EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.persistence.dao.hibernate.common;

import java.util.ArrayList;

import java.util.List;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.apache.lucene.analysis.standard.StandardAnalyzer;

import org.apache.lucene.queryparser.classic.ParseException;

import org.apache.lucene.queryparser.classic.QueryParser;

import org.hibernate.Criteria;

import org.hibernate.Query;

import org.hibernate.Session;

import org.hibernate.criterion.Criterion;

import org.hibernate.criterion.Order;

import org.hibernate.criterion.Projections;

import org.hibernate.criterion.Restrictions;

import org.hibernate.envers.query.AuditEntity;

import org.hibernate.envers.query.AuditQuery;

import org.hibernate.search.FullTextSession;

import org.hibernate.search.Search;

import org.hibernate.search.SearchFactory;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.common.Credit;

import eu.etaxonomy.cdm.model.common.IAnnotatableEntity;

import eu.etaxonomy.cdm.model.common.IdentifiableEntity;

import eu.etaxonomy.cdm.model.common.IdentifiableSource;

import eu.etaxonomy.cdm.model.common.LSID;

import eu.etaxonomy.cdm.model.common.MarkerType;

import eu.etaxonomy.cdm.model.media.Rights;

import eu.etaxonomy.cdm.model.term.DefinedTerm;

import eu.etaxonomy.cdm.persistence.dao.QueryParseException;

import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;

import eu.etaxonomy.cdm.persistence.dao.common.Restriction;

import eu.etaxonomy.cdm.persistence.dto.SortableTaxonNodeQueryResult;

import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;

import eu.etaxonomy.cdm.persistence.query.MatchMode;

import eu.etaxonomy.cdm.persistence.query.OrderHint;

public class IdentifiableDaoBase<T extends IdentifiableEntity>

        extends AnnotatableDaoImpl<T>

        implements IIdentifiableDao<T>{

    @SuppressWarnings("unused")

    private static final Logger logger = Logger.getLogger(IdentifiableDaoBase.class);

    protected String defaultField = "titleCache_tokenized";

    protected Class<? extends T> indexedClasses[];

    public IdentifiableDaoBase(Class<T> type) {

        super(type);

    }

    @Override

    public List<T> findByTitle(String queryString) {

        return findByTitle(queryString, null);

    }

    @Override

    public List<T> findByTitle(String queryString, CdmBase sessionObject) {

        /**

         *  FIXME why do we need to call update in a find* method? I don't know for sure

         *  that this is a good idea . . .

         */

        Session session = getSession();

        if ( sessionObject != null ) {

            session.update(sessionObject);

        }

        checkNotInPriorView("IdentifiableDaoBase.findByTitle(String queryString, CdmBase sessionObject)");

        Criteria crit = session.createCriteria(type);

        crit.add(Restrictions.ilike("titleCache", queryString));

        @SuppressWarnings("unchecked")

		List<T> results = crit.list();

        List<String> propertyPaths = null;

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public List<String> findTitleCache(Class<? extends T> clazz, String queryString,

    		Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, MatchMode matchMode){

        Query query = prepareFindTitleCache(clazz, queryString, pageSize,

                pageNumber, matchMode, false);

        @SuppressWarnings("unchecked")

        List<String> result = query.list();

        return result;

    }

    @Override

    public Long countTitleCache(Class<? extends T> clazz, String queryString, MatchMode matchMode){

        Query query = prepareFindTitleCache(clazz, queryString, null,

                null, matchMode, true);

        Long result = (Long)query.uniqueResult();

        return result;

    }

    /**

     * @param clazz filter by class - can be null to include all instances of type T

     * @param queryString the query string to filter by

     * @param pageSize

     * @param pageNumber

     * @param matchmode use a particular type of matching (can be null - defaults to exact matching)

     * @return

     */

    private Query prepareFindTitleCache(Class<? extends T> clazz,

            String queryString, Integer pageSize, Integer pageNumber,

            MatchMode matchMode, boolean doCount) {

        if(clazz == null) {

            clazz = type;

