cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ClassificationServiceImpl.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.api.service;
  11
  12 import java.util.ArrayList;
  13 import java.util.Arrays;
  14 import java.util.Collection;
  15 import java.util.Collections;
  16 import java.util.Comparator;
  17 import java.util.HashMap;
  18 import java.util.HashSet;
  19 import java.util.List;
  20 import java.util.Map;
  21 import java.util.Set;
  22 import java.util.TreeMap;
  23 import java.util.UUID;
  24 import java.util.stream.Collectors;
  25
  26 import javax.persistence.EntityNotFoundException;
  27
  28 import org.apache.commons.collections.CollectionUtils;
  29 import org.apache.commons.lang.StringUtils;
  30 import org.apache.log4j.Logger;
  31 import org.springframework.beans.factory.annotation.Autowired;
  32 import org.springframework.stereotype.Service;
  33 import org.springframework.transaction.annotation.Transactional;
  34
  35 import eu.etaxonomy.cdm.api.service.config.CreateHierarchyForClassificationConfigurator;
  36 import eu.etaxonomy.cdm.api.service.config.NodeDeletionConfigurator.ChildHandling;
  37 import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
  38 import eu.etaxonomy.cdm.api.service.dto.EntityDTO;
  39 import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
  40 import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
  41 import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
  42 import eu.etaxonomy.cdm.api.service.pager.Pager;
  43 import eu.etaxonomy.cdm.api.service.pager.PagerUtils;
  44 import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;
  45 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  46 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  47 import eu.etaxonomy.cdm.compare.taxon.ITaxonNodeComparator;
  48 import eu.etaxonomy.cdm.compare.taxon.TaxonNodeSortMode;
  49 import eu.etaxonomy.cdm.exception.FilterException;
  50 import eu.etaxonomy.cdm.exception.UnpublishedException;
  51 import eu.etaxonomy.cdm.model.common.CdmBase;
  52 import eu.etaxonomy.cdm.model.common.ITreeNode;
  53 import eu.etaxonomy.cdm.model.common.MarkerType;
  54 import eu.etaxonomy.cdm.model.common.TreeIndex;
  55 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  56 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  57 import eu.etaxonomy.cdm.model.media.Media;
  58 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  59 import eu.etaxonomy.cdm.model.media.MediaUtils;
  60 import eu.etaxonomy.cdm.model.name.INonViralName;
  61 import eu.etaxonomy.cdm.model.name.Rank;
  62 import eu.etaxonomy.cdm.model.name.TaxonName;
  63 import eu.etaxonomy.cdm.model.taxon.Classification;
  64 import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
  65 import eu.etaxonomy.cdm.model.taxon.Synonym;
  66 import eu.etaxonomy.cdm.model.taxon.Taxon;
  67 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  68 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  69 import eu.etaxonomy.cdm.model.term.DefinedTermBase;
  70 import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
  71 import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
  72 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
  73 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
  74 import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;
  75 import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
  76 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
  77 import eu.etaxonomy.cdm.persistence.dto.TaxonStatus;
  78 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  79 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  80 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  81 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  82
  83 /**
  84  * @author n.hoffmann
  85  * @since Sep 21, 2009
  86  */
  87 @Service
  88 @Transactional(readOnly = true)
  89 public class ClassificationServiceImpl
  90              extends IdentifiableServiceBase<Classification, IClassificationDao>
  91              implements IClassificationService {
  92
  93     private static final Logger logger = Logger.getLogger(ClassificationServiceImpl.class);
  94
  95     @Autowired
  96     private ITaxonNodeDao taxonNodeDao;
  97
  98     @Autowired
  99     private ITaxonDao taxonDao;
 100
 101     @Autowired
 102     private ITaxonNodeService taxonNodeService;
 103
 104     @Autowired
 105     private IDefinedTermDao termDao;
 106
 107     @Autowired
 108     private IBeanInitializer defaultBeanInitializer;
 109
 110     @Override
 111     @Autowired
 112     protected void setDao(IClassificationDao dao) {
 113         this.dao = dao;
 114     }
 115
 116     private Comparator<? super TaxonNode> taxonNodeComparator;
 117
 118     @Autowired
 119     public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){
 120         this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;
 121     }
 122
 123     @Override
 124     public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths){
 125         Classification tree = dao.load(classificationUuid);
 126         TaxonNode node = tree.getNode(taxon);
 127
 128         return loadTaxonNode(node.getUuid(), propertyPaths);
 129     }
 130
 131     public TaxonNode loadTaxonNode(UUID taxonNodeUuid, List<String> propertyPaths){
 132         return taxonNodeDao.load(taxonNodeUuid, propertyPaths);
 133     }
 134
 135     @Override
 136     public List<TaxonNode> listRankSpecificRootNodes(Classification classification,
 137             TaxonNode subtree, Rank rank,
 138             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
 139         return pageRankSpecificRootNodes(classification, subtree, rank, includeUnpublished, pageSize, pageIndex, propertyPaths).getRecords();
 140     }
 141
 142     @Override
 143     public List<TaxonNodeDto> listRankSpecificRootNodeDtos(Classification classification, TaxonNode subtree,
 144             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode,
 145             List<String> propertyPaths) {
 146         List<TaxonNode> list = listRankSpecificRootNodes(classification, subtree, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
 147         return list.stream().filter(e ->  e != null).map(e -> new TaxonNodeDto(e)).sorted(sortMode.newComparator()).collect(Collectors.toList());
 148     }
 149
 150     @Override
 151     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank,
 152             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
 153         return pageRankSpecificRootNodes(classification, null, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
 154     }
 155
 156     @Override
 157     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree, Rank rank,
 158             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
