EDIT

// $Id$

/**

* 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.api.service;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Collection;

import java.util.Collections;

import java.util.Comparator;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.TreeMap;

import java.util.UUID;

import org.apache.commons.collections.CollectionUtils;

import org.apache.log4j.Logger;

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

import org.springframework.stereotype.Service;

import org.springframework.transaction.annotation.Transactional;

import eu.etaxonomy.cdm.api.service.config.CreateHierarchyForClassificationConfigurator;

import eu.etaxonomy.cdm.api.service.config.NodeDeletionConfigurator.ChildHandling;

import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;

import eu.etaxonomy.cdm.api.service.dto.EntityDTO;

import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;

import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.api.service.pager.PagerUtils;

import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;

import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;

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

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

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

import eu.etaxonomy.cdm.model.description.DescriptionElementBase;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

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

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

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

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

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

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

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

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

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

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.persistence.dao.initializer.IBeanInitializer;

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.ClassificationLookupDTO;

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

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

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

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

import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;

import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;

/**

 * @author n.hoffmann

 * @created Sep 21, 2009

 */

@Service

@Transactional(readOnly = true)

public class ClassificationServiceImpl extends IdentifiableServiceBase<Classification, IClassificationDao>

    implements IClassificationService {

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

    @Autowired

    private ITaxonNodeDao taxonNodeDao;

    @Autowired

    private ITaxonDao taxonDao;

    @Autowired

    private ITaxonNodeService taxonNodeService;

    @Autowired

    private IBeanInitializer defaultBeanInitializer;

    @Override

    @Autowired

    protected void setDao(IClassificationDao dao) {

        this.dao = dao;

    }

    private Comparator<? super TaxonNode> taxonNodeComparator;

    @Autowired

    public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){

        this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;

    }

    @Override

    public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths){

        Classification tree = dao.load(classificationUuid);

        TaxonNode node = tree.getNode(taxon);

        return loadTaxonNode(node.getUuid(), propertyPaths);

    }

    @Override

    @Deprecated // use loadTaxonNode(UUID, List<String>) instead

    public TaxonNode loadTaxonNode(TaxonNode taxonNode, List<String> propertyPaths){

        return taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);

    }

    public TaxonNode loadTaxonNode(UUID taxonNodeUuid, List<String> propertyPaths){

        return taxonNodeDao.load(taxonNodeUuid, propertyPaths);

    }

    @Override

    public List<TaxonNode> listRankSpecificRootNodes(Classification classification, Rank rank, Integer pageSize,

            Integer pageIndex, List<String> propertyPaths) {

        return pageRankSpecificRootNodes(classification, rank, pageSize, pageIndex, propertyPaths).getRecords();

    }

    @Override

    public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank, Integer pageSize,

            Integer pageIndex, List<String> propertyPaths) {

        long[] numberOfResults = dao.countRankSpecificRootNodes(classification, rank);

        long totalNumberOfResults = numberOfResults[0] + (numberOfResults.length > 1 ? numberOfResults[1] : 0);

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

        if (AbstractPagerImpl.hasResultsInRange(totalNumberOfResults, pageIndex, pageSize)) { // no point checking again

            Integer limit = PagerUtils.limitFor(pageSize);

            Integer start = PagerUtils.startFor(pageSize, pageIndex);

            Integer remainingLimit = limit;

            int[] queryIndexes = rank == null ? new int[]{0} : new int[]{0,1};

            for(int queryIndex: queryIndexes) {

                if(start != null && start > numberOfResults[queryIndex]) {

                    // start in next query with new start value

                    start = start - (int)numberOfResults[queryIndex];

                    continue;

                }

                List<TaxonNode> perQueryResults = dao.listRankSpecificRootNodes(classification, rank, remainingLimit, start, propertyPaths, queryIndex);

                results.addAll(perQueryResults);

                if(remainingLimit != null ){

                    remainingLimit = remainingLimit - results.size();

                    if(remainingLimit <= 0) {

                        // no need to run further queries if first query returned enough items!

                        break;

                    }

                    // start at with fist item of next query to fetch the remaining items

                    start = 0;

                }

            }

        }

//        long start_t = System.currentTimeMillis();

        Collections.sort(results, taxonNodeComparator); // TODO is ordering during the hibernate query in the dao possible?