        }

        String what = (doCount ? "count(distinct e.titleCache)": "distinct e.titleCache");

        if(matchMode != null){

            queryString	= matchMode.queryStringFrom(queryString);

        }

        String hql = "select " + what + " from  " + clazz.getName() + " e where e.titleCache like '" + queryString + "'";

        Query query = getSession().createQuery(hql);

        if(pageSize != null && !doCount) {

            query.setMaxResults(pageSize);

            if(pageNumber != null) {

                query.setFirstResult(pageNumber * pageSize);

            }

        }

        return query;

    }

    @Override

    public <S extends T> List<S> findByTitle(Class<S> clazz, String queryString, MatchMode matchmode, List<Criterion> criterion, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {

        return findByParam(clazz, "titleCache", queryString, matchmode, criterion, pageSize, pageNumber, orderHints, propertyPaths);

    }

    @Override

    public <S extends T> List<S> findByReferenceTitle(Class<S> clazz, String queryString, MatchMode matchmode, List<Criterion> criterion, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {

        return findByParam(clazz, "title", queryString, matchmode, criterion, pageSize, pageNumber, orderHints, propertyPaths);

    }

    @Override

    public <S extends T> List<S> findByTitleWithRestrictions(Class<S> clazz, String queryString, MatchMode matchmode, List<Restriction<?>> restrictions, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {

        return findByParamWithRestrictions(clazz, "titleCache", queryString, matchmode, restrictions, pageSize, pageNumber, orderHints, propertyPaths);

    }

    @Override

    public <S extends T> List<S> findByReferenceTitleWithRestrictions(Class<S> clazz, String queryString, MatchMode matchmode, List<Restriction<?>> restrictions, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {

        return findByParamWithRestrictions(clazz, "title", queryString, matchmode, restrictions, pageSize, pageNumber, orderHints, propertyPaths);

    }

    @Override

    public List<T> findByTitle(String queryString, MatchMode matchmode, int page, int pagesize, List<Criterion> criteria) {

        checkNotInPriorView("IdentifiableDaoBase.findByTitle(String queryString, MATCH_MODE matchmode, int page, int pagesize, List<Criterion> criteria)");

        Criteria crit = getSession().createCriteria(type);

        if (matchmode == MatchMode.EXACT) {

            crit.add(Restrictions.eq("titleCache", matchmode.queryStringFrom(queryString)));

        } else {

//			crit.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString)));

            crit.add(Restrictions.like("titleCache", matchmode.queryStringFrom(queryString)));

        }

        if (pagesize >= 0) {

            crit.setMaxResults(pagesize);

        }

        if(criteria != null){

            for (Criterion criterion : criteria) {

                crit.add(criterion);

            }

        }

        crit.addOrder(Order.asc("titleCache"));

        int firstItem = (page - 1) * pagesize;

        crit.setFirstResult(firstItem);

        @SuppressWarnings("unchecked")

        List<T> results = crit.list();

        List<String> propertyPaths = null;

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public long countRights(T identifiableEntity) {

        checkNotInPriorView("IdentifiableDaoBase.countRights(T identifiableEntity)");

        Query query = getSession().createQuery("select count(rights) from " + type.getSimpleName() + " identifiableEntity join identifiableEntity.rights rights where identifiableEntity = :identifiableEntity");

        query.setParameter("identifiableEntity",identifiableEntity);

        return (Long)query.uniqueResult();

    }

    @Override

    public long countSources(T identifiableEntity) {

        checkNotInPriorView("IdentifiableDaoBase.countSources(T identifiableEntity)");

        Query query = getSession().createQuery("SELECT COUNT(source) FROM "+identifiableEntity.getClass().getName() + " ie JOIN ie.sources source WHERE ie = :identifiableEntity");

        query.setParameter("identifiableEntity", identifiableEntity);

        return (Long)query.uniqueResult();