 159         long[] numberOfResults = dao.countRankSpecificRootNodes(classification, subtree, includeUnpublished, rank);
 160         long totalNumberOfResults = numberOfResults[0] + (numberOfResults.length > 1 ? numberOfResults[1] : 0);
 161
 162         List<TaxonNode> results = new ArrayList<>();
 163
 164         if (AbstractPagerImpl.hasResultsInRange(totalNumberOfResults, pageIndex, pageSize)) { // no point checking again
 165             Integer limit = PagerUtils.limitFor(pageSize);
 166             Integer start = PagerUtils.startFor(pageSize, pageIndex);
 167
 168             Integer remainingLimit = limit;
 169             int[] queryIndexes = rank == null ? new int[]{0} : new int[]{0,1};
 170
 171             for(int queryIndex: queryIndexes) {
 172                 if(start != null && start > numberOfResults[queryIndex]) {
 173                     // start in next query with new start value
 174                     start = start - (int)numberOfResults[queryIndex];
 175                     continue;
 176                 }
 177
 178                 List<TaxonNode> perQueryResults = dao.listRankSpecificRootNodes(classification,
 179                         subtree, rank, includeUnpublished, remainingLimit,
 180                         start, propertyPaths, queryIndex);
 181                 results.addAll(perQueryResults);
 182                 if(remainingLimit != null ){
 183                     remainingLimit = remainingLimit - results.size();
 184                     if(remainingLimit <= 0) {
 185                         // no need to run further queries if first query returned enough items!
 186                         break;
 187                     }
 188                     // start at with fist item of next query to fetch the remaining items
 189                     start = 0;
 190                 }
 191             }
 192         }
 193 //        long start_t = System.currentTimeMillis();
 194         Collections.sort(results, taxonNodeComparator); // TODO is ordering during the hibernate query in the dao possible?
 195 //        System.err.println("service.pageRankSpecificRootNodes() - Collections.sort(results,  taxonNodeComparator) " + (System.currentTimeMillis() - start_t));
 196         return new DefaultPagerImpl<>(pageIndex, totalNumberOfResults, pageSize, results);
 197
 198     }
 199
 200     @Override
 201     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank,
 202             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 203         return loadTreeBranch(taxonNode, null, baseRank, includeUnpublished, propertyPaths);
 204     }
 205
 206     @Override
 207     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank,
 208             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 209
 210         TaxonNode thisNode = taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
 211         if(baseRank != null){
 212             baseRank = (Rank) termDao.load(baseRank.getUuid());
 213         }
 214         if (!includeUnpublished && thisNode.getTaxon() != null && !thisNode.getTaxon().isPublish()){
 215             throw new UnpublishedException("Final taxon in tree branch is unpublished.");
 216         }
 217
 218         List<TaxonNode> pathToRoot = new ArrayList<>();
 219         pathToRoot.add(thisNode);
 220
 221         while(!thisNode.isTopmostNode()){
 222             //TODO why do we need to deproxy here?
 223             //     without this thisNode.getParent() will return NULL in
 224             //     some cases (environment dependend?) even if the parent exits
 225             TaxonNode parentNode = CdmBase.deproxy(thisNode).getParent();
 226
 227             if(parentNode == null){
 228                 throw new NullPointerException("Taxon node " + thisNode + " must have a parent since it is not top most");
 229             }
 230             if(parentNode.getTaxon() == null){
 231                 throw new NullPointerException("The taxon associated with taxon node " + parentNode + " is NULL");
 232             }
 233             if(!includeUnpublished && !parentNode.getTaxon().isPublish()){
 234                 throw new UnpublishedException("Some taxon in tree branch is unpublished.");
 235             }
 236             if(parentNode.getTaxon().getName() == null){
 237                 throw new NullPointerException("The name of the taxon associated with taxonNode " + parentNode + " is NULL");
 238             }
 239
 240             Rank parentNodeRank = (parentNode.getTaxon().getName() == null) ? null : parentNode.getTaxon().getName().getRank();
 241             // stop if the next parent is higher than the baseRank
 242             if(baseRank != null && parentNodeRank != null && baseRank.isLower(parentNodeRank)){
 243                 break;
 244             }
 245             if((subtree!= null && !subtree.isAncestor(parentNode) )){
 246                 break;
 247             }
 248
 249             pathToRoot.add(parentNode);
 250             thisNode = parentNode;
 251         }
 252
 253         // initialize and invert order of nodes in list
 254         defaultBeanInitializer.initializeAll(pathToRoot, propertyPaths);
 255         Collections.reverse(pathToRoot);
 256
 257         return pathToRoot;
 258     }
 259
 260     @Override
 261     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank,
 262             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 263         return loadTreeBranchToTaxon(taxon, classification, null, baseRank, includeUnpublished, propertyPaths);
 264     }
 265
 266     @Override
 267     public List<TaxonNodeDto> loadTreeBranchDTOsToTaxon(Taxon taxon, Classification classification,
 268             TaxonNode subtree, Rank baseRank,
 269             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException {
 270         List<TaxonNode> list = loadTreeBranchToTaxon(taxon, classification, subtree, baseRank, includeUnpublished, propertyPaths);
 271         return list.stream().map(e -> new TaxonNodeDto(e)).collect(Collectors.toList());
 272     }
 273
 274     @Override
 275     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 276             TaxonNode subtree, Rank baseRank,
 277             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 278
 279         UUID nodeUuid = getTaxonNodeUuidByTaxonUuid(classification.getUuid(), taxon.getUuid());
 280         TaxonNode node = taxonNodeService.find(nodeUuid);
 281         if(node == null){
 282             logger.warn("The specified taxon is not found in the given tree.");
 283             return null;
 284         }else if (subtree != null && !node.isDescendant(subtree)){
 285             //TODO handle as exception? E.g. FilterException, AccessDeniedException?
