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.taxon;

import java.math.BigInteger;

import java.util.ArrayList;

import java.util.Collection;

import java.util.Collections;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.hibernate.Criteria;

import org.hibernate.Hibernate;

import org.hibernate.Query;

import org.hibernate.criterion.Projections;

import org.hibernate.criterion.Restrictions;

import org.springframework.beans.factory.annotation.Autowired;

import org.springframework.beans.factory.annotation.Qualifier;

import org.springframework.stereotype.Repository;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.taxon.Classification;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;

import eu.etaxonomy.cdm.model.taxon.UuidAndTitleCacheTaxonComparator;

import eu.etaxonomy.cdm.persistence.dao.hibernate.common.AnnotatableDaoImpl;

import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;

import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;

import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;

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

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

/**

 * @author a.mueller

 * @since 16.06.2009

 */

@Repository

@Qualifier("taxonNodeDaoHibernateImpl")

public class TaxonNodeDaoHibernateImpl extends AnnotatableDaoImpl<TaxonNode>

		implements ITaxonNodeDao {

	@SuppressWarnings("unused")

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

	@Autowired

	private ITaxonDao taxonDao;

	@Autowired

	private IClassificationDao classificationDao;

	public TaxonNodeDaoHibernateImpl() {

		super(TaxonNode.class);

	}

	@Override

	public UUID delete(TaxonNode persistentObject, boolean deleteChildren){

		Taxon taxon = persistentObject.getTaxon();

		taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);

		/*Session session = this.getSession();

		Query query = session.createQuery("from TaxonNode t where t.taxon = :taxon");

		query.setParameter("taxon", taxon);

		List result = query.list();*/

		if (taxon != null){

		    Hibernate.initialize(taxon);

		    Hibernate.initialize(taxon.getTaxonNodes());

			Set<TaxonNode> nodes = taxon.getTaxonNodes();

			//Hibernate.initialize(taxon.getTaxonNodes());

			for (TaxonNode node:nodes) {

			    node = HibernateProxyHelper.deproxy(node, TaxonNode.class);

			    if (node.equals(persistentObject)){

			        if (node.hasChildNodes()){

			            Iterator<TaxonNode> childNodes = node.getChildNodes().iterator();

			            TaxonNode childNode;

			            List<TaxonNode> listForDeletion = new ArrayList<TaxonNode>();

	                    while (childNodes.hasNext()){

	                        childNode = childNodes.next();

	                        listForDeletion.add(childNode);

	                        childNodes.remove();

	                    }

	                    for (TaxonNode deleteNode:listForDeletion){

	                        delete(deleteNode, deleteChildren);

	                    }

	                }

			        taxon.removeTaxonNode(node, deleteChildren);

			        taxonDao.saveOrUpdate(taxon);

    				taxon = HibernateProxyHelper.deproxy(taxonDao.findByUuid(taxon.getUuid()), Taxon.class);

    				taxonDao.delete(taxon);

			    }

			}

		}

		UUID result = super.delete(persistentObject);

		return result;

	}

	@Override

	public List<TaxonNode> getTaxonOfAcceptedTaxaByClassification(Classification classification, Integer start, Integer end) {

		int classificationId = classification.getId();

		String limit = "";

		if(start !=null && end != null){

		    limit = "LIMIT "+start+"," +end;

		}

		//FIXME write test

        String queryString = "SELECT DISTINCT nodes.*,taxa.titleCache FROM TaxonNode AS nodes LEFT JOIN TaxonBase AS taxa ON nodes.taxon_id = taxa.id WHERE taxa.DTYPE = 'Taxon' AND nodes.classification_id = " + classificationId + " ORDER BY taxa.titleCache " + limit;

        @SuppressWarnings("unchecked")

        List<TaxonNode> result  = getSession().createSQLQuery(queryString).addEntity(TaxonNode.class).list();

       return result;

	}

    @Override

    public int countTaxonOfAcceptedTaxaByClassification(Classification classification){

        int classificationId = classification.getId();

