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
  25 import javax.persistence.EntityNotFoundException;
  26
  27 import org.apache.commons.collections.CollectionUtils;
  28 import org.apache.commons.lang.StringUtils;
  29 import org.apache.log4j.Logger;
  30 import org.springframework.beans.factory.annotation.Autowired;
  31 import org.springframework.stereotype.Service;
  32 import org.springframework.transaction.annotation.Transactional;
  33
  34 import eu.etaxonomy.cdm.api.service.config.CreateHierarchyForClassificationConfigurator;
  35 import eu.etaxonomy.cdm.api.service.config.NodeDeletionConfigurator.ChildHandling;
  36 import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
  37 import eu.etaxonomy.cdm.api.service.dto.EntityDTO;
  38 import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
  39 import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
  40 import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
  41 import eu.etaxonomy.cdm.api.service.pager.Pager;
  42 import eu.etaxonomy.cdm.api.service.pager.PagerUtils;
  43 import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;
  44 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  45 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  46 import eu.etaxonomy.cdm.exception.UnpublishedException;
  47 import eu.etaxonomy.cdm.hibernate.HHH_9751_Util;
  48 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  49 import eu.etaxonomy.cdm.model.common.CdmBase;
  50 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  51 import eu.etaxonomy.cdm.model.common.ITreeNode;
  52 import eu.etaxonomy.cdm.model.common.MarkerType;
  53 import eu.etaxonomy.cdm.model.common.TreeIndex;
  54 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  55 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  56 import eu.etaxonomy.cdm.model.media.Media;
  57 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  58 import eu.etaxonomy.cdm.model.media.MediaUtils;
  59 import eu.etaxonomy.cdm.model.name.INonViralName;
  60 import eu.etaxonomy.cdm.model.name.Rank;
  61 import eu.etaxonomy.cdm.model.name.TaxonName;
  62 import eu.etaxonomy.cdm.model.reference.Reference;
  63 import eu.etaxonomy.cdm.model.taxon.Classification;
  64 import eu.etaxonomy.cdm.model.taxon.ITaxonNodeComparator;
  65 import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
  66 import eu.etaxonomy.cdm.model.taxon.Synonym;
  67 import eu.etaxonomy.cdm.model.taxon.Taxon;
  68 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  69 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  70 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  71 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
  72 import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
  73 import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
  74 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
  75 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
  76 import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
  77 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
  78 import eu.etaxonomy.cdm.persistence.dto.TaxonStatus;
  79 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  80 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  81 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  82 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  83
  84 /**
  85  * @author n.hoffmann
  86  * @since Sep 21, 2009
  87  */
  88 @Service
  89 @Transactional(readOnly = true)
  90 public class ClassificationServiceImpl
  91              extends IdentifiableServiceBase<Classification, IClassificationDao>
  92              implements IClassificationService {
  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     @Transactional(readOnly = false)
 137     public UpdateResult cloneClassification(UUID classificationUuid,
 138                 String name, Reference sec, TaxonRelationshipType relationshipType) {
 139         UpdateResult result = new UpdateResult();
 140         Classification classification = load(classificationUuid);
 141         Classification clone = Classification.NewInstance(name);
 142         clone.setReference(sec);
 143
 144         //clone taxa and taxon nodes
 145         List<TaxonNode> childNodes = classification.getRootNode().getChildNodes();
 146         for (TaxonNode taxonNode : childNodes) {
 147                 addChildTaxa(taxonNode, null, clone, relationshipType);
 148         }
 149         dao.saveOrUpdate(clone);
 150         result.setCdmEntity(clone);
 151         return result;
 152     }
 153
 154     private void addChildTaxa(TaxonNode originalParentNode, TaxonNode cloneParentNode, Classification classification, TaxonRelationshipType relationshipType){
 155         Reference reference = classification.getReference();
 156         Taxon cloneTaxon = (Taxon) HibernateProxyHelper.deproxy(originalParentNode.getTaxon(), Taxon.class).clone();
 157         cloneTaxon.setSec(reference);