//        System.err.println("service.pageRankSpecificRootNodes() - Collections.sort(results,  taxonNodeComparator) " + (System.currentTimeMillis() - start_t));

        return new DefaultPagerImpl<TaxonNode>(pageIndex, (int) totalNumberOfResults, pageSize, results);

    }

    /**

     * @implements {@link IClassificationService#loadTreeBranch(TaxonNode, Rank, List)

     * @see eu.etaxonomy.cdm.api.service.ITaxonService#loadTreeBranchTo(eu.etaxonomy.cdm.model.taxon.TaxonNode, eu.etaxonomy.cdm.model.name.Rank, java.util.List)

     * FIXME Candidate for harmonization

     * move to classification service

     */

    @Override

    public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, List<String> propertyPaths){

        TaxonNode thisNode = taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);

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

        pathToRoot.add(thisNode);

        while(!thisNode.isTopmostNode()){

            //TODO why do we need to deproxy here?

            //     without this thisNode.getParent() will return NULL in

            //     some cases (environment dependend?) even if the parent exits

            TaxonNode parentNode = CdmBase.deproxy(thisNode, TaxonNode.class).getParent();

            if(parentNode == null){

                throw new NullPointerException("taxonNode " + thisNode + " must have a parent since it is not top most");

            }

            if(parentNode.getTaxon() == null){

                throw new NullPointerException("The taxon associated with taxonNode " + parentNode + " is NULL");

            }

            if(parentNode.getTaxon().getName() == null){

                throw new NullPointerException("The name of the taxon associated with taxonNode " + parentNode + " is NULL");

            }

            Rank parentNodeRank = parentNode.getTaxon().getName() == null ? null : parentNode.getTaxon().getName().getRank();

            // stop if the next parent is higher than the baseRank

            if(baseRank != null && parentNodeRank != null && baseRank.isLower(parentNodeRank)){

                break;

            }

            pathToRoot.add(parentNode);

            thisNode = parentNode;

        }

        // initialize and invert order of nodes in list

        defaultBeanInitializer.initializeAll(pathToRoot, propertyPaths);

        Collections.reverse(pathToRoot);

        return pathToRoot;

    }

    @Override

    public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank, List<String> propertyPaths){

        Classification tree = dao.load(classification.getUuid());

        taxon = (Taxon) taxonDao.load(taxon.getUuid());

        TaxonNode node = tree.getNode(taxon);

        if(node == null){

            logger.warn("The specified taxon is not found in the given tree.");

            return null;

        }

        return loadTreeBranch(node, baseRank, propertyPaths);

    }

    @Override

    public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,

            List<String> propertyPaths) {

        taxonNode = taxonNodeDao.load(taxonNode.getUuid());

        List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());

        defaultBeanInitializer.initializeAll(childNodes, propertyPaths);

        Collections.sort(childNodes, taxonNodeComparator);

        return childNodes;

    }

    @Override

    public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,

            Integer pageIndex, List<String> propertyPaths){

        Classification classification = dao.load(classificationUuid);

        Taxon taxon = (Taxon) taxonDao.load(taxonUuid);

        List<TaxonNode> results = dao.listChildrenOf(taxon, classification, pageSize, pageIndex, propertyPaths);

        Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao

        return results;

    }

    @Override

    public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,

            Integer pageIndex, List<String> propertyPaths){

        Classification classification = dao.load(classificationUuid);

        Taxon taxon = (Taxon) taxonDao.load(taxonUuid);

        long numberOfResults = dao.countSiblingsOf(taxon, classification);

        List<TaxonNode> results;

        if(PagerUtils.hasResultsInRange(numberOfResults, pageIndex, pageSize)) {

            results = dao.listSiblingsOf(taxon, classification, pageSize, pageIndex, propertyPaths);

            Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao

        } else {

            results = new ArrayList<>();

        }

        return new DefaultPagerImpl<TaxonNode>(pageIndex, numberOfResults, pageSize, results);

    }

    @Override

    public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,

            Integer pageIndex, List<String> propertyPaths){

        Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, pageSize, pageIndex, propertyPaths);

        return pager.getRecords();