    }

    @Override

    public List<Rights> getRights(T identifiableEntity, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {

        checkNotInPriorView("IdentifiableDaoBase.getRights(T identifiableEntity, Integer pageSize, Integer pageNumber, List<String> propertyPaths)");

        Query query = getSession().createQuery("select rights from " + type.getSimpleName() + " identifiableEntity join identifiableEntity.rights rights where identifiableEntity = :identifiableEntity");

        query.setParameter("identifiableEntity",identifiableEntity);

        setPagingParameter(query, pageSize, pageNumber);

        @SuppressWarnings("unchecked")

        List<Rights> results = query.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

//    @Override  //TODO add to interface, maybe add property path

    public List<Credit> getCredits(T identifiableEntity, Integer pageSize, Integer pageNumber) {

        checkNotInPriorView("IdentifiableDaoBase.getCredits(T identifiableEntity, Integer pageSize, Integer pageNumber)");

        Query query = getSession().createQuery("select credits from " + type.getSimpleName() + " identifiableEntity join identifiableEntity.credits credits where identifiableEntity = :identifiableEntity");

        query.setParameter("identifiableEntity",identifiableEntity);

        setPagingParameter(query, pageSize, pageNumber);

        @SuppressWarnings("unchecked")

        List<Credit> result = query.list();

        return result;

    }

    @Override

    public List<IdentifiableSource> getSources(T identifiableEntity, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {

        checkNotInPriorView("IdentifiableDaoBase.getSources(T identifiableEntity, Integer pageSize, Integer pageNumber)");

        Query query = getSession().createQuery("SELECT source FROM "+ identifiableEntity.getClass().getName()+ " ie JOIN ie.sources source WHERE ie.id = :id");

        query.setParameter("id",identifiableEntity.getId());

        setPagingParameter(query, pageSize, pageNumber);

        @SuppressWarnings("unchecked")

        List<IdentifiableSource> results = query.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public List<T> findOriginalSourceByIdInSource(String idInSource, String idNamespace) {

        checkNotInPriorView("IdentifiableDaoBase.findOriginalSourceByIdInSource(String idInSource, String idNamespace)");

        Query query = getSession().createQuery(

                "Select c from " + type.getSimpleName() + " as c " +

                "inner join c.sources as source " +

                "where source.idInSource = :idInSource " +

                    " AND source.idNamespace = :idNamespace"

            );

        query.setString("idInSource", idInSource);

        query.setString("idNamespace", idNamespace);

        //TODO integrate reference in where

        @SuppressWarnings("unchecked")

        List<T> result = query.list();

        return result;

    }

    @Override

    public T find(LSID lsid) {

        checkNotInPriorView("IdentifiableDaoBase.find(LSID lsid)");

        Criteria criteria = getSession().createCriteria(type);

        criteria.add(Restrictions.eq("lsid.authority", lsid.getAuthority()));

        criteria.add(Restrictions.eq("lsid.namespace", lsid.getNamespace()));

        criteria.add(Restrictions.eq("lsid.object", lsid.getObject()));

        if(lsid.getRevision() != null) {

            criteria.add(Restrictions.eq("lsid.revision", lsid.getRevision()));

        }

        @SuppressWarnings("unchecked")

		T object = (T)criteria.uniqueResult();

        if(object != null) {

            return object;

        } else {

            AuditQuery query = getAuditReader().createQuery().forRevisionsOfEntity(type, false, true);

            query.add(AuditEntity.property("lsid_authority").eq(lsid.getAuthority()));

            query.add(AuditEntity.property("lsid_namespace").eq(lsid.getNamespace()));

            query.add(AuditEntity.property("lsid_object").eq(lsid.getObject()));

            if(lsid.getRevision() != null) {

                query.add(AuditEntity.property("lsid_revision").eq(lsid.getRevision()));

            }

            query.addOrder(AuditEntity.revisionNumber().asc());

            query.setMaxResults(1);

            query.setFirstResult(0);

            @SuppressWarnings("unchecked")