 158                 String microReference = null;
 159                 List<TaxonNode> originalChildNodes = originalParentNode.getChildNodes();
 160                 HHH_9751_Util.removeAllNull(originalChildNodes);
 161
 162                 //add relation between taxa
 163                 if (relationshipType != null){
 164                     cloneTaxon.addTaxonRelation(originalParentNode.getTaxon(), relationshipType, reference, microReference);
 165                 }
 166
 167                 TaxonNode cloneChildNode = null;
 168         //add taxon node to either parent node or classification (no parent node)
 169         if(cloneParentNode==null){
 170                 cloneChildNode = classification.addChildTaxon(cloneTaxon, reference, microReference);
 171         }
 172         else{
 173                 cloneChildNode = cloneParentNode.addChildTaxon(cloneTaxon, reference, microReference);
 174         }
 175         taxonNodeDao.saveOrUpdate(cloneChildNode);
 176         //add children
 177                 for (TaxonNode originalChildNode : originalChildNodes) {
 178                 addChildTaxa(originalChildNode, cloneChildNode, classification, relationshipType);
 179         }
 180     }
 181
 182     /**
 183      * {@inheritDoc}
 184      */
 185     @Override
 186     public List<TaxonNode> listRankSpecificRootNodes(Classification classification, Rank rank,
 187             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
 188         return pageRankSpecificRootNodes(classification, rank, includeUnpublished, pageSize, pageIndex, propertyPaths).getRecords();
 189     }
 190
 191     @Override
 192     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank,
 193             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
 194         long[] numberOfResults = dao.countRankSpecificRootNodes(classification, includeUnpublished, rank);
 195         long totalNumberOfResults = numberOfResults[0] + (numberOfResults.length > 1 ? numberOfResults[1] : 0);
 196
 197         List<TaxonNode> results = new ArrayList<>();
 198
 199         if (AbstractPagerImpl.hasResultsInRange(totalNumberOfResults, pageIndex, pageSize)) { // no point checking again
 200             Integer limit = PagerUtils.limitFor(pageSize);
 201             Integer start = PagerUtils.startFor(pageSize, pageIndex);
 202
 203             Integer remainingLimit = limit;
 204             int[] queryIndexes = rank == null ? new int[]{0} : new int[]{0,1};
 205
 206             for(int queryIndex: queryIndexes) {
 207                 if(start != null && start > numberOfResults[queryIndex]) {
 208                     // start in next query with new start value
 209                     start = start - (int)numberOfResults[queryIndex];
 210                     continue;
 211                 }
 212
 213                 List<TaxonNode> perQueryResults = dao.listRankSpecificRootNodes(classification,
 214                         rank, includeUnpublished, remainingLimit, start, propertyPaths, queryIndex);
 215                 results.addAll(perQueryResults);
 216                 if(remainingLimit != null ){
 217                     remainingLimit = remainingLimit - results.size();
 218                     if(remainingLimit <= 0) {
 219                         // no need to run further queries if first query returned enough items!
 220                         break;
 221                     }
 222                     // start at with fist item of next query to fetch the remaining items
 223                     start = 0;
 224                 }
 225             }
 226         }
 227 //        long start_t = System.currentTimeMillis();
 228         Collections.sort(results, taxonNodeComparator); // TODO is ordering during the hibernate query in the dao possible?
 229 //        System.err.println("service.pageRankSpecificRootNodes() - Collections.sort(results,  taxonNodeComparator) " + (System.currentTimeMillis() - start_t));
 230         return new DefaultPagerImpl<>(pageIndex, totalNumberOfResults, pageSize, results);
 231
 232     }
 233
 234
 235     /**
 236      * {@inheritDoc}
 237      */
 238     @Override
 239     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank,
 240             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 241
 242         TaxonNode thisNode = taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
 243         if(baseRank != null){
 244             baseRank = (Rank) termDao.load(baseRank.getUuid());
 245         }
 246         if (!includeUnpublished && thisNode.getTaxon() != null && !thisNode.getTaxon().isPublish()){
 247             throw new UnpublishedException("Final taxon in tree branch is unpublished.");
 248         }
 249
 250         List<TaxonNode> pathToRoot = new ArrayList<>();
 251         pathToRoot.add(thisNode);
 252
 253         while(!thisNode.isTopmostNode()){
 254             //TODO why do we need to deproxy here?