    }

    @Override

    public TaxonNode getTaxonNodeByUuid(UUID uuid) {

        return taxonNodeDao.findByUuid(uuid);

    }

    @Override

    public ITaxonTreeNode getTreeNodeByUuid(UUID uuid){

        ITaxonTreeNode treeNode = taxonNodeDao.findByUuid(uuid);

        if(treeNode == null){

            treeNode = dao.findByUuid(uuid);

        }

        return treeNode;

    }

    @Override

    public TaxonNode getRootNode(UUID classificationUuid){

        return dao.getRootNode(classificationUuid);

    }

    @Override

    public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        return dao.list(limit, start, orderHints, propertyPaths);

    }

    @Override

    public UUID removeTaxonNode(TaxonNode taxonNode) {

        return taxonNodeDao.delete(taxonNode);

    }

    @Override

    public UUID removeTreeNode(ITaxonTreeNode treeNode) {

        if(treeNode instanceof Classification){

            return dao.delete((Classification) treeNode);

        }else if(treeNode instanceof TaxonNode){

            return taxonNodeDao.delete((TaxonNode)treeNode);

        }

        return null;

    }

    @Override

    public UUID saveTaxonNode(TaxonNode taxonNode) {

        return taxonNodeDao.save(taxonNode).getUuid();

    }

    @Override

    public Map<UUID, TaxonNode> saveTaxonNodeAll(

            Collection<TaxonNode> taxonNodeCollection) {

        return taxonNodeDao.saveAll(taxonNodeCollection);

    }

    @Override

    public UUID saveTreeNode(ITaxonTreeNode treeNode) {

        if(treeNode instanceof Classification){

            return dao.save((Classification) treeNode).getUuid();

        }else if(treeNode instanceof TaxonNode){

            return taxonNodeDao.save((TaxonNode)treeNode).getUuid();

        }

        return null;

    }

    @Override

    public List<TaxonNode> getAllNodes(){

        return taxonNodeDao.list(null,null);

    }

    @Override

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

        return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid),  limit, pattern);

    }

    @Override

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

        return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification,  limit, pattern);

    }

    @Override

    public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid ) {

        return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null);

    }

    @Override

    public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification ) {

        return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null);

    }

    @Override

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

        return dao.getUuidAndTitleCache(limit, pattern);

    }

    @Override

    public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(

            TaxonNode taxonNode, List<String> propertyPaths, int size,

            int height, int widthOrDuration, String[] mimeTypes) {

        TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<UUID, List<MediaRepresentation>>();

        List<Media> taxonMedia = new ArrayList<Media>();

        List<MediaRepresentation> mediaRepresentations = new ArrayList<MediaRepresentation>();

        //add all media of the children to the result map

        if (taxonNode != null){

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

            nodes.add(loadTaxonNode(taxonNode, propertyPaths));

            nodes.addAll(loadChildNodesOfTaxonNode(taxonNode, propertyPaths));

            if (nodes != null){

                for(TaxonNode node : nodes){

                    Taxon taxon = node.getTaxon();

                    for (TaxonDescription taxonDescription: taxon.getDescriptions()){

                        for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){

                            for(Media media : descriptionElement.getMedia()){

                                taxonMedia.add(media);

                                //find the best matching representation

                                mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes));

                            }

                        }

                    }

                    result.put(taxon.getUuid(), mediaRepresentations);

                }

            }

        }

        return result;

    }

    @Override

    public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(Taxon taxon, Classification taxTree, List<String> propertyPaths, int size, int height, int widthOrDuration, String[] mimeTypes){

        TaxonNode node = taxTree.getNode(taxon);

        return getAllMediaForChildNodes(node, propertyPaths, size, height, widthOrDuration, mimeTypes);

    }

    @Override

    @Transactional(readOnly = false)

    public void updateTitleCache(Class<? extends Classification> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<Classification> cacheStrategy, IProgressMonitor monitor) {

        if (clazz == null){

            clazz = Classification.class;

        }

        super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);

    }

    /**

     *

     * @param allNodesOfClassification

     * @return null - if  allNodesOfClassification is empty <br>

     */

    private Map<String, List<TaxonNode>> getSortedGenusList(Collection<TaxonNode> allNodesOfClassification){