        //FIXME write test

        String queryString = "SELECT DISTINCT COUNT('nodes.*') FROM TaxonNode AS nodes LEFT JOIN TaxonBase AS taxa ON nodes.taxon_id = taxa.id WHERE taxa.DTYPE = 'Taxon' AND nodes.classification_id = " + classificationId;

         @SuppressWarnings("unchecked")

        List<BigInteger> result = getSession().createSQLQuery(queryString).list();

         return result.get(0).intValue ();

    }

    @Override

    public List<UuidAndTitleCache<TaxonNode>> listChildNodesAsUuidAndTitleCache(UuidAndTitleCache<TaxonNode> parent) {

        String queryString = "select tn.uuid, tn.id, tx.titleCache from TaxonNode tn INNER JOIN tn.taxon as tx where tn.parent.uuid = :parentId";

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

        query.setParameter("parentId", parent.getUuid());

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

        @SuppressWarnings("unchecked")

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

        for(Object[] object : result){

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

        }

        return list;

    }

    @Override

    public List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(UuidAndTitleCache<TaxonNode> parent) {

        String queryString = "select tn from TaxonNode tn INNER JOIN tn.taxon as tx where tn.parent.uuid = :parentId";

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

        query.setParameter("parentId", parent.getUuid());

        List<TaxonNodeDto> list = new ArrayList<>();

        @SuppressWarnings("unchecked")

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

        for(TaxonNode object : result){

            list.add(new TaxonNodeDto(object));

        }

        return list;

    }

    @Override

    public List<UuidAndTitleCache<TaxonNode>> getUuidAndTitleCache(Integer limit, String pattern, UUID classificationUuid) {

        String queryString = "select tn.uuid, tn.id, tx.titleCache, tx.name.rank from TaxonNode tn "

        		+ "INNER JOIN tn.taxon as tx "

        		+ "INNER JOIN tn.classification as cls "

        		+ "WHERE tx.titleCache like :pattern ";

        if(classificationUuid!=null){

        	queryString += "AND cls.uuid = :classificationUuid";

        }

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

        query.setParameter("pattern", pattern.toLowerCase()+"%");

        query.setParameter("classificationUuid", classificationUuid);

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

        @SuppressWarnings("unchecked")

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

        if (result != null){

            Collections.sort(result, new UuidAndTitleCacheTaxonComparator());

        }

        for(Object[] object : result){

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

        }

        return list;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public UuidAndTitleCache<TaxonNode> getParentUuidAndTitleCache(UuidAndTitleCache<TaxonNode> child) {

        String queryString = "select tn.parent.uuid, tn.parent.id, tn.parent.taxon.titleCache, tn.parent.classification.titleCache "

                + " from TaxonNode tn"

                + " LEFT OUTER JOIN tn.parent.taxon"

                + " where tn.id = :childId";

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

        query.setParameter("childId", child.getId());

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

        @SuppressWarnings("unchecked")

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

        for(Object[] object : result){

            UUID uuid = (UUID) object[0];

            Integer id = (Integer) object[1];

            String taxonTitleCache = (String) object[2];

            String classificationTitleCache = (String) object[3];

            if(taxonTitleCache!=null){

                list.add(new UuidAndTitleCache<TaxonNode>(uuid,id, taxonTitleCache));

            }

            else{

                list.add(new UuidAndTitleCache<TaxonNode>(uuid,id, classificationTitleCache));

            }

        }

        if(list.size()==1){

            return list.iterator().next();

        }

        return null;

    }

    @Override

    public List<TaxonNode> listChildrenOf(TaxonNode node, Integer pageSize, Integer pageIndex, List<String> propertyPaths, boolean recursive){

    	if (recursive == true){

    		Criteria crit = getSession().createCriteria(TaxonNode.class);

    		crit.add( Restrictions.like("treeIndex", node.treeIndex()+ "%") );

    		if(pageSize != null) {

                crit.setMaxResults(pageSize);

                if(pageIndex != null) {

                    crit.setFirstResult(pageIndex * pageSize);

                } else {

                    crit.setFirstResult(0);

                }

            }

    		@SuppressWarnings("unchecked")

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

    		results.remove(node);

    		defaultBeanInitializer.initializeAll(results, propertyPaths);

    		return results;