 286             logger.warn("The specified taxon is not found for the given subtree.");
 287             return null;
 288         }
 289
 290         return loadTreeBranch(node, subtree, baseRank, includeUnpublished, propertyPaths);
 291     }
 292
 293
 294     @Override
 295     public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
 296             List<String> propertyPaths) {
 297         taxonNode = taxonNodeDao.load(taxonNode.getUuid());
 298         List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
 299         defaultBeanInitializer.initializeAll(childNodes, propertyPaths);
 300         Collections.sort(childNodes, taxonNodeComparator);
 301         return childNodes;
 302     }
 303
 304     @Override
 305     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid,
 306             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 307         try {
 308             return listChildNodesOfTaxon(taxonUuid, classificationUuid, null, includeUnpublished, pageSize, pageIndex, propertyPaths);
 309         } catch (FilterException e) {
 310             throw new RuntimeException(e);  //this should not happen as filter is null
 311         }
 312     }
 313
 314     @Override
 315     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid,
 316             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException{
 317
 318         Classification classification = dao.load(classificationUuid);
 319         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 320         TaxonNode subtree = taxonNodeDao.load(subtreeUuid);
 321         if (subtreeUuid != null && subtree == null){
 322             throw new FilterException("Taxon node for subtree filter can not be found in database", true);
 323         }
 324
 325         List<TaxonNode> results = dao.listChildrenOf(
 326                 taxon, classification, subtree, includeUnpublished, pageSize, pageIndex, propertyPaths);
 327         Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
 328         return results;
 329     }
 330
 331     @Override
 332     public List<TaxonNodeDto> listChildNodeDtosOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
 333             Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode, List<String> propertyPaths) throws FilterException{
 334         Classification classification = dao.load(classificationUuid);
 335         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 336         TaxonNode subtree = taxonNodeDao.load(subtreeUuid);
 337         if (subtreeUuid != null && subtree == null){
 338             throw new FilterException("Taxon node for subtree filter can not be found in database", true);
 339         }
 340
 341         List<TaxonNode> results = dao.listChildrenOf(
 342                 taxon, classification, subtree, includeUnpublished, pageSize, pageIndex, propertyPaths);
 343         Comparator<TaxonNodeDto> comparator = sortMode.newComparator();
 344         // TODO order during the hibernate query in the dao?
 345         List<TaxonNodeDto> dtos = results.stream().map(e -> new TaxonNodeDto(e)).sorted(comparator).collect(Collectors.toList());
 346         return dtos;
 347     }
 348
 349     @Override
 350     public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 351             Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 352
 353         Classification classification = dao.load(classificationUuid);
 354         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 355
 356         long numberOfResults = dao.countSiblingsOf(taxon, classification, includeUnpublished);
 357
 358         List<TaxonNode> results;
 359         if(PagerUtils.hasResultsInRange(numberOfResults, pageIndex, pageSize)) {
 360             results = dao.listSiblingsOf(taxon, classification, includeUnpublished, pageSize, pageIndex, propertyPaths);
 361             Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
 362         } else {
 363             results = new ArrayList<>();
 364         }
 365
 366         return new DefaultPagerImpl<>(pageIndex, numberOfResults, pageSize, results);
 367     }
 368
 369     @Override
 370     public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 371             Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 372
 373         Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, includeUnpublished, pageSize, pageIndex, propertyPaths);
 374         return pager.getRecords();
 375     }
 376
 377     @Override
 378     public ITaxonTreeNode getTreeNodeByUuid(UUID uuid){
 379         ITaxonTreeNode treeNode = taxonNodeDao.findByUuid(uuid);
 380         if(treeNode == null){
 381             treeNode = dao.findByUuid(uuid);
 382         }
 383
 384         return treeNode;
 385     }
 386
 387     @Override
 388     public TaxonNode getRootNode(UUID classificationUuid){
 389         return dao.getRootNode(classificationUuid);
 390     }
 391
 392     @Override
 393     public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
 394         return dao.list(limit, start, orderHints, propertyPaths);
 395     }
 396
 397     @Override
 398     public UUID removeTreeNode(ITaxonTreeNode treeNode) {
 399         if(treeNode instanceof Classification){
 400             return dao.delete((Classification) treeNode);
 401         }else if(treeNode instanceof TaxonNode){
 402             return taxonNodeDao.delete((TaxonNode)treeNode);
 403         }
 404         return null;
 405     }
 406
 407     @Override
 408     public Map<UUID, TaxonNode> saveTaxonNodeAll(
 409             Collection<TaxonNode> taxonNodeCollection) {
 410         return taxonNodeDao.saveAll(taxonNodeCollection);
 411     }
 412
 413     @Override
 414     public UUID saveClassification(Classification classification) {
 415
 416        taxonNodeDao.saveOrUpdateAll(classification.getAllNodes());
 417        UUID result =dao.saveOrUpdate(classification);
 418        return result;
 419     }
 420
 421     @Override
 422     public UUID saveTreeNode(ITaxonTreeNode treeNode) {
 423         if(treeNode instanceof Classification){
 424             return dao.save((Classification) treeNode).getUuid();
 425         }else if(treeNode instanceof TaxonNode){
 426             return taxonNodeDao.save((TaxonNode)treeNode).getUuid();
 427         }
 428         return null;
 429     }
 430
 431     @Override
 432     public List<TaxonNode> getAllNodes(){