 255             //     without this thisNode.getParent() will return NULL in
 256             //     some cases (environment dependend?) even if the parent exits
 257             TaxonNode parentNode = CdmBase.deproxy(thisNode).getParent();
 258
 259             if(parentNode == null){
 260                 throw new NullPointerException("Taxon node " + thisNode + " must have a parent since it is not top most");
 261             }
 262             if(parentNode.getTaxon() == null){
 263                 throw new NullPointerException("The taxon associated with taxon node " + parentNode + " is NULL");
 264             }
 265             if(!includeUnpublished && !parentNode.getTaxon().isPublish()){
 266                 throw new UnpublishedException("Some taxon in tree branch is unpublished.");
 267             }
 268             if(parentNode.getTaxon().getName() == null){
 269                 throw new NullPointerException("The name of the taxon associated with taxonNode " + parentNode + " is NULL");
 270             }
 271
 272             Rank parentNodeRank = (parentNode.getTaxon().getName() == null) ? null : parentNode.getTaxon().getName().getRank();
 273             // stop if the next parent is higher than the baseRank
 274             if(baseRank != null && parentNodeRank != null && baseRank.isLower(parentNodeRank)){
 275                 break;
 276             }
 277
 278             pathToRoot.add(parentNode);
 279             thisNode = parentNode;
 280         }
 281
 282         // initialize and invert order of nodes in list
 283         defaultBeanInitializer.initializeAll(pathToRoot, propertyPaths);
 284         Collections.reverse(pathToRoot);
 285
 286         return pathToRoot;
 287     }
 288
 289     @Override
 290     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank,
 291             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
 292
 293         UUID nodeUuid = getTaxonNodeUuidByTaxonUuid(classification.getUuid(), taxon.getUuid());
 294         TaxonNode node = taxonNodeService.find(nodeUuid);
 295         if(node == null){
 296             logger.warn("The specified taxon is not found in the given tree.");
 297             return null;
 298         }
 299         return loadTreeBranch(node, baseRank, includeUnpublished, propertyPaths);
 300     }
 301
 302
 303     @Override
 304     public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
 305             List<String> propertyPaths) {
 306         taxonNode = taxonNodeDao.load(taxonNode.getUuid());
 307         List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
 308         defaultBeanInitializer.initializeAll(childNodes, propertyPaths);
 309         Collections.sort(childNodes, taxonNodeComparator);
 310         return childNodes;
 311     }
 312
 313     @Override
 314     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid,
 315             boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 316
 317         Classification classification = dao.load(classificationUuid);
 318         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 319
 320         List<TaxonNode> results = dao.listChildrenOf(
 321                 taxon, classification, includeUnpublished, pageSize, pageIndex, propertyPaths);
 322         Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
 323         return results;
 324     }
 325
 326     @Override
 327     public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 328             Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 329
 330         Classification classification = dao.load(classificationUuid);
 331         Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
 332
 333         long numberOfResults = dao.countSiblingsOf(taxon, classification, includeUnpublished);
 334
 335         List<TaxonNode> results;
 336         if(PagerUtils.hasResultsInRange(numberOfResults, pageIndex, pageSize)) {
 337             results = dao.listSiblingsOf(taxon, classification, includeUnpublished, pageSize, pageIndex, propertyPaths);
 338             Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
 339         } else {
 340             results = new ArrayList<>();
 341         }
 342
 343         return new DefaultPagerImpl<>(pageIndex, numberOfResults, pageSize, results);
 344     }
 345
 346     @Override
 347     public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 348             Integer pageSize, Integer pageIndex, List<String> propertyPaths){
 349
 350         Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, includeUnpublished, pageSize, pageIndex, propertyPaths);
 351         return pager.getRecords();
 352     }
 353
 354     @Override
 355     public ITaxonTreeNode getTreeNodeByUuid(UUID uuid){
 356         ITaxonTreeNode treeNode = taxonNodeDao.findByUuid(uuid);
 357         if(treeNode == null){
 358             treeNode = dao.findByUuid(uuid);
 359         }
 360
 361         return treeNode;
 362     }
 363
 364     @Override
 365     public TaxonNode getRootNode(UUID classificationUuid){
 366         return dao.getRootNode(classificationUuid);
 367     }
 368
 369     @Override
 370     public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
 371         return dao.list(limit, start, orderHints, propertyPaths);
 372     }
 373
 374     @Override
 375     public UUID removeTaxonNode(TaxonNode taxonNode) {
 376         return taxonNodeDao.delete(taxonNode);
 377     }
 378     @Override
 379     public UUID removeTreeNode(ITaxonTreeNode treeNode) {
 380         if(treeNode instanceof Classification){