    	}else{

    		return classificationDao.listChildrenOf(node.getTaxon(), node.getClassification(), pageSize, pageIndex, propertyPaths);

    	}

    }

    @Override

	public Long countChildrenOf(TaxonNode node, Classification classification,

			boolean recursive) {

		if (recursive == true){

			Criteria crit = getSession().createCriteria(TaxonNode.class);

    		crit.add( Restrictions.like("treeIndex", node.treeIndex()+ "%") );

    		crit.setProjection(Projections.rowCount());

    		return ((Integer)crit.uniqueResult().hashCode()).longValue();

		}else{

			return classificationDao.countChildrenOf(node.getTaxon(), classification);

		}

	}

    /**

     * {@inheritDoc}

     */

    @Override

    public List<TaxonNodeAgentRelation> listTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid,

            UUID agentUuid, UUID rankUuid, UUID relTypeUuid, Integer start, Integer limit, List<String> propertyPaths) {

        StringBuilder hql = prepareListTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid, false);

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

        if(limit != null) {

            query.setMaxResults(limit);

            if(start != null) {

                query.setFirstResult(start);

            }

        }

        setParamsForListTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid, query);

        @SuppressWarnings("unchecked")

        List<TaxonNodeAgentRelation> records = query.list();

        if(propertyPaths != null) {

            defaultBeanInitializer.initializeAll(records, propertyPaths);

        }

        return records;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public long countTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid, UUID agentUuid, UUID rankUuid, UUID relTypeUuid) {

        StringBuilder hql = prepareListTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid, true);

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

        setParamsForListTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid, query);

        Long count = Long.parseLong(query.uniqueResult().toString());

        return count;

    }

    /**

     * @param taxonUuid

     * @param classificationUuid

     * @param agentUuid

     * @param relTypeUuid TODO

     * @param doCount TODO

     * @param rankId

     *     limit to taxa having this rank, only applies if <code>taxonUuid = null</code>

     * @return

     */

    private StringBuilder prepareListTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid, UUID agentUuid, UUID rankUuid, UUID relTypeUuid, boolean doCount) {

        StringBuilder hql = new StringBuilder();

        String join_fetch_mode = doCount ? "join" : "join fetch";

        if(doCount) {

            hql.append("select count(tnar)");

        } else {

            hql.append("select tnar");

        }

        hql.append(" from TaxonNodeAgentRelation as tnar ");

        if(taxonUuid != null) {

            // taxonUuid is search filter, do not fetch it

            hql.append(" join tnar.taxonNode as tn join tn.taxon as t ");

        } else {

            hql.append(join_fetch_mode).append(" tnar.taxonNode as tn ").append(join_fetch_mode).append(" tn.taxon as t ");

            if(rankUuid != null) {

                hql.append(" join t.name as n ");

            }

        }

        hql.append(" join tn.classification as c ");

        if(agentUuid != null) {

            // agentUuid is search filter, do not fetch it

//            hql.append(" join tnar.agent as a ");

            hql.append(join_fetch_mode).append(" tnar.agent as a ");

        } else {

            hql.append(join_fetch_mode).append(" tnar.agent as a ");

        }

        hql.append(" where 1 = 1 ");

        if(relTypeUuid != null) {

            hql.append(" and tnar.type.uuid = :relTypeUuid ");

        }

        if(taxonUuid != null) {

            hql.append(" and t.uuid = :taxonUuid ");

        } else {

            if(rankUuid != null) {

                hql.append(" and n.rank.uuid = :rankUuid ");

            }

        }

        if(classificationUuid != null) {

            hql.append(" and c.uuid = :classificationUuid ");

        }

        if(agentUuid != null) {

            hql.append(" and a.uuid = :agentUuid ");

        }

        hql.append(" order by a.titleCache");

        return hql;

    }

    /**

     * @param taxonUuid

     * @param classificationUuid

     * @param agentUuid

     * @param relTypeUuid TODO

     * @param query

     * @param rankId TODO

     */

    private void setParamsForListTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid, UUID agentUuid,