 433         return taxonNodeDao.list(null,null);
 434     }
 435
 436     @Override
 437     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications, boolean includeDoubtful) {
 438         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid),  limit, pattern, searchForClassifications, includeDoubtful);
 439     }
 440
 441     @Override
 442     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,  Integer limit, String pattern, boolean searchForClassifications) {
 443         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification,  limit, pattern, searchForClassifications);
 444     }
 445
 446     @Override
 447     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, boolean searchForClassifications ) {
 448         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null, searchForClassifications);
 449     }
 450
 451     @Override
 452     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, boolean searchForClassifications ) {
 453         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null, searchForClassifications);
 454     }
 455
 456     @Override
 457     public List<UuidAndTitleCache<Classification>> getUuidAndTitleCache(Integer limit, String pattern) {
 458         return dao.getUuidAndTitleCache(limit, pattern);
 459     }
 460
 461     @Override
 462     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(
 463             TaxonNode taxonNode, List<String> propertyPaths, int size,
 464             int height, int widthOrDuration, String[] mimeTypes) {
 465
 466         TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<>();
 467         List<MediaRepresentation> mediaRepresentations = new ArrayList<>();
 468
 469         //add all media of the children to the result map
 470         if (taxonNode != null){
 471
 472             List<TaxonNode> nodes = new ArrayList<>();
 473
 474             nodes.add(loadTaxonNode(taxonNode.getUuid(), propertyPaths));
 475             nodes.addAll(loadChildNodesOfTaxonNode(taxonNode, propertyPaths));
 476
 477             for(TaxonNode node : nodes){
 478                 Taxon taxon = node.getTaxon();
 479                 for (TaxonDescription taxonDescription: taxon.getDescriptions()){
 480                     for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){
 481                         for(Media media : descriptionElement.getMedia()){
 482                             //find the best matching representation
 483                             mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes, MediaUtils.MissingValueStrategy.MAX));
 484                         }
 485                     }
 486                 }
 487                 result.put(taxon.getUuid(), mediaRepresentations);
 488             }
 489         }
 490
 491         return result;
 492     }
 493
 494     @Override
 495     @Transactional(readOnly = false)
 496     public UpdateResult updateCaches(Class<? extends Classification> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<Classification> cacheStrategy, IProgressMonitor monitor) {
 497         if (clazz == null){
 498             clazz = Classification.class;
 499         }
 500         return super.updateCachesImpl(clazz, stepSize, cacheStrategy, monitor);
 501     }
 502
 503     /**
 504      *
 505      * @param allNodesOfClassification
 506      * @return null - if  allNodesOfClassification is empty <br>
 507      */
 508
 509     private Map<String, List<TaxonNode>> getSortedGenusList(Collection<TaxonNode> allNodesOfClassification){
 510
 511         if(allNodesOfClassification == null || allNodesOfClassification.isEmpty()){
 512                 return null;
 513         }
 514         Map<String, List<TaxonNode>> sortedGenusMap = new HashMap<>();
 515         for(TaxonNode node:allNodesOfClassification){
 516                 Taxon taxon = node.getTaxon();
 517                 INonViralName name = taxon.getName();
 518                 String genusOrUninomial = name.getGenusOrUninomial();
 519                 //if rank unknown split string and take first word
 520                 if(genusOrUninomial == null){
 521                         String titleCache = taxon.getTitleCache();
 522                         String[] split = titleCache.split("\\s+");
 523                         for(String s:split){
 524                                 genusOrUninomial = s;
 525                                 break;
 526                         }
 527                 }
 528                 //if node has children
 529
 530                 //retrieve list from map if not create List
 531                 if(sortedGenusMap.containsKey(genusOrUninomial)){
 532                         List<TaxonNode> list = sortedGenusMap.get(genusOrUninomial);
 533                         list.add(node);
 534                         sortedGenusMap.put(genusOrUninomial, list);
 535                 }else{
 536                         //create List for genus
 537                         List<TaxonNode> list = new ArrayList<>();
 538                         list.add(node);
 539                         sortedGenusMap.put(genusOrUninomial, list);
 540                 }
 541         }
 542         return sortedGenusMap;
 543     }
 544
 545     /**
 546      *
 547      * creates new Classification and parent TaxonNodes at genus level
 548      *
 549      *
 550      * @param map GenusMap which holds a name (Genus) and all the same Taxa as a list
 551      * @param classification you want to improve the hierarchy (will not be modified)
 552      * @param configurator to change certain settings, if null then standard settings will be taken
 553      * @return new classification with parentNodes for each entry in the map
 554      */
 555     @SuppressWarnings({ "unchecked" })
 556         @Transactional(readOnly = false)
 557         @Override
 558     public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator){
 559         UpdateResult result = new UpdateResult();
 560         classification = dao.findByUuid(classification.getUuid());
 561         Map<String, List<TaxonNode>> map = getSortedGenusList(classification.getAllNodes());
 562
 563         final String APPENDIX = "repaired";
 564         String titleCache = StringUtils.isBlank(classification.getTitleCache()) ? " " : classification.getTitleCache() ;
 565         //TODO classification clone???
