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.Comparator;

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.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;

import org.hibernate.Criteria;

import org.hibernate.Hibernate;

import org.hibernate.criterion.Projections;

import org.hibernate.criterion.Restrictions;

import org.hibernate.query.Query;

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.name.Rank;

import eu.etaxonomy.cdm.model.name.TaxonName;

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

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

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

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

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

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.TaxonRelationship;

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

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

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.dao.taxon.ITaxonRelationshipDao;

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

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

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

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

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

/**

 * @author a.mueller

 * @since 16.06.2009

 */

@Repository

@Qualifier("taxonNodeDaoHibernateImpl")

public class TaxonNodeDaoHibernateImpl extends AnnotatableDaoBaseImpl<TaxonNode>

		implements ITaxonNodeDao {

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

    private static final int DEFAULT_SET_SUBTREE_PARTITION_SIZE = 100;

	@Autowired

	private ITaxonDao taxonDao;

	@Autowired

	private IClassificationDao classificationDao;

    @Autowired

    private ITaxonRelationshipDao taxonRelDao;

	public TaxonNodeDaoHibernateImpl() {

		super(TaxonNode.class);

	}

	@Override

	public UUID delete(TaxonNode persistentObject, boolean deleteChildren){

		Taxon taxon = persistentObject.getTaxon();

		taxon = HibernateProxyHelper.deproxy(taxon);

		/*Session session = this.getSession();

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

		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);

			    if (node.equals(persistentObject)){

			        if (node.hasChildNodes()){

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

			            TaxonNode childNode;

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

	                    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<TaxonNodeDto> listChildNodesAsUuidAndTitleCache(TaxonNodeDto parent) {

        String queryString =

                  " SELECT tn.uuid, tn.id, t.titleCache "

                + " FROM TaxonNode tn "

                + "    INNER JOIN tn.taxon AS t "

                + " WHERE tn.parent.uuid = :parentId";

        Query<Object[]> query =  getSession().createQuery(queryString, Object[].class);

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

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

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

        for(Object[] object : result){

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

        }

        return list;

    }

    @Override

    public List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(TaxonNodeDto parent) {

        String queryString =

                 " SELECT tn "

               + " FROM TaxonNode tn "

               + "    INNER JOIN tn.taxon AS t "

               + " WHERE tn.parent.uuid = :parentId";

        Query<TaxonNode> query =  getSession().createQuery(queryString, TaxonNode.class);

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

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

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

        for(TaxonNode object : result){

            list.add(new TaxonNodeDto(object));

        }

        return list;

    }

    @Override

    public List<TaxonNodeDto> getUuidAndTitleCache(Integer limit, String pattern, UUID classificationUuid, boolean includeDoubtful) {

        Query<SortableTaxonNodeQueryResult> query = createQueryForUuidAndTitleCache(limit, classificationUuid, pattern, includeDoubtful);

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

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

        if(logger.isTraceEnabled()){

            logger.trace("number of matches:" + result.size());

            result.stream().forEach(o -> logger.trace("uuid: " + o.getTaxonNodeUuid() + " titleCache:" + o.getTaxonTitleCache() + " rank: " + o.getNameRank()));

        }

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

//        int index = limit;

        for(SortableTaxonNodeQueryResult stnqr : result){

//            if (index > 0){

                list.add(new TaxonNodeDto(stnqr.getTaxonNodeUuid(),stnqr.getTaxonNodeId(), stnqr.getTaxonTitleCache()));

//                index --;

//            }

        }

        return list;

    }

    private Query<SortableTaxonNodeQueryResult> createQueryForUuidAndTitleCache(Integer limit, UUID classificationUuid, String pattern, boolean includeDoubtful){

        String doubtfulPattern = "";

        String queryString = "SELECT new " + SortableTaxonNodeQueryResult.class.getName() + "("

                + " node.uuid, node.id, node.treeIndex, t.uuid, t.titleCache, rank, parent.uuid"

                + ") "

                + " FROM TaxonNode AS node "

                + "   JOIN node.taxon as t " // FIXME why not inner join here?

                + "   INNER JOIN t.name AS name "

                + "   LEFT OUTER JOIN node.parent as parent"

                + "   LEFT OUTER JOIN name.rank AS rank "

                + " WHERE ";

      if (classificationUuid != null){

          queryString = queryString + " node.classification.uuid like :classificationUuid " ;

      }

      if (pattern == null){

          pattern = "*";

      }

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

          limit = null;

      } else{

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

              pattern += "%";

          }

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

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

          if (classificationUuid != null){

              queryString = queryString + " AND ";

          }

          queryString = queryString + " (t.titleCache LIKE (:pattern) " ;

          doubtfulPattern = "?" + pattern;

          if (includeDoubtful){

              queryString = queryString + " OR t.titleCache LIKE (:doubtfulPattern))";

          }else{

              queryString = queryString + ")";

          }

      }

      Query<SortableTaxonNodeQueryResult> query =  getSession().createQuery(queryString, SortableTaxonNodeQueryResult.class);

      if (pattern != null){

          query.setParameter("pattern", pattern);