            UUID rankUuid, UUID relTypeUuid, Query query) {

        if(taxonUuid != null) {

            query.setParameter("taxonUuid", taxonUuid);

        } else {

            if(rankUuid != null) {

                query.setParameter("rankUuid", rankUuid);

            }

        }

        if(classificationUuid != null) {

            query.setParameter("classificationUuid", classificationUuid);

        }

        if(agentUuid != null) {

            query.setParameter("agentUuid", agentUuid);

        }

        if(relTypeUuid != null) {

            query.setParameter("relTypeUuid", relTypeUuid);

        }

    }

    @Override

    public Map<TreeIndex, Integer> rankOrderIndexForTreeIndex(List<TreeIndex> treeIndexes,

            Integer minRankOrderIndex,

            Integer maxRankOrderIndex) {

        Map<TreeIndex, Integer> result = new HashMap<>();

        if (treeIndexes == null || treeIndexes.isEmpty()){

            return result;

        }

        String hql = " SELECT tn.treeIndex, r.orderIndex "

                + " FROM TaxonNode tn JOIN tn.taxon t JOIN t.name n JOIN n.rank r "

                + " WHERE tn.treeIndex IN (:treeIndexes) ";

        if (minRankOrderIndex != null){

            hql += " AND r.orderIndex <= :minOrderIndex";

        }

        if (maxRankOrderIndex != null){

            hql += " AND r.orderIndex >= :maxOrderIndex";

        }

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

        query.setParameterList("treeIndexes", TreeIndex.toString(treeIndexes));

        if (minRankOrderIndex != null){

            query.setParameter("minOrderIndex", minRankOrderIndex);

        }

        if (maxRankOrderIndex != null){

            query.setParameter("maxOrderIndex", maxRankOrderIndex);

        }

        @SuppressWarnings("unchecked")

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

        for (Object[] o : list){

            result.put(TreeIndex.NewInstance((String)o[0]), (Integer)o[1]);

        }

        return result;

    }

    @Override

    public Map<TreeIndex, UuidAndTitleCache<?>> taxonUuidsForTreeIndexes(Collection<TreeIndex> treeIndexes) {

        Map<TreeIndex, UuidAndTitleCache<?>> result = new HashMap<>();

        if (treeIndexes == null || treeIndexes.isEmpty()){

            return result;

        }

        String hql = " SELECT tn.treeIndex, t.uuid, tnb.titleCache "

                + " FROM TaxonNode tn JOIN tn.taxon t Join t.name tnb "

                + " WHERE tn.treeIndex IN (:treeIndexes) ";

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

        query.setParameterList("treeIndexes", TreeIndex.toString(treeIndexes));

        @SuppressWarnings("unchecked")

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

        for (Object[] o : list){

            result.put(TreeIndex.NewInstance((String)o[0]), new UuidAndTitleCache<>((UUID)o[1], null, (String)o[2]));

        }

        return result;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public int countSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec,

            boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {

        String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.COUNT);

        if (!overwriteExisting){

            queryStr += " AND t.sec IS NULL ";

        }

        return countResult(queryStr);

    }

    /**

     * @param queryStr

     * @return

     */

    protected int countResult(String queryStr) {

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

        return ((Long)query.uniqueResult()).intValue();

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public int countSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec,

            boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {

        String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.COUNT);

        if (!overwriteExisting){

            queryStr += " AND syn.sec IS NULL ";

        }

        return countResult(queryStr);

    }

    /**

     * {@inheritDoc}

     */

    //#3465

    @Override

    public Set<TaxonBase> setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec,

            boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail, IProgressMonitor monitor) {

        //for some reason this does not work, maybe because the listeners are not activated,

        //but also the first taxon for some reason does not get updated in terms of secundum, but only by the update listener

//        String where = "SELECT t.id FROM TaxonNode tn JOIN tn.taxon t " +

//                " WHERE tn.treeIndex like '%s%%' ORDER BY t.id";

//        where = String.format(where, subTreeIndex.toString());

//        Query query1 = getSession().createQuery(where);

//        List l = query1.list();

//

//        String hql = "UPDATE Taxon SET sec = :newSec, publish=false WHERE id IN (" + where + ")";

