theValueSetCodeAccumulator);
        }

        private org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
                Class<? extends IBaseResource> type =
                                getFhirContext().getResourceDefinition("ValueSet").getImplementingClass();
                IBaseResource valueSet = myJpaStorageResourceParser.toResource(type, theResourceTable, null, false);
                return myVersionCanonicalizer.valueSetToCanonical(valueSet);
        }

        @Override
        public CodeValidationResult validateCodeIsInPreExpandedValueSet(
                        ConceptValidationOptions theOptions,
                        IBaseResource theValueSet,
                        String theSystem,
                        String theCode,
                        String theDisplay,
                        IBaseDatatype theCoding,
                        IBaseDatatype theCodeableConcept) {
                ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
                org.hl7.fhir.r4.model.ValueSet valueSetR4 = myVersionCanonicalizer.valueSetToCanonical(theValueSet);
                org.hl7.fhir.r4.model.Coding codingR4 = myVersionCanonicalizer.codingToCanonical((IBaseCoding) theCoding);
                org.hl7.fhir.r4.model.CodeableConcept codeableConcept =
                                myVersionCanonicalizer.codeableConceptToCanonical(theCodeableConcept);

                return validateCodeIsInPreExpandedValueSet(
                                theOptions, valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConcept);
        }

        @Override
        public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
                ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
                org.hl7.fhir.r4.model.ValueSet valueSetR4 = myVersionCanonicalizer.valueSetToCanonical(theValueSet);
                return isValueSetPreExpandedForCodeValidation(valueSetR4);
        }

        @Override
        public LookupCodeResult lookupCode(
                        ValidationSupportContext theValidationSupportContext,
                        String theSystem,
                        String theCode,
                        String theDisplayLanguage) {
                return lookupCode(theSystem, theCode, theDisplayLanguage);
        }

        private static class TermCodeSystemVersionDetails {

                private final long myPid;
                private final String myCodeSystemVersionId;

                public TermCodeSystemVersionDetails(long thePid, String theCodeSystemVersionId) {
                        myPid = thePid;
                        myCodeSystemVersionId = theCodeSystemVersionId;
                }
        }

        public static class Job implements HapiJob {
                @Autowired
                private ITermReadSvc myTerminologySvc;

                @Override
                public void execute(JobExecutionContext theContext) {
                        myTerminologySvc.preExpandDeferredValueSetsToTerminologyTables();
                }
        }

        /**
         * Properties returned from method buildSearchScroll
         */
        private static final class SearchProperties {
                private SearchScroll<EntityReference> mySearchScroll;
                private Optional<PredicateFinalStep> myExpansionStepOpt;
                private List<String> myIncludeOrExcludeCodes;

                public SearchScroll<EntityReference> getSearchScroll() {
                        return mySearchScroll;
                }

                public void setSearchScroll(SearchScroll<EntityReference> theSearchScroll) {
                        mySearchScroll = theSearchScroll;
                }

                public Optional<PredicateFinalStep> getExpansionStepOpt() {
                        return myExpansionStepOpt;
                }

                public void setExpansionStepOpt(Optional<PredicateFinalStep> theExpansionStepOpt) {
                        myExpansionStepOpt = theExpansionStepOpt;
                }

                public List<String> getIncludeOrExcludeCodes() {
                        return myIncludeOrExcludeCodes;
                }

                public void setIncludeOrExcludeCodes(List<String> theIncludeOrExcludeCodes) {
                        myIncludeOrExcludeCodes = theIncludeOrExcludeCodes;
                }
        }

        static boolean isValueSetDisplayLanguageMatch(ValueSetExpansionOptions theExpansionOptions, String theStoredLang) {
                if (theExpansionOptions == null) {
                        return true;
                }

                if (theExpansionOptions.getTheDisplayLanguage() == null || theStoredLang == null) {
                        return true;
                }

                return theExpansionOptions.getTheDisplayLanguage().equalsIgnoreCase(theStoredLang);
        }

        @Nonnull
        private static String createMessageAppendForDisplayMismatch(
                        String theCodeSystemUrl, String theDisplay, String theExpectedDisplay) {
                return " - Concept Display \"" + theDisplay + "\" does not match expected \"" + theExpectedDisplay
                                + "\" for CodeSystem: " + theCodeSystemUrl;
        }

        @Nonnull
        private static String createMessageAppendForCodeNotFoundInCodeSystem(String theCodeSystemUrl) {
                return " - Code is not found in CodeSystem: " + theCodeSystemUrl;
        }