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

    		return null;

    	}

    	Map<String, List<TaxonNode>> sortedGenusMap = new HashMap<String, List<TaxonNode>>();

    	for(TaxonNode node:allNodesOfClassification){

    		final TaxonNode tn = node;

    		Taxon taxon = node.getTaxon();

    		NonViralName name = CdmBase.deproxy(taxon.getName(), NonViralName.class);

    		String genusOrUninomial = name.getGenusOrUninomial();

    		//if rank unknown split string and take first word

    		if(genusOrUninomial == null){

    			String titleCache = taxon.getTitleCache();

    			String[] split = titleCache.split("\\s+");

    			for(String s:split){

    				genusOrUninomial = s;

    				break;

    			}

    		}

    		//if node has children

    		//retrieve list from map if not create List

    		if(sortedGenusMap.containsKey(genusOrUninomial)){

    			List<TaxonNode> list = sortedGenusMap.get(genusOrUninomial);

    			list.add(node);

    			sortedGenusMap.put(genusOrUninomial, list);

    		}else{

    			//create List for genus

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

    			list.add(node);

    			sortedGenusMap.put(genusOrUninomial, list);

    		}

    	}

    	return sortedGenusMap;

    }

    /**

     *

     * creates new Classification and parent TaxonNodes at genus level

     *

     *

     * @param map GenusMap which holds a name (Genus) and all the same Taxa as a list

     * @param classification you want to improve the hierarchy (will not be modified)

     * @param configurator to change certain settings, if null then standard settings will be taken

     * @return new classification with parentNodes for each entry in the map

     */

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

	@Transactional(readOnly = false)

	@Override

    public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator){

        UpdateResult result = new UpdateResult();

    	classification = dao.findByUuid(classification.getUuid());

    	Map<String, List<TaxonNode>> map = getSortedGenusList(classification.getAllNodes());

    	final String APPENDIX = "repaired";

    	String titleCache = org.apache.commons.lang.StringUtils.isBlank(classification.getTitleCache()) ? " " : classification.getTitleCache() ;

    	//TODO classification clone???

    	Classification newClassification = Classification.NewInstance(titleCache +" "+ APPENDIX);

    	newClassification.setReference(classification.getReference());

    	for(Map.Entry<String, List<TaxonNode>> entry:map.entrySet()){

    		String genus = entry.getKey();

    		List<TaxonNode> listOfTaxonNodes = entry.getValue();

    		TaxonNode parentNode = null;

    		//Search for genus in list

    		for(TaxonNode tNode:listOfTaxonNodes){

    			//take that taxonNode as parent and remove from list with all it possible children

    			//FIXME NPE for name

    			TaxonNameBase name = tNode.getTaxon().getName();

				NonViralName nonViralName = CdmBase.deproxy(name, NonViralName.class);

    			if(nonViralName.getNameCache().equalsIgnoreCase(genus)){

    				TaxonNode clone = (TaxonNode) tNode.clone();

    				if(!tNode.hasChildNodes()){

    					//FIXME remove classification

//    					parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());

    					parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());

    					//remove taxonNode from list because just added to classification

    					result.addUpdatedObject(tNode);

    					listOfTaxonNodes.remove(tNode);

    				}else{

    					//get all childNodes

    					//save prior Hierarchy and remove them from the list

    					List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tNode, clone, result);

//    					parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());

      					//FIXME remove classification

    					parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());

    					//remove taxonNode from list because just added to classification

    					result.addUpdatedObject(tNode);

    					listOfTaxonNodes.remove(tNode);

    					if(copyAllChildrenToTaxonNode != null){

    						listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);

    					}

    				}

    				break;

    			}

    		}

    		if(parentNode == null){

    			//if no match found in list, create parentNode

    			NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();

    			NonViralName nonViralName = parser.parseFullName(genus);

    			TaxonNameBase taxonNameBase = nonViralName;

    			//TODO Sec via configurator

    			Taxon taxon = Taxon.NewInstance(taxonNameBase, null);

    			parentNode = newClassification.addChildTaxon(taxon, 0, null, null);

    			result.addUpdatedObject(parentNode);