      }

      if (includeDoubtful){

          query.setParameter("doubtfulPattern", doubtfulPattern);

      }

      if(classificationUuid != null){

          query.setParameter("classificationUuid", classificationUuid);

      }

      if (limit != null){

          query.setMaxResults(limit);

      }

      return query;

    }

    @Override

    public TaxonNodeDto getParentUuidAndTitleCache(TaxonNodeDto 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<Object[]> query =  getSession().createQuery(queryString, Object[].class);

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

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

        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 TaxonNodeDto(uuid,id, taxonTitleCache));

            }

            else{

                list.add(new TaxonNodeDto(uuid,id, classificationTitleCache));

            }

        }

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

            return list.iterator().next();

        }

        return null;

    }

    @Override

    public List<TaxonNode> listChildrenOf(TaxonNode node, Integer pageSize, Integer pageIndex,

            boolean recursive, boolean includeUnpublished, List<String> propertyPaths, Comparator<TaxonNode> comparator){

        return listChildrenOfRecursive(node,new ArrayList<>(), pageSize, pageIndex, recursive, includeUnpublished, propertyPaths, comparator);

    }

    private List<TaxonNode> listChildrenOfRecursive(TaxonNode node, List<TaxonNode> previousResult, Integer pageSize, Integer pageIndex,

            boolean recursive, boolean includeUnpublished, List<String> propertyPaths, Comparator<TaxonNode> comparator){

        if (recursive == true && comparator == null ){

    		Criteria crit = childrenOfCriteria(node, includeUnpublished);

    		this.addPageSizeAndNumber(crit, pageSize, pageIndex);

    		@SuppressWarnings("unchecked")

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

    		results.remove(node);

    		defaultBeanInitializer.initializeAll(results, propertyPaths);

    		return results;

    	} else if (recursive == true){

    	    List<TaxonNode> children = node.getChildNodes();

    	    Collections.sort(children, comparator);

    	    for (TaxonNode child: children){

    	        if (!previousResult.contains(child)){

    	            previousResult.add(child);

    	        }

    	        if (child.hasChildNodes()){

    	            previousResult = listChildrenOfRecursive(child, previousResult, pageSize, pageIndex,

    	                    recursive, includeUnpublished, propertyPaths, comparator);

    	        }

    	    }

    	    return previousResult;

        } else{

    		return classificationDao.listChildrenOf(node.getTaxon(), node.getClassification(), null,

    		       includeUnpublished, pageSize, pageIndex, propertyPaths);

    	}

    }

    @Override

	public Long countChildrenOf(TaxonNode node, Classification classification,

			boolean recursive, boolean includeUnpublished) {

		if (recursive == true){

			Criteria crit = childrenOfCriteria(node, includeUnpublished);

    		crit.setProjection(Projections.rowCount());

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

		}else{

			return classificationDao.countChildrenOf(

			        node.getTaxon(), classification, null, includeUnpublished);

		}

	}

    private Criteria childrenOfCriteria(TaxonNode node, boolean includeUnpublished) {

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

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

        if (!includeUnpublished){

            crit.createCriteria("taxon").add( Restrictions.eq("publish", Boolean.TRUE));

        }

        return crit;

    }

    @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<TaxonNodeAgentRelation> query =  getSession().createQuery(hql.toString(), TaxonNodeAgentRelation.class);

        if(limit != null) {

            query.setMaxResults(limit);

            if(start != null) {

                query.setFirstResult(start);

            }

        }

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

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

        if(propertyPaths != null) {

            defaultBeanInitializer.initializeAll(records, propertyPaths);

        }

        return records;

    }

    @Override

    public <S extends TaxonNode> List<S> list(Class<S> type, List<Restriction<?>> restrictions, Integer limit,

            Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        // TODO Auto-generated method stub

        return list(type, restrictions, limit, start, orderHints, propertyPaths, INCLUDE_UNPUBLISHED);

    }

    @Override

    public <S extends TaxonNode> List<S> list(Class<S> type, List<Restriction<?>> restrictions, Integer limit,

            Integer start, List<OrderHint> orderHints, List<String> propertyPaths, boolean includePublished) {

        Criteria criteria = createCriteria(type, restrictions, false);

        if(!includePublished){

            criteria.add(Restrictions.eq("taxon.publish", true));

        }

        addLimitAndStart(criteria, limit, start);

        addOrder(criteria, orderHints);

        @SuppressWarnings("unchecked")

        List<S> result = criteria.list();

        defaultBeanInitializer.initializeAll(result, propertyPaths);

        return result;

    }

    @Override

    public long count(Class<? extends TaxonNode> type, List<Restriction<?>> restrictions) {

        return count(type, restrictions, INCLUDE_UNPUBLISHED);

    }

    @Override

    public long count(Class<? extends TaxonNode> type, List<Restriction<?>> restrictions, boolean includePublished) {

        Criteria criteria = createCriteria(type, restrictions, false);

        if(!includePublished){

            criteria.add(Restrictions.eq("taxon.publish", true));