        @VisibleForTesting
        public static void setForceDisableHibernateSearchForUnitTest(boolean theForceDisableHibernateSearchForUnitTest) {
                ourForceDisableHibernateSearchForUnitTest = theForceDisableHibernateSearchForUnitTest;
        }

        static boolean isPlaceholder(DomainResource theResource) {
                boolean retVal = false;
                Extension extension = theResource.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
                if (extension != null && extension.hasValue() && extension.getValue() instanceof BooleanType) {
                        retVal = ((BooleanType) extension.getValue()).booleanValue();
                }
                return retVal;
        }

        /**
         * This is only used for unit tests to test failure conditions
         */
        static void invokeRunnableForUnitTest() {
                if (myInvokeOnNextCallForUnitTest != null) {
                        Runnable invokeOnNextCallForUnitTest = myInvokeOnNextCallForUnitTest;
                        myInvokeOnNextCallForUnitTest = null;
                        invokeOnNextCallForUnitTest.run();
                }
        }

        @VisibleForTesting
        public static void setInvokeOnNextCallForUnitTest(Runnable theInvokeOnNextCallForUnitTest) {
                myInvokeOnNextCallForUnitTest = theInvokeOnNextCallForUnitTest;
        }

        static List<TermConcept> toPersistedConcepts(
                        List<CodeSystem.ConceptDefinitionComponent> theConcept, TermCodeSystemVersion theCodeSystemVersion) {
                ArrayList<TermConcept> retVal = new ArrayList<>();

                for (CodeSystem.ConceptDefinitionComponent next : theConcept) {
                        if (isNotBlank(next.getCode())) {
                                TermConcept termConcept = toTermConcept(next, theCodeSystemVersion);
                                retVal.add(termConcept);
                        }
                }

                return retVal;
        }

        @Nonnull
        static TermConcept toTermConcept(
                        CodeSystem.ConceptDefinitionComponent theConceptDefinition, TermCodeSystemVersion theCodeSystemVersion) {
                TermConcept termConcept = new TermConcept();
                termConcept.setCode(theConceptDefinition.getCode());
                termConcept.setCodeSystemVersion(theCodeSystemVersion);
                termConcept.setDisplay(theConceptDefinition.getDisplay());
                termConcept.addChildren(
                                toPersistedConcepts(theConceptDefinition.getConcept(), theCodeSystemVersion), RelationshipTypeEnum.ISA);

                for (CodeSystem.ConceptDefinitionDesignationComponent designationComponent :
                                theConceptDefinition.getDesignation()) {
                        if (isNotBlank(designationComponent.getValue())) {
                                TermConceptDesignation designation = termConcept.addDesignation();
                                designation.setLanguage(designationComponent.hasLanguage() ? designationComponent.getLanguage() : null);
                                if (designationComponent.hasUse()) {
                                        designation.setUseSystem(
                                                        designationComponent.getUse().hasSystem()
                                                                        ? designationComponent.getUse().getSystem()
                                                                        : null);
                                        designation.setUseCode(
                                                        designationComponent.getUse().hasCode()
                                                                        ? designationComponent.getUse().getCode()
                                                                        : null);
                                        designation.setUseDisplay(
                                                        designationComponent.getUse().hasDisplay()
                                                                        ? designationComponent.getUse().getDisplay()
                                                                        : null);
                                }
                                designation.setValue(designationComponent.getValue());
                        }
                }

                for (CodeSystem.ConceptPropertyComponent next : theConceptDefinition.getProperty()) {
                        TermConceptProperty property = new TermConceptProperty();

                        property.setKey(next.getCode());
                        property.setConcept(termConcept);
                        property.setCodeSystemVersion(theCodeSystemVersion);

                        if (next.getValue() instanceof StringType) {
                                property.setType(TermConceptPropertyTypeEnum.STRING);
                                property.setValue(next.getValueStringType().getValue());
                        } else if (next.getValue() instanceof Coding) {
                                Coding nextCoding = next.getValueCoding();
                                property.setType(TermConceptPropertyTypeEnum.CODING);
                                property.setCodeSystem(nextCoding.getSystem());
                                property.setValue(nextCoding.getCode());
                                property.setDisplay(nextCoding.getDisplay());
                        } else if (next.getValue() != null) {
                                // TODO: LOINC has properties of type BOOLEAN that we should handle
                                ourLog.warn("Don't know how to handle properties of type: "
                                                + next.getValue().getClass());
                                continue;
                        }

                        termConcept.getProperties().add(property);
                }
                return termConcept;
        }

        static boolean isDisplayLanguageMatch(String theReqLang, String theStoredLang) {
                // NOTE: return the designation when one of then is not specified.
                if (theReqLang == null || theStoredLang == null) return true;

                return theReqLang.equalsIgnoreCase(theStoredLang);
        }
}