 566         Classification newClassification = Classification.NewInstance(titleCache +" "+ APPENDIX);
 567         newClassification.setReference(classification.getReference());
 568
 569         for(Map.Entry<String, List<TaxonNode>> entry:map.entrySet()){
 570                 String genus = entry.getKey();
 571                 List<TaxonNode> listOfTaxonNodes = entry.getValue();
 572                 TaxonNode parentNode = null;
 573                 //Search for genus in list
 574                 for(TaxonNode tNode:listOfTaxonNodes){
 575                         //take that taxonNode as parent and remove from list with all it possible children
 576                         //FIXME NPE for name
 577                         TaxonName name = tNode.getTaxon().getName();
 578                         if(name.getNameCache().equalsIgnoreCase(genus)){
 579                                 TaxonNode clone = tNode.clone();
 580                                 if(!tNode.hasChildNodes()){
 581                                         //FIXME remove classification
 582 //                                      parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
 583                                         parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
 584                                         //remove taxonNode from list because just added to classification
 585                                         result.addUpdatedObject(tNode);
 586                                         listOfTaxonNodes.remove(tNode);
 587                                 }else{
 588                                         //get all childNodes
 589                                         //save prior Hierarchy and remove them from the list
 590                                         List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tNode, clone, result);
 591 //                                      parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
 592                                         //FIXME remove classification
 593                                         parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
 594                                         //remove taxonNode from list because just added to classification
 595                                         result.addUpdatedObject(tNode);
 596                                         listOfTaxonNodes.remove(tNode);
 597                                         if(copyAllChildrenToTaxonNode != null){
 598                                                 listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
 599                                         }
 600                                 }
 601                                 break;
 602                         }
 603                 }
 604                 if(parentNode == null){
 605                         //if no match found in list, create parentNode
 606                         NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
 607                         TaxonName TaxonName = (TaxonName)parser.parseFullName(genus);
 608                         //TODO Sec via configurator
 609                         Taxon taxon = Taxon.NewInstance(TaxonName, null);
 610                         parentNode = newClassification.addChildTaxon(taxon, 0, null, null);
 611                         result.addUpdatedObject(parentNode);
 612                 }
 613                 //iterate over the rest of the list
 614                 for(TaxonNode tn : listOfTaxonNodes){
 615                         //if TaxonNode has a parent and this is not the classification then skip it
 616                         //and add to new classification via the parentNode as children of it
 617                         //this should assures to keep the already existing hierarchy
 618                         //FIXME: Assert is not rootnode --> entrypoint is not classification in future but rather rootNode
 619
 620                         if(!tn.isTopmostNode()){
 621                                 continue; //skip to next taxonNode
 622                         }
 623
 624                         TaxonNode clone = tn.clone();
 625                         //FIXME: citation from node
 626                         //TODO: addchildNode without citation and references
 627 //                      TaxonNode taxonNode = parentNode.addChildNode(clone, classification.getCitation(), classification.getMicroReference());
 628                         TaxonNode taxonNode = parentNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
 629                         result.addUnChangedObject(clone);
 630                         if(tn.hasChildNodes()){
 631                                 //save hierarchy in new classification
 632                                 List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tn, taxonNode, result);
 633                                 if(copyAllChildrenToTaxonNode != null){
 634                                         listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
 635                                 }
 636                         }
 637                 }
 638         }
 639         dao.saveOrUpdate(newClassification);
 640         result.setCdmEntity(newClassification);
 641         return result;
 642     }
 643
 644     /**
 645      *
 646      * recursive method to get all childnodes of taxonNode in classification.