 381             return dao.delete((Classification) treeNode);
 382         }else if(treeNode instanceof TaxonNode){
 383             return taxonNodeDao.delete((TaxonNode)treeNode);
 384         }
 385         return null;
 386     }
 387     @Override
 388     public UUID saveTaxonNode(TaxonNode taxonNode) {
 389         return taxonNodeDao.save(taxonNode).getUuid();
 390     }
 391
 392     @Override
 393     public Map<UUID, TaxonNode> saveTaxonNodeAll(
 394             Collection<TaxonNode> taxonNodeCollection) {
 395         return taxonNodeDao.saveAll(taxonNodeCollection);
 396     }
 397
 398     @Override
 399     public UUID saveClassification(Classification classification) {
 400
 401        taxonNodeDao.saveOrUpdateAll(classification.getAllNodes());
 402        UUID result =dao.saveOrUpdate(classification);
 403        return result;
 404     }
 405
 406     @Override
 407     public UUID saveTreeNode(ITaxonTreeNode treeNode) {
 408         if(treeNode instanceof Classification){
 409             return dao.save((Classification) treeNode).getUuid();
 410         }else if(treeNode instanceof TaxonNode){
 411             return taxonNodeDao.save((TaxonNode)treeNode).getUuid();
 412         }
 413         return null;
 414     }
 415
 416     @Override
 417     public List<TaxonNode> getAllNodes(){
 418         return taxonNodeDao.list(null,null);
 419     }
 420
 421     @Override
 422     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications) {
 423         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid),  limit, pattern, searchForClassifications);
 424     }
 425
 426     @Override
 427     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification,  Integer limit, String pattern, boolean searchForClassifications) {
 428         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification,  limit, pattern, searchForClassifications);
 429     }
 430
 431     @Override
 432     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, boolean searchForClassifications ) {
 433         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null, searchForClassifications);
 434     }
 435
 436     @Override
 437     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, boolean searchForClassifications ) {
 438         return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null, searchForClassifications);
 439     }
 440
 441     @Override
 442     public List<UuidAndTitleCache<Classification>> getUuidAndTitleCache(Integer limit, String pattern) {
 443         return dao.getUuidAndTitleCache(limit, pattern);
 444     }
 445
 446     @Override
 447     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(
 448             TaxonNode taxonNode, List<String> propertyPaths, int size,
 449             int height, int widthOrDuration, String[] mimeTypes) {
 450
 451         TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<>();
 452         List<Media> taxonMedia = new ArrayList<>();
 453         List<MediaRepresentation> mediaRepresentations = new ArrayList<>();
 454
 455         //add all media of the children to the result map
 456         if (taxonNode != null){
 457
 458             List<TaxonNode> nodes = new ArrayList<>();
 459
 460             nodes.add(loadTaxonNode(taxonNode.getUuid(), propertyPaths));
 461             nodes.addAll(loadChildNodesOfTaxonNode(taxonNode, propertyPaths));
 462
 463             for(TaxonNode node : nodes){
 464                 Taxon taxon = node.getTaxon();
 465                 for (TaxonDescription taxonDescription: taxon.getDescriptions()){
 466                     for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){
 467                         for(Media media : descriptionElement.getMedia()){
 468                             taxonMedia.add(media);
 469
 470                             //find the best matching representation
 471                             mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes));
 472                         }
 473                     }
 474                 }
 475                 result.put(taxon.getUuid(), mediaRepresentations);
 476             }
 477         }
 478
 479         return result;
 480     }
 481
 482     @Override
 483     @Transactional(readOnly = false)
 484     public void updateTitleCache(Class<? extends Classification> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<Classification> cacheStrategy, IProgressMonitor monitor) {
 485         if (clazz == null){
 486             clazz = Classification.class;
 487         }
 488         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 489     }
 490
 491     /**
 492      *
 493      * @param allNodesOfClassification
 494      * @return null - if  allNodesOfClassification is empty <br>
 495      */
 496
 497     private Map<String, List<TaxonNode>> getSortedGenusList(Collection<TaxonNode> allNodesOfClassification){
 498
 499         if(allNodesOfClassification == null || allNodesOfClassification.isEmpty()){
 500                 return null;
 501         }
 502         Map<String, List<TaxonNode>> sortedGenusMap = new HashMap<>();
 503         for(TaxonNode node:allNodesOfClassification){
 504                 Taxon taxon = node.getTaxon();
 505                 INonViralName name = taxon.getName();
 506                 String genusOrUninomial = name.getGenusOrUninomial();
 507                 //if rank unknown split string and take first word
 508                 if(genusOrUninomial == null){
 509                         String titleCache = taxon.getTitleCache();