			List<Object[]> objs = query.getResultList();

            if(objs.isEmpty()) {

                return null;

            } else {

                @SuppressWarnings("unchecked")

				T result = (T)objs.get(0)[0];

                return result;

            }

        }

    }

    @SuppressWarnings("deprecation")

    @Override

    public String getTitleCache(UUID uuid, boolean refresh){

        if (! refresh){

            String queryStr = String.format("SELECT titleCache FROM %s t WHERE t.uuid = '%s'", type.getSimpleName() , uuid.toString());

            Query query = getSession().createQuery(queryStr);

            List<?> list = query.list();

            return list.isEmpty()? null : (String)list.get(0);

        }else{

            T entity = this.findByUuid(uuid);

            if (entity == null){

                return null;

            }

            entity.setTitleCache(null);

            return entity.getTitleCache();

        }

    }

    @Override

    public long countByTitle(Class<? extends T> clazz, String queryString,  MatchMode matchmode, List<Criterion> criterion) {

        return countByParam(clazz, "titleCache",queryString,matchmode,criterion);

    }

    @Override

    public long countByReferenceTitle(Class<? extends T> clazz, String queryString, MatchMode matchmode, List<Criterion> criterion) {

        return countByParam(clazz, "title",queryString,matchmode,criterion);

    }

    @Override

    public long countByTitleWithRestrictions(Class<? extends T> clazz, String queryString,	MatchMode matchmode, List<Restriction<?>> restrictions) {

        return countByParamWithRestrictions(clazz, "titleCache", queryString, matchmode, restrictions);

    }

    @Override

    public long countByReferenceTitleWithRestrictions(Class<? extends T> clazz, String queryString,	MatchMode matchmode, List<Restriction<?>> restrictions) {

        return countByParamWithRestrictions(clazz, "title", queryString, matchmode, restrictions);

    }

    @Override

    public long count(Class<? extends T> clazz, String queryString) {

        checkNotInPriorView("IdentifiableDaoBase.count(Class<? extends T> clazz, String queryString)");

        QueryParser queryParser = new QueryParser(defaultField , new StandardAnalyzer());

        try {

            org.apache.lucene.search.Query query = queryParser.parse(queryString);

            FullTextSession fullTextSession = Search.getFullTextSession(this.getSession());

            org.hibernate.search.FullTextQuery fullTextQuery = null;

            if(clazz == null) {

                fullTextQuery = fullTextSession.createFullTextQuery(query, type);

            } else {

                fullTextQuery = fullTextSession.createFullTextQuery(query, clazz);

            }

            int  result = fullTextQuery.getResultSize();

            return result;

        } catch (ParseException e) {

            throw new QueryParseException(e, queryString);

        }

    }

    @Override

    public void optimizeIndex() {

        FullTextSession fullTextSession = Search.getFullTextSession(getSession());

        SearchFactory searchFactory = fullTextSession.getSearchFactory();

        for(Class<?> clazz : indexedClasses) {

            searchFactory.optimize(clazz); // optimize the indices ()

        }

        fullTextSession.flushToIndexes();

    }

    @Override

    public void purgeIndex() {

        FullTextSession fullTextSession = Search.getFullTextSession(getSession());

        for(Class<?> clazz : indexedClasses) {

            fullTextSession.purgeAll(clazz); // remove all objects of type t from indexes

        }

        fullTextSession.flushToIndexes();

    }

    @Override

    public void rebuildIndex() {

        FullTextSession fullTextSession = Search.getFullTextSession(getSession());

        for(T t : list(null,null)) { // re-index all objects

            fullTextSession.index(t);

        }

        fullTextSession.flushToIndexes();

    }

    @Override

    public List<T> search(Class<? extends T> clazz, String queryString,	Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,List<String> propertyPaths) {

        checkNotInPriorView("IdentifiableDaoBase.search(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,List<String> propertyPaths)");