 647      *
 648      * @param classification just for References and Citation, can be null
 649      * @param copyFromNode TaxonNode with Children
 650      * @param copyToNode TaxonNode which will receive the children
 651      * @return List of ChildNode which has been added. If node has no children returns null
 652      */
 653    private List<TaxonNode> copyAllChildrenToTaxonNode(TaxonNode copyFromNode, TaxonNode copyToNode, UpdateResult result) {
 654                 List<TaxonNode> childNodes;
 655                 if(!copyFromNode.hasChildNodes()){
 656                         return null;
 657                 }else{
 658                         childNodes = copyFromNode.getChildNodes();
 659                 }
 660                 for(TaxonNode childNode:childNodes){
 661                         TaxonNode clone = childNode.clone();
 662                         result.addUnChangedObject(clone);
 663                         if(childNode.hasChildNodes()){
 664                                 copyAllChildrenToTaxonNode(childNode, clone, result);
 665                         }
 666                         //FIXME: citation from node instead of classification
 667 //                      copyToNode.addChildNode(clone,classification.getCitation(), classification.getMicroReference());
 668                         copyToNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
 669                 }
 670                 return childNodes;
 671         }
 672
 673     @Override
 674     public ClassificationLookupDTO classificationLookup(Classification classification) {
 675         return dao.classificationLookup(classification);
 676     }
 677
 678     @Override
 679     @Transactional
 680     public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config){
 681         DeleteResult result = new DeleteResult();
 682         Classification classification = dao.findByUuid(classificationUuid);
 683         if (classification == null){
 684             result.addException(new IllegalArgumentException("The classification does not exist in database."));
 685             result.setAbort();
 686             return result;
 687         }
 688         if (!classification.hasChildNodes()){
 689             dao.delete(classification);
 690             result.addDeletedObject(classification);
 691             return result;
 692         }
 693         if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)){
 694 //            TaxonNode root = classification.getRootNode();
 695 //            result.includeResult(taxonNodeService.deleteTaxonNode(HibernateProxyHelper.deproxy(root), config));
 696 //            result.addDeletedObject(classification);
 697             dao.delete(classification);
 698             result.addDeletedObject(classification);
 699             return result;
 700         }
 701
 702
 703         return result;
 704     }
 705
 706     @Override
 707     public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> originalTaxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank){
 708         List<GroupedTaxonDTO> result = new ArrayList<>();
 709
 710         //get treeindex for each taxonUUID
 711         Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
 712
 713         //build treeindex list (or tree)
 714         //TODO make it work with TreeIndex or move there
 715         List<String> treeIndexClosureStr = new ArrayList<>();
 716         for (TreeIndex treeIndex : taxonIdTreeIndexMap.values()){
 717             String[] splits = treeIndex.toString().substring(1).split(ITreeNode.separator);
 718             String currentIndex = ITreeNode.separator;
 719             for (String split : splits){
 720                 if (split.equals("")){
 721                     continue;
 722                 }
 723                 currentIndex += split + ITreeNode.separator;
 724                 if (!treeIndexClosureStr.contains(currentIndex) && !split.startsWith(ITreeNode.treePrefix)){
 725                     treeIndexClosureStr.add(currentIndex);
 726                 }
 727             }
 728         }
 729
 730         //get rank sortindex for all parent taxa with sortindex <= minRank and sortIndex >= maxRank (if available)
 731         Integer minRankOrderIndex = minRank == null ? null : minRank.getOrderIndex();
 732         Integer maxRankOrderIndex = maxRank == null ? null : maxRank.getOrderIndex();
 733         List<TreeIndex> treeIndexClosure = TreeIndex.NewListInstance(treeIndexClosureStr);
 734
 735         Map<TreeIndex, Integer> treeIndexSortIndexMapTmp = taxonNodeDao.rankOrderIndexForTreeIndex(treeIndexClosure, minRankOrderIndex, maxRankOrderIndex);
 736
 737         //remove all treeindex with "exists child in above map(and child.sortindex > xxx)
 738         List<TreeIndex> treeIndexList = TreeIndex.sort(treeIndexSortIndexMapTmp.keySet());
 739
 740         Map<TreeIndex, Integer> treeIndexSortIndexMap = new HashMap<>();
 741         TreeIndex lastTreeIndex = null;
 742         for (TreeIndex treeIndex : treeIndexList){
 743             if (lastTreeIndex != null && lastTreeIndex.hasChild(treeIndex)){
 744                 treeIndexSortIndexMap.remove(lastTreeIndex);
 745             }
 746             treeIndexSortIndexMap.put(treeIndex, treeIndexSortIndexMapTmp.get(treeIndex));
 747             lastTreeIndex = treeIndex;
 748         }
 749
 750         //get taxonID for treeIndexes
 751         Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(treeIndexSortIndexMap.keySet());
 752
 753         //fill result list
 754         for (UUID originalTaxonUuid : originalTaxonUuids){
 755             GroupedTaxonDTO item = new GroupedTaxonDTO();
 756             result.add(item);
 757             item.setTaxonUuid(originalTaxonUuid);
 758             TreeIndex groupTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