    		}

    		//iterate over the rest of the list

    		for(TaxonNode tn : listOfTaxonNodes){

    			//if TaxonNode has a parent and this is not the classification then skip it

    			//and add to new classification via the parentNode as children of it

    			//this should assures to keep the already existing hierarchy

    			//FIXME: Assert is not rootnode --> entrypoint is not classification in future but rather rootNode

    			if(!tn.isTopmostNode()){

    				continue; //skip to next taxonNode

    			}

    			TaxonNode clone = (TaxonNode) tn.clone();

    			//FIXME: citation from node

    			//TODO: addchildNode without citation and references

//    			TaxonNode taxonNode = parentNode.addChildNode(clone, classification.getCitation(), classification.getMicroReference());

    			TaxonNode taxonNode = parentNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());

    			result.addUnChangedObject(clone);

    			if(tn.hasChildNodes()){

    				//save hierarchy in new classification

    				List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tn, taxonNode, result);

    				if(copyAllChildrenToTaxonNode != null){

    					listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);

    				}

    			}

    		}

    	}

    	dao.saveOrUpdate(newClassification);

    	result.setCdmEntity(newClassification);

    	return result;

    }

    /**

     *

     * recursive method to get all childnodes of taxonNode in classification.

     *

     * @param classification just for References and Citation, can be null

     * @param copyFromNode TaxonNode with Children

     * @param copyToNode TaxonNode which will receive the children

     * @return List of ChildNode which has been added. If node has no children returns null

     */

   private List<TaxonNode> copyAllChildrenToTaxonNode(TaxonNode copyFromNode, TaxonNode copyToNode, UpdateResult result) {

		List<TaxonNode> childNodes;

		if(!copyFromNode.hasChildNodes()){

			return null;

		}else{

			childNodes = copyFromNode.getChildNodes();

		}

		for(TaxonNode childNode:childNodes){

			TaxonNode clone = (TaxonNode) childNode.clone();

			result.addUnChangedObject(clone);

			if(childNode.hasChildNodes()){

				copyAllChildrenToTaxonNode(childNode, clone, result);

			}

			//FIXME: citation from node instead of classification

//			copyToNode.addChildNode(clone,classification.getCitation(), classification.getMicroReference());

			copyToNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());

		}

		return childNodes;

	}

    /**

     * {@inheritDoc}

     */

    @Override

    public ClassificationLookupDTO classificationLookup(Classification classification) {

        return dao.classificationLookup(classification);

    }

    @Override

    public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config){

        DeleteResult result = new DeleteResult();

        Classification classification = dao.findByUuid(classificationUuid);

        if (classification == null){

            result.addException(new IllegalArgumentException("The classification does not exist in database."));

            result.setAbort();

            return result;

        }

        if (!classification.hasChildNodes()){

            dao.delete(classification);

        }

        if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE) ){

            TaxonNode root = classification.getRootNode();

            taxonNodeDao.delete(root, true);

            dao.delete(classification);

        }

        return result;

    }

    @Override

    public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> originalTaxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank){

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

        //get treeindex for each taxonUUID

        Map<UUID, String> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);

        //build treeindex list (or tree)

        List<String> treeIndexClosure = new ArrayList<>();

        for (String treeIndex : taxonIdTreeIndexMap.values()){

            String[] splits = treeIndex.substring(1).split(ITreeNode.separator);

            String currentIndex = ITreeNode.separator;

            for (String split : splits){

                if (split.equals("")){

                    continue;

                }

                currentIndex += split + ITreeNode.separator;

                if (!treeIndexClosure.contains(currentIndex) && !split.startsWith(ITreeNode.treePrefix)){

                    treeIndexClosure.add(currentIndex);

                }

            }

        }

        //get rank sortindex for all parent taxa with sortindex <= minRank and sortIndex >= maxRank (if available)

        Integer minRankOrderIndex = minRank == null ? null : minRank.getOrderIndex();

        Integer maxRankOrderIndex = maxRank == null ? null : maxRank.getOrderIndex();

        Map<String, Integer> treeIndexSortIndexMapTmp = taxonNodeDao.rankOrderIndexForTreeIndex(treeIndexClosure, minRankOrderIndex, maxRankOrderIndex);