        QueryParser queryParser = new QueryParser(defaultField, new StandardAnalyzer());

        try {

            org.apache.lucene.search.Query query = queryParser.parse(queryString);

            FullTextSession fullTextSession = Search.getFullTextSession(getSession());

            org.hibernate.search.FullTextQuery fullTextQuery = null;

            if(clazz == null) {

                fullTextQuery = fullTextSession.createFullTextQuery(query, type);

            } else {

                fullTextQuery = fullTextSession.createFullTextQuery(query, clazz);

            }

            addOrder(fullTextQuery,orderHints);

            if(pageSize != null) {

                fullTextQuery.setMaxResults(pageSize);

                if(pageNumber != null) {

                    fullTextQuery.setFirstResult(pageNumber * pageSize);

                } else {

                    fullTextQuery.setFirstResult(0);

                }

            }

            @SuppressWarnings("unchecked")

			List<T> result = fullTextQuery.list();

            defaultBeanInitializer.initializeAll(result, propertyPaths);

            return result;

        } catch (ParseException e) {

            throw new QueryParseException(e, queryString);

        }

    }

    @Override

    public String suggestQuery(String string) {

        throw new UnsupportedOperationException("suggestQuery is not supported for objects of class " + type.getName());

    }

    @Override

    public long countByTitle(String queryString) {

        return countByTitle(queryString, null);

    }

    @Override

    public long countByTitle(String queryString, CdmBase sessionObject) {

        Session session = getSession();

        if ( sessionObject != null ) {

            session.update(sessionObject);

        }

        checkNotInPriorView("IdentifiableDaoBase.countByTitle(String queryString, CdmBase sessionObject)");

        Criteria crit = session.createCriteria(type);

        crit.add(Restrictions.ilike("titleCache", queryString))

            .setProjection(Projections.rowCount());

        long result =  (Long)crit.uniqueResult();

        return result;

    }

    @Override

    public long countByTitle(String queryString, MatchMode matchMode, List<Criterion> criteria) {

        checkNotInPriorView("IdentifiableDaoBase.findByTitle(String queryString, MATCH_MODE matchmode, int page, int pagesize, List<Criterion> criteria)");

        Criteria crit = getCriteria(type);

        if (matchMode == MatchMode.EXACT) {

            crit.add(Restrictions.eq("titleCache", matchMode.queryStringFrom(queryString)));

        } else {

//			crit.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString)));

            crit.add(Restrictions.like("titleCache", matchMode.queryStringFrom(queryString)));

        }

        if(criteria != null){

            for (Criterion criterion : criteria) {

                crit.add(criterion);

            }

        }

        crit.setProjection(Projections.rowCount());

        long result = (Long)crit.uniqueResult();

        return result;

    }

	@Override

	public <S extends T> long countByIdentifier(Class<S> clazz,

			String identifier, DefinedTerm identifierType, MatchMode matchMode) {

		checkNotInPriorView("IdentifiableDaoBase.countByIdentifier(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode)");

		Class<?> clazzParam = clazz == null ? type : clazz;

		String queryString = "SELECT count(*) FROM " + clazzParam.getSimpleName() + " as c " +

	                "INNER JOIN c.identifiers as ids " +

	                "WHERE (1=1) ";

		if (matchMode == null){

		    matchMode = MatchMode.EXACT;

		}

		if (identifier != null){

			queryString += " AND ids.identifier LIKE '" + matchMode.queryStringFrom(identifier)  + "'";

		}

		if (identifierType != null){

        	queryString += " AND ids.type = :type";

        }

		Query query = getSession().createQuery(queryString);

        if (identifierType != null){

        	query.setEntity("type", identifierType);

        }

		return (Long)query.uniqueResult();

	}

	@Override

	public <S extends T> List<Object[]> findByIdentifier(

			Class<S> clazz, String identifier, DefinedTerm identifierType,

			MatchMode matchMode, boolean includeEntity,

			Integer pageSize, Integer pageNumber, List<String> propertyPaths) {

		checkNotInPriorView("IdentifiableDaoBase.findByIdentifier(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");