 759             String groupIndexX = TreeIndex.toString(groupTreeIndex);
 760             while (groupTreeIndex != null){
 761                 if (treeIndexTaxonIdMap.get(groupTreeIndex) != null){
 762                     UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
 763                     item.setGroupTaxonUuid(uuidAndLabel.getUuid());
 764                     item.setGroupTaxonName(uuidAndLabel.getTitleCache());
 765                     break;
 766                 }else{
 767                     groupTreeIndex = groupTreeIndex.parent();
 768 //                    int index = groupIndex.substring(0, groupIndex.length()-1).lastIndexOf(ITreeNode.separator);
 769 //                    groupIndex = index < 0 ? null : groupIndex.substring(0, index+1);
 770                 }
 771             }
 772         }
 773
 774         return result;
 775     }
 776
 777     @Override
 778     public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> originalTaxonUuids, UUID classificationUuid,
 779             MarkerType markerType, Boolean flag) {
 780
 781         List<GroupedTaxonDTO> result = new ArrayList<>();
 782
 783         //get treeindex for each taxonUUID
 784         Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
 785
 786         //get all marked tree indexes
 787         Set<TreeIndex> markedTreeIndexes = dao.getMarkedTreeIndexes(markerType, flag);
 788
 789         Map<TreeIndex, TreeIndex> groupedMap = TreeIndex.group(markedTreeIndexes, taxonIdTreeIndexMap.values());
 790         Set<TreeIndex> notNullGroups = new HashSet<>(groupedMap.values());
 791         notNullGroups.remove(null);
 792
 793         //get taxonInfo for treeIndexes
 794         Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(notNullGroups);
 795
 796         //fill result list
 797         for (UUID originalTaxonUuid : originalTaxonUuids){
 798             GroupedTaxonDTO item = new GroupedTaxonDTO();
 799             result.add(item);
 800             item.setTaxonUuid(originalTaxonUuid);
 801
 802             TreeIndex toBeGroupedTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
 803             TreeIndex groupTreeIndex = groupedMap.get(toBeGroupedTreeIndex);
 804             UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
 805             if (uuidAndLabel != null){
 806                 item.setGroupTaxonUuid(uuidAndLabel.getUuid());
 807                 item.setGroupTaxonName(uuidAndLabel.getTitleCache());
 808             }
 809         }
 810
 811         return result;
 812     }
 813
 814     @Override
 815     public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid) {
 816         Map<UUID, UUID> map = dao.getTaxonNodeUuidByTaxonUuid(classificationUuid, Arrays.asList(taxonUuid));
 817         UUID taxonNodeUuid = map.get(taxonUuid);
 818         return taxonNodeUuid;
 819     }
 820
 821     @Override
 822     public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonBaseUuid,
 823             Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
 824             TaxonNodeSortMode sortMode) {
 825
 826         TaxonInContextDTO result = new TaxonInContextDTO();
 827
 828         TaxonBase<?> taxonBase = taxonDao.load(taxonBaseUuid);
 829         if (taxonBase == null){
 830             throw new EntityNotFoundException("Taxon with uuid " + taxonBaseUuid + " not found in datasource");
 831         }
 832         boolean isSynonym = false;
 833         Taxon acceptedTaxon;
 834         if (taxonBase.isInstanceOf(Synonym.class)){
 835             isSynonym = true;
 836             Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
 837             acceptedTaxon = synonym.getAcceptedTaxon();
 838             if (acceptedTaxon == null) {
 839                 throw new EntityNotFoundException("Accepted taxon not found for synonym"  );
 840             }
 841             TaxonStatus taxonStatus = TaxonStatus.Synonym;
 842             if (synonym.getName()!= null && acceptedTaxon.getName() != null
 843                     && synonym.getName().getHomotypicalGroup().equals(acceptedTaxon.getName().getHomotypicalGroup())){
 844                 taxonStatus = TaxonStatus.SynonymObjective;
 845             }
 846             result.setTaxonStatus(taxonStatus);
 847
 848         }else{
 849             acceptedTaxon = CdmBase.deproxy(taxonBase, Taxon.class);
 850             result.setTaxonStatus(TaxonStatus.Accepted);
 851         }
 852         UUID acceptedTaxonUuid = acceptedTaxon.getUuid();
 853
 854         UUID taxonNodeUuid = getTaxonNodeUuidByTaxonUuid(classificationUuid, acceptedTaxonUuid);
 855         if (taxonNodeUuid == null) {
 856             throw new EntityNotFoundException("Taxon not found in classficiation with uuid " + classificationUuid + ". Either classification does not exist or does not contain taxon/synonym with uuid " + taxonBaseUuid );
 857         }
 858         result.setTaxonNodeUuid(taxonNodeUuid);
 859
 860         //TODO make it a dao call
 861         Taxon parentTaxon = getParentTaxon(classificationUuid, acceptedTaxon);
 862         if (parentTaxon != null){
 863             result.setParentTaxonUuid(parentTaxon.getUuid());
 864             result.setParentTaxonLabel(parentTaxon.getTitleCache());
 865             if (parentTaxon.getName() != null){
 866                 result.setParentNameLabel(parentTaxon.getName().getTitleCache());
 867             }
 868         }
 869
 870         result.setTaxonUuid(taxonBaseUuid);
 871         result.setClassificationUuid(classificationUuid);
 872         if (taxonBase.getSec() != null){
 873             result.setSecundumUuid(taxonBase.getSec().getUuid());
 874             result.setSecundumLabel(taxonBase.getSec().getTitleCache());
 875         }
 876         result.setTaxonLabel(taxonBase.getTitleCache());
 877
 878         TaxonName name = taxonBase.getName();