        }

        criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));

        return (Long) criteria.uniqueResult();

    }

    @Override

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

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

        Query<Long> query =  getSession().createQuery(hql.toString(), Long.class);

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

        Long count = query.uniqueResult();

        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;

    }

    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<Object[]> query =  getSession().createQuery(hql, Object[].class);

        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<Object[]> query =  getSession().createQuery(hql, Object[].class);

        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;

    }

    @Override

    public List<TaxonNodeDto> getParentTaxonNodeDtoForRank(

            Classification classification, Rank rank, TaxonBase<?> taxonBase) {

        Taxon taxon = null;

        if (taxonBase instanceof Taxon) {

            taxon = CdmBase.deproxy(taxonBase, Taxon.class);

        }else {

            taxon = CdmBase.deproxy(((Synonym)taxonBase).getAcceptedTaxon());

        }

        TaxonNode node = null;

        if (taxon != null) {

            node = taxon.getTaxonNode(classification);

        }

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

        if (node != null) {

            String treeIndex = node.treeIndex();

            List<Integer> ancestorNodeIds = TreeIndex.NewInstance(treeIndex).parentNodeIds(false);

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

            Criteria taxonCrit = nodeCrit.createCriteria("taxon");

            Criteria nameCrit = taxonCrit.createCriteria("name");

            nodeCrit.add(Restrictions.in("id", ancestorNodeIds));

            nodeCrit.add(Restrictions.eq("classification", classification));

            nameCrit.add(Restrictions.eq("rank", rank));

            @SuppressWarnings("unchecked")

            List<TaxonNode> list = nodeCrit.list();

            for (TaxonNode rankNode : list){

                TaxonNodeDto dto = new TaxonNodeDto(rankNode);

                result.add(dto);

            }

        }

        return result;

    }

    @Override

    public List<TaxonNodeDto> getParentTaxonNodeDtoForRank(

            Classification classification, Rank rank, TaxonName name) {

    	Set<TaxonBase> taxa = name.getTaxonBases();

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

    	for (TaxonBase<?> taxonBase:taxa) {

    	    List<TaxonNodeDto> tmpList = getParentTaxonNodeDtoForRank(classification, rank, taxonBase);

    	    for (TaxonNodeDto tmpDto : tmpList){

    	        boolean exists = false; //an equal method does not yet exist for TaxonNodeDto therefore this workaround

    	        for (TaxonNodeDto dto: result){

    	            if (dto.getTreeIndex().equals(tmpDto.getTreeIndex())){

    	                exists = true;

    	            }

    	        }

    	        if (!exists){

    	            result.add(tmpDto);

    	        }

    	    }

    	}

    	return result;

    }

    @Override

    public int countSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec,

            boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {

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

        if (!overwriteExisting){

            queryStr += " AND t.secSource.citation IS NULL ";

        }

        return countResult(queryStr);

    }

    private int countResult(String queryStr) {

        Query<Long> query = getSession().createQuery(queryStr, Long.class);

        return query.uniqueResult().intValue();

    }

    @Override

    public int countSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec,

            boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {

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

        if (!overwriteExisting){

            queryStr += " AND syn.secSource.citation IS NULL ";

        }

        return countResult(queryStr);

    }

    @Override

    public int countSecundumForSubtreeRelations(TreeIndex subTreeIndex, Reference newSec,

            boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {

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

        return countResult(queryStr);

    }

    //#3465

    @Override

    public Set<CdmBase> 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 = forSubtreeAcceptedQueryStr(includeSharedTaxa, subTreeIndex, false, SelectMode.ID);

        if (!overwriteExisting){

            queryStr += " AND t.secSource.citation IS NULL ";

        }

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

    }

    @Override

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

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

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

        if (!overwriteExisting){

            queryStr += " AND syn.secSource.citation IS NULL ";

        }

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

    }

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

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

        Query<Integer> query = getSession().createQuery(queryStr, Integer.class);

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

        for (List<Integer> taxonIdList : partitionList){

            @SuppressWarnings({ "unchecked", "rawtypes" })

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

            for (T taxonBase : taxonList){

                if (taxonBase != null){

                    taxonBase = CdmBase.deproxy(taxonBase);

                    SecundumSource secSourceBefore = taxonBase.getSecSource();

                    Reference refBefore = taxonBase.getSec();

                    String refDetailBefore = taxonBase.getSecMicroReference();

                    if (newSec == null && taxonBase.getSec() !=null

                            || newSec != null && (taxonBase.getSec() == null || !newSec.equals(taxonBase.getSec()) )){

                        taxonBase.setSec(newSec);

                    }

                    if (emptyDetail){

                        if (taxonBase.getSecMicroReference() != null){

                            taxonBase.setSecMicroReference(null);

                        }

                    }

                    //compute updated objects

                    SecundumSource secSourceAfter = taxonBase.getSecSource();

                    if (!CdmUtils.nullSafeEqual(secSourceBefore, secSourceAfter)){

                        result.add(taxonBase);