		Class<?> clazzParam = clazz == null ? type : clazz;

		String queryString = "SELECT ids.type, ids.identifier, %s "

		        + "FROM %s as c " +

                " INNER JOIN c.identifiers as ids " +

                " WHERE (1=1) ";

		queryString = String.format(queryString, (includeEntity ? "c":"c.uuid, c.titleCache") , clazzParam.getSimpleName());

		//matchMode and identifier

		if (matchMode == null){

		    matchMode = MatchMode.EXACT;

		}

		if (identifier != null){

			queryString += " AND ids.identifier LIKE '" + matchMode.queryStringFrom(identifier)  + "'";

		}

        if (identifierType != null){

        	queryString += " AND ids.type = :type";

        }

        //order

        queryString +=" ORDER BY ids.type.uuid, ids.identifier, c.uuid ";

		Query query = getSession().createQuery(queryString);

		//parameters

		if (identifierType != null){

        	query.setEntity("type", identifierType);

        }

        //paging

        setPagingParameter(query, pageSize, pageNumber);

        @SuppressWarnings("unchecked")

		List<Object[]> results = query.list();

        //initialize

        if (includeEntity){

        	List<S> entities = new ArrayList<>();

        	for (Object[] result : results){

        		@SuppressWarnings("unchecked")

				S entity = (S)result[2];

        		entities.add(entity);

        	}

        	defaultBeanInitializer.initializeAll(entities, propertyPaths);

        }

        return results;

	}

    @Override

    public <S extends T> long countByMarker(Class<S> clazz, MarkerType markerType,

            Boolean markerValue) {

        checkNotInPriorView("IdentifiableDaoBase.countByMarker(T clazz, MarkerType markerType, Boolean markerValue)");

        if (markerType == null){

            return 0;

        }

        Class<?> clazzParam = clazz == null ? type : clazz;

        String queryString = "SELECT count(*) FROM " + clazzParam.getSimpleName() + " as c " +

                    "INNER JOIN c.markers as mks " +

                    "WHERE (1=1) ";

        if (markerValue != null){

            queryString += " AND mks.flag = :flag";

        }

        queryString += " AND mks.markerType = :type";

        Query query = getSession().createQuery(queryString);

        query.setEntity("type", markerType);

        if (markerValue != null){

            query.setBoolean("flag", markerValue);

        }

        Long c = (Long)query.uniqueResult();

        return c;

    }

	@Override

    public <S extends T> List<Object[]> findByMarker(

            Class<S> clazz, MarkerType markerType,

            Boolean markerValue, boolean includeEntity, Integer pageSize, Integer pageNumber,

            List<String> propertyPaths) {

        checkNotInPriorView("IdentifiableDaoBase.findByMarker(T clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)");

        if (markerType == null){

            return new ArrayList<>();

        }

        Class<?> clazzParam = clazz == null ? type : clazz;

        String queryString = "SELECT mks.markerType, mks.flag, %s FROM %s as c " +

                " INNER JOIN c.markers as mks " +

                " WHERE (1=1) ";

        queryString = String.format(queryString, (includeEntity ? "c":"c.uuid, c.titleCache") , clazzParam.getSimpleName());

        //Matchmode and identifier

        if (markerValue != null){

            queryString += " AND mks.flag = :flag";

        }

        queryString += " AND mks.markerType = :type";

        //order

        queryString +=" ORDER BY mks.markerType.uuid, mks.flag, c.uuid ";

        Query query = getSession().createQuery(queryString);

        //parameters

        query.setEntity("type", markerType);

        if (markerValue != null){

            query.setBoolean("flag", markerValue);

        }

        //paging

        setPagingParameter(query, pageSize, pageNumber);

        @SuppressWarnings("unchecked")

        List<Object[]> results = query.list();

        //initialize

        if (includeEntity){

            List<S> entities = new ArrayList<>();

            for (Object[] result : results){

            	@SuppressWarnings("unchecked")