 879         result.setNameUuid(name.getUuid());
 880         result.setNameLabel(name.getTitleCache());
 881         result.setNameWithoutAuthor(name.getNameCache());
 882         result.setGenusOrUninomial(name.getGenusOrUninomial());
 883         result.setInfraGenericEpithet(name.getInfraGenericEpithet());
 884         result.setSpeciesEpithet(name.getSpecificEpithet());
 885         result.setInfraSpecificEpithet(name.getInfraSpecificEpithet());
 886
 887         result.setAuthorship(name.getAuthorshipCache());
 888
 889         Rank rank = name.getRank();
 890         if (rank != null){
 891             result.setRankUuid(rank.getUuid());
 892             String rankLabel = rank.getAbbreviation();
 893             if (StringUtils.isBlank(rankLabel)){
 894                 rankLabel = rank.getLabel();
 895             }
 896             result.setRankLabel(rankLabel);
 897         }
 898
 899         boolean recursive = false;
 900         Integer pageSize = null;
 901         Integer pageIndex = null;
 902         Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, includeUnpublished, doSynonyms,
 903                 sortMode, pageSize, pageIndex);
 904
 905         //children
 906         if(! isSynonym) {
 907             for (TaxonNodeDto childDto : children.getRecords()){
 908                 if (doChildren && childDto.getTaxonStatus().equals(TaxonStatus.Accepted)){
 909                     EntityDTO<Taxon> child = new EntityDTO<Taxon>(childDto.getTaxonUuid(), childDto.getTitleCache());
 910                     result.addChild(child);
 911                 }else if (doSynonyms && childDto.getTaxonStatus().isSynonym()){
 912                     EntityDTO<Synonym> child = new EntityDTO<>(childDto.getTaxonUuid(), childDto.getTitleCache());
 913                     result.addSynonym(child);
 914                 }
 915             }
 916         }else{
 917             result.setAcceptedTaxonUuid(acceptedTaxonUuid);
 918             String nameTitel = acceptedTaxon.getName() == null ? null : acceptedTaxon.getName().getTitleCache();
 919             result.setAcceptedTaxonLabel(acceptedTaxon.getTitleCache());
 920             result.setAcceptedNameLabel(nameTitel);
 921         }
 922
 923         //marked ancestors
 924         if (ancestorMarkers != null && !ancestorMarkers.isEmpty()){
 925             @SuppressWarnings("rawtypes")
 926             List<DefinedTermBase> markerTypesTerms = termDao.list(ancestorMarkers, pageSize, null, null, null);
 927             List<MarkerType> markerTypes = new ArrayList<>();
 928             for (DefinedTermBase<?> term : markerTypesTerms){
 929                 if (term.isInstanceOf(MarkerType.class)){
 930                     markerTypes.add(CdmBase.deproxy(term, MarkerType.class));
 931                 }
 932             }
 933             if (! markerTypes.isEmpty()){
 934                 TaxonNode node = taxonNodeDao.findByUuid(taxonNodeUuid);
 935                 handleAncestorsForMarkersRecursive(result, markerTypes, node);
 936             }
 937         }
 938
 939         return result;
 940     }
 941
 942     private Taxon getParentTaxon(UUID classificationUuid, Taxon acceptedTaxon) {
 943         if (classificationUuid == null){
 944             return null;
 945         }
 946         TaxonNode parent = null;
 947         for (TaxonNode node : acceptedTaxon.getTaxonNodes()){
 948             if (classificationUuid.equals(node.getClassification().getUuid())){
 949                 parent = node.getParent();
 950             }
 951         }
 952         if (parent != null){
 953             return parent.getTaxon();
 954         }
 955         return null;
 956     }
 957
 958     private void handleAncestorsForMarkersRecursive(TaxonInContextDTO result, List<MarkerType> markerTypes, TaxonNode node) {
 959        for (MarkerType type : markerTypes){
 960             Taxon taxon = node.getTaxon();
 961             if (taxon != null && taxon.hasMarker(type, true)){
 962                 String label =  taxon.getName() == null? taxon.getTitleCache() : taxon.getName().getTitleCache();
 963                 MarkedEntityDTO<Taxon> dto = new MarkedEntityDTO<>(type, true, taxon.getUuid(), label);
 964                 result.addMarkedAncestor(dto);
 965             }
 966         }
 967         TaxonNode parentNode = node.getParent();
 968         if (parentNode != null){
 969             handleAncestorsForMarkersRecursive(result, markerTypes, parentNode);
 970         }
 971     }
 972
 973     @Override
 974     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 975             Classification classification) {
 976         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, false);
 977     }
 978
 979     @Override
 980     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 981             UUID classificationUuid) {
 982         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, false);
 983     }
 984
 985     @Override
 986     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 987             UUID classificationUuid, Integer limit, String pattern) {
 988         return  getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid,  limit, pattern, false);
 989     }
 990
 991     @Override
 992     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 993             Classification classification, Integer limit, String pattern) {
 994         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, false);
 995     }
 996
 997     @Override
 998     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 999             UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications) {
1000         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1001                 classificationUuid, limit, pattern, searchForClassifications, false);
1002     }
1003 }