        //remove all treeindex with "exists child in above map(and child.sortindex > xxx)

        List<String> treeIndexList = new ArrayList<>(treeIndexSortIndexMapTmp.keySet());

        Collections.sort(treeIndexList, new TreeIndexComparator());

        Map<String, Integer> treeIndexSortIndexMap = new HashMap<>();

        String lastTreeIndex = null;

        for (String treeIndex : treeIndexList){

            if (lastTreeIndex != null && treeIndex.startsWith(lastTreeIndex)){

                treeIndexSortIndexMap.remove(lastTreeIndex);

            }

            treeIndexSortIndexMap.put(treeIndex, treeIndexSortIndexMapTmp.get(treeIndex));

            lastTreeIndex = treeIndex;

        }

        //get taxonID for treeIndexes

        Map<String, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(treeIndexSortIndexMap.keySet());

        //fill result list

        for (UUID originalTaxonUuid : originalTaxonUuids){

            GroupedTaxonDTO item = new GroupedTaxonDTO();

            result.add(item);

            item.setTaxonUuid(originalTaxonUuid);

            String groupIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);

            while (groupIndex != null){

                if (treeIndexTaxonIdMap.get(groupIndex) != null){

                    UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupIndex);

                    item.setGroupTaxonUuid(uuidAndLabel.getUuid());

                    item.setGroupTaxonName(uuidAndLabel.getTitleCache());

                    break;

                }else{

                    int index = groupIndex.substring(0, groupIndex.length()-1).lastIndexOf(ITreeNode.separator);

                    groupIndex = index<0 ? null : groupIndex.substring(0, index+1);

                }

            }

        }

        return result;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid) {

        Map<UUID, UUID> map = dao.getTaxonNodeUuidByTaxonUuid(classificationUuid, Arrays.asList(taxonUuid));

        UUID taxonNodeUuid = map.get(taxonUuid);

        return taxonNodeUuid;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonUuid,

            Boolean doChildren, Boolean doSynonyms, List<UUID> ancestorMarkers,

            NodeSortMode sortMode) {

        TaxonInContextDTO result = new TaxonInContextDTO();

        TaxonBase<?> taxonBase = taxonDao.load(taxonUuid);

        TaxonNameBase<?,?> name = taxonBase.getName();

        result.setNameUuid(name.getUuid());

        result.setNameLabel(name.getTitleCache());

        if (name.isInstanceOf(NonViralName.class)){

            NonViralName<?> nvn = CdmBase.deproxy(name, NonViralName.class);

            result.setNameWithoutAuthor(nvn.getNameCache());

            result.setGenusOrUninomial(nvn.getGenusOrUninomial());

            result.setInfraGenericEpithet(nvn.getInfraGenericEpithet());

            result.setSpeciesEpithet(nvn.getSpecificEpithet());

            result.setInfraSpecificEpithet(nvn.getInfraSpecificEpithet());

            result.setAuthorship(nvn.getAuthorshipCache());

            Rank rank = name.getRank();

            if (rank != null){

                result.setRankUuid(rank.getUuid());

                result.setRankLabel(rank.getTitleCache());

            }

        }

        UUID taxonNodeUuid = getTaxonNodeUuidByTaxonUuid(classificationUuid, taxonUuid);

        result.setTaxonNodeUuid(taxonNodeUuid);

        boolean recursive = false;

        int pageSize = Integer.MAX_VALUE;

        int pageIndex = 0;

        Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, doSynonyms, sortMode, pageSize, pageIndex);

        //children

        for (TaxonNodeDto childDto : children.getRecords()){

            if (doChildren && childDto.getStatus().equals(TaxonStatus.Accepted)){

                EntityDTO<Taxon> child = new EntityDTO<Taxon>(childDto.getTaxonUuid(), childDto.getTitleCache());

                result.addChild(child);

            }else if (doSynonyms && childDto.getStatus().isSynonym()){

                EntityDTO<Synonym> child = new EntityDTO<Synonym>(childDto.getTaxonUuid(), childDto.getTitleCache());

                result.addSynonym(child);

            }

        }

        //marked ancestors

        return result;

    }

}