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

//        query.setParameter("newSec", newSec);

//        int n = query.executeUpdate();

        String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);

        if (!overwriteExisting){

            queryStr += " AND t.sec IS NULL ";

        }

        return setSecundum(newSec, emptyDetail, queryStr, monitor);

    }

    @Override

    public Set<TaxonBase> setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec,

            boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail, IProgressMonitor monitor) {

        String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);

        if (!overwriteExisting){

            queryStr += " AND syn.sec IS NULL ";

        }

        return setSecundum(newSec, emptyDetail, queryStr, monitor);

    }

    /**

     * @param newSec

     * @param emptyDetail

     * @param queryStr

     * @param monitor

     * @return

     */

    @SuppressWarnings("unchecked")

    private <T extends TaxonBase<?>> Set<T> setSecundum(Reference newSec, boolean emptyDetail, String queryStr, IProgressMonitor monitor) {

        Set<T> result = new HashSet<>();

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

        List<List<Integer>> partitionList = splitIdList(query.list(), DEFAULT_PARTITION_SIZE);

        for (List<Integer> taxonIdList : partitionList){

            List<TaxonBase> taxonList = taxonDao.loadList(taxonIdList, null);

            for (TaxonBase taxonBase : taxonList){

                if (taxonBase != null){

                    taxonBase = taxonDao.load(taxonBase.getUuid());

                    taxonBase.setSec(newSec);

                    if (emptyDetail){

                        taxonBase.setSecMicroReference(null);

                    }

                    result.add((T)CdmBase.deproxy(taxonBase));

                    monitor.worked(1);

                    if (monitor.isCanceled()){

                        return result;

                    }

                }

            }

        }

        return result;

    }

    private List<List<Integer>> splitIdList(List<Integer> idList, Integer size){

        List<List<Integer>> result = new ArrayList<>();

        for (int i = 0; (i*size)<idList.size(); i++) {

            int upper = Math.min((i+1)*size, idList.size());

            result.add(idList.subList(i*size, upper));

        }

        return result;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public int countPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, boolean publish, boolean includeSharedTaxa) {

        String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.COUNT);

        queryStr += " AND t.publish != :publish ";

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

        query.setBoolean("publish", publish);

        return ((Long)query.uniqueResult()).intValue();

//        return countResult(queryStr);

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public int countPublishForSubtreeSynonyms(TreeIndex subTreeIndex, boolean publish, boolean includeSharedTaxa) {

        String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.COUNT);

        queryStr += " AND syn.publish != :publish ";

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

        query.setBoolean("publish", publish);

        return ((Long)query.uniqueResult()).intValue();

//      return countResult(queryStr);

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public Set<TaxonBase> setPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, boolean publish,

            boolean includeSharedTaxa, IProgressMonitor monitor) {

        String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);

        queryStr += " AND t.publish != :publish ";

        return setPublish(publish, queryStr, monitor);

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public Set<TaxonBase> setPublishForSubtreeSynonyms(TreeIndex subTreeIndex, boolean publish,

            boolean includeSharedTaxa, IProgressMonitor monitor) {

        String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);

        queryStr += " AND syn.publish != :publish ";

        return setPublish(publish, queryStr, monitor);

    }

    private static final int DEFAULT_PARTITION_SIZE = 100;

    /**

     * @param publish

     * @param queryStr

     * @return

     */

    private <T extends TaxonBase<?>> Set<T> setPublish(boolean publish, String queryStr, IProgressMonitor monitor) {

        Set<T> result = new HashSet<>();

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

        query.setBoolean("publish", publish);

        @SuppressWarnings("unchecked")

        List<List<Integer>> partitionList = splitIdList(query.list(), DEFAULT_PARTITION_SIZE);

        for (List<Integer> taxonIdList : partitionList){

            List<TaxonBase> taxonList = taxonDao.loadList(taxonIdList, null);

            for (TaxonBase taxonBase : taxonList){

                if (taxonBase != null){

                    taxonBase.setPublish(publish);

                    result.add((T)CdmBase.deproxy(taxonBase));

                    monitor.worked(1);

                    if (monitor.isCanceled()){

                        return result;