				S entity = (S)result[2];

        		entities.add(entity);

            }

            defaultBeanInitializer.initializeAll(entities, propertyPaths);

        }

        return results;

    }

    @Override

    public List<UuidAndTitleCache<T>> getUuidAndTitleCacheByMarker(Integer limit, String pattern, MarkerType markerType){

        if (markerType == null){

            return new ArrayList<>();

        }

        String queryString = "SELECT c.uuid, c.titleCache FROM %s as c " +

                " INNER JOIN c.markers as mks " +

                " WHERE (1=1) ";

        queryString = String.format(queryString, type.getSimpleName());

        queryString += " AND mks.markerType = :type";

        if (pattern != null){

            queryString += " AND c.titleCache like :pattern";

            pattern = pattern.replace("*", "%");

            pattern = pattern.replace("?", "_");

            pattern = pattern + "%";

        }

        Query query = getSession().createQuery(queryString);

        if (pattern != null){

            query.setParameter("pattern", pattern);

        }

        //parameters

        query.setEntity("type", markerType);

        query.setMaxResults(limit);

        @SuppressWarnings("unchecked")

        List<Object[]> results = query.list();

        List<UuidAndTitleCache<T>> uuidAndTitleCacheResult = new ArrayList<>();

        for (Object[] result:results){

            uuidAndTitleCacheResult.add(new UuidAndTitleCache<>((UUID)result[0], (String)result[1]));

        }

        return uuidAndTitleCacheResult;

    }

    @Override

    public List<UuidAndTitleCache<T>> getUuidAndTitleCache(Integer limit, String pattern){

        return getUuidAndTitleCache(type, limit, pattern);

    }

    @Override

    public <S extends T> List<UuidAndTitleCache<S>> getUuidAndTitleCache(Class<S> clazz, Integer limit, String pattern){

        Session session = getSession();

        if (clazz == null){

            clazz = (Class)this.type;

        }

        Query query = session.createQuery(

                "SELECT new " + SortableTaxonNodeQueryResult.class.getName() + "("

                + " uuid, id, titleCache "

                + ") "

                + " FROM " + clazz.getSimpleName()

                + (pattern!=null ? " WHERE titleCache LIKE :pattern" : ""));

        if(pattern!=null){

            pattern = pattern.replace("*", "%");

            pattern = pattern.replace("?", "_");

            pattern = pattern + "%";

            query.setParameter("pattern", pattern);

        }

        if (limit != null){

           query.setMaxResults(limit);

        }

        return getUuidAndTitleCache(query);

    }

    @Override

    public List<UuidAndTitleCache<T>> getUuidAndTitleCache(){

        return getUuidAndTitleCache(type, null, null);

    }

    protected <E extends IAnnotatableEntity> List<UuidAndTitleCache<E>> getUuidAndAbbrevTitleCache(Query query){

        List<UuidAndTitleCache<E>> list = new ArrayList<>();

		@SuppressWarnings("unchecked")

        List<Object[]> result = query.list();

        for(Object[] object : result){

            list.add(new UuidAndTitleCache<E>((UUID) object[0],(Integer) object[1], (String) object[3], (String) object[2]));

        }

        return list;

    }

    protected <E extends IAnnotatableEntity> List<UuidAndTitleCache<E>> getUuidAndTitleCache(Query query){

        List<UuidAndTitleCache<E>> list = new ArrayList<>();

		@SuppressWarnings("unchecked")

        List<Object> result = query.list();

        for(Object obj : result){

            if (obj instanceof SortableTaxonNodeQueryResult) {

                SortableTaxonNodeQueryResult stnqr = (SortableTaxonNodeQueryResult) obj;

                list.add(new UuidAndTitleCache<>(stnqr.getTaxonNodeUuid(),stnqr.getTaxonNodeId(), stnqr.getTaxonTitleCache()));

            }else{

                Object[] object = (Object[])obj;

                list.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));

            }

        }