                    }

                }

            }

        }

        return result;

    }

    /**

     * @param includeSharedTaxa

     * @param subTreeIndex

     * @return

     */

    private String synonymForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex, SelectMode mode) {

        String queryStr = "SELECT " + mode.hql("syn")

                + " FROM TaxonNode tn JOIN tn.taxon t JOIN t.synonyms syn"

                + " WHERE tn.treeIndex like '%s%%' ";

        if (!includeSharedTaxa){

            queryStr += " AND t.taxonNodes.size <= 1  ";

        }

        queryStr = String.format(queryStr, subTreeIndex.toString());

        return queryStr;

    }

    private enum SelectMode{

        COUNT(" count(*) "),

        ID ("id "),

        UUID("uuid "),

        FULL("");

        private String hql;

        SelectMode(String hql){

            this.hql = hql;

        }

        public String hql(String prefix){

            switch (this){

            case ID:

            case UUID:

                return CdmUtils.Nz(prefix)+"." + hql;

            case FULL:

                return CdmUtils.Nz(prefix) + hql;

            case COUNT:

            default: return hql;

            }

        }

    }

    private String acceptedForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex, SelectMode mode) {

        String queryStr = "SELECT " + mode.hql("t")

                + " FROM TaxonNode tn JOIN tn.taxon t "

                + " WHERE tn.treeIndex like '%s%%' ";

        if (!includeSharedTaxa){

            queryStr += " AND t.taxonNodes.size <= 1  ";

        }

        queryStr = String.format(queryStr, subTreeIndex.toString());

        return queryStr;

    }

    @Override

    public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, Integer limit, String pattern, boolean searchForClassifications) {

        int classificationId = classification.getId();

        // StringBuffer excludeUuids = new StringBuffer();

   //, taxon.name.rank

         String queryString = "SELECT nodes.uuid, nodes.id,  taxon.titleCache, taxon.name.rank FROM TaxonNode AS nodes JOIN nodes.taxon as taxon WHERE nodes.classification.id = " + classificationId ;

         if (pattern != null){

             if (pattern.equals("?")){

                 limit = null;

             } else{

                 if (!pattern.endsWith("*")){

                     pattern += "%";

                 }

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

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

                 queryString = queryString + " AND taxon.titleCache like (:pattern) " ;

             }

         }

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

         if (limit != null){

             query.setMaxResults(limit);

         }

         if (pattern != null && !pattern.equals("?")){

             query.setParameter("pattern", pattern);

         }

         @SuppressWarnings("unchecked")

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

         if (searchForClassifications){

             queryString = "SELECT nodes.uuid, nodes.id,  nodes.classification.titleCache, NULLIF(1,1) FROM TaxonNode AS nodes WHERE nodes.classification.id = " + classificationId + " AND nodes.taxon IS NULL";

             if (pattern != null){

                 if (pattern.equals("?")){

                     limit = null;

                 } else{

                     if (!pattern.endsWith("*")){

                         pattern += "%";

                     }

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

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

                     queryString = queryString + " AND nodes.classification.titleCache like (:pattern) " ;

                 }

             }

              query = getSession().createQuery(queryString);

             if (limit != null){

                 query.setMaxResults(limit);

             }

             if (pattern != null && !pattern.equals("?")){

                 query.setParameter("pattern", pattern);

             }

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

             result.addAll(resultClassifications);

         }

         if(result.size() == 0){

             return null;

         }else{

             List<UuidAndTitleCache<TaxonNode>> list = new ArrayList<UuidAndTitleCache<TaxonNode>>(result.size());

             if (result != null && !result.isEmpty()){

                 if (result.iterator().next().length == 4){

                     Collections.sort(result, new UuidAndTitleCacheTaxonComparator());

                 }

             }

             for (Object object : result){

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

                 UUID uuid = (UUID)objectArray[0];

                 Integer id = (Integer) objectArray[1];

                 String titleCache = (String) objectArray[2];

                 list.add(new UuidAndTitleCache<TaxonNode>(TaxonNode.class, uuid, id, titleCache));