 510                         String[] split = titleCache.split("\\s+");
 511                         for(String s:split){
 512                                 genusOrUninomial = s;
 513                                 break;
 514                         }
 515                 }
 516                 //if node has children
 517
 518                 //retrieve list from map if not create List
 519                 if(sortedGenusMap.containsKey(genusOrUninomial)){
 520                         List<TaxonNode> list = sortedGenusMap.get(genusOrUninomial);
 521                         list.add(node);
 522                         sortedGenusMap.put(genusOrUninomial, list);
 523                 }else{
 524                         //create List for genus
 525                         List<TaxonNode> list = new ArrayList<>();
 526                         list.add(node);
 527                         sortedGenusMap.put(genusOrUninomial, list);
 528                 }
 529         }
 530         return sortedGenusMap;
 531     }
 532
 533     /**
 534      *
 535      * creates new Classification and parent TaxonNodes at genus level
 536      *
 537      *
 538      * @param map GenusMap which holds a name (Genus) and all the same Taxa as a list
 539      * @param classification you want to improve the hierarchy (will not be modified)
 540      * @param configurator to change certain settings, if null then standard settings will be taken
 541      * @return new classification with parentNodes for each entry in the map
 542      */
 543     @SuppressWarnings({ "unchecked" })
 544         @Transactional(readOnly = false)
 545         @Override
 546     public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator){
 547         UpdateResult result = new UpdateResult();
 548         classification = dao.findByUuid(classification.getUuid());
 549         Map<String, List<TaxonNode>> map = getSortedGenusList(classification.getAllNodes());
 550
 551         final String APPENDIX = "repaired";
 552         String titleCache = StringUtils.isBlank(classification.getTitleCache()) ? " " : classification.getTitleCache() ;
 553         //TODO classification clone???
 554         Classification newClassification = Classification.NewInstance(titleCache +" "+ APPENDIX);
 555         newClassification.setReference(classification.getReference());
 556
 557         for(Map.Entry<String, List<TaxonNode>> entry:map.entrySet()){
 558                 String genus = entry.getKey();
 559                 List<TaxonNode> listOfTaxonNodes = entry.getValue();
 560                 TaxonNode parentNode = null;
 561                 //Search for genus in list
 562                 for(TaxonNode tNode:listOfTaxonNodes){
 563                         //take that taxonNode as parent and remove from list with all it possible children
 564                         //FIXME NPE for name
 565                         TaxonName name = tNode.getTaxon().getName();
 566                         if(name.getNameCache().equalsIgnoreCase(genus)){
 567                                 TaxonNode clone = (TaxonNode) tNode.clone();
 568                                 if(!tNode.hasChildNodes()){
 569                                         //FIXME remove classification
 570 //                                      parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
 571                                         parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
 572                                         //remove taxonNode from list because just added to classification
 573                                         result.addUpdatedObject(tNode);
 574                                         listOfTaxonNodes.remove(tNode);
 575                                 }else{
 576                                         //get all childNodes
 577                                         //save prior Hierarchy and remove them from the list
 578                                         List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tNode, clone, result);
 579 //                                      parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
 580                                         //FIXME remove classification
 581                                         parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
 582                                         //remove taxonNode from list because just added to classification
 583                                         result.addUpdatedObject(tNode);
 584                                         listOfTaxonNodes.remove(tNode);
 585                                         if(copyAllChildrenToTaxonNode != null){
 586                                                 listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
 587                                         }
 588                                 }
 589                                 break;
 590                         }
 591                 }
 592                 if(parentNode == null){
 593                         //if no match found in list, create parentNode
 594                         NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
 595                         TaxonName TaxonName = (TaxonName)parser.parseFullName(genus);
 596                         //TODO Sec via configurator
 597                         Taxon taxon = Taxon.NewInstance(TaxonName, null);
 598                         parentNode = newClassification.addChildTaxon(taxon, 0, null, null);
 599                         result.addUpdatedObject(parentNode);
 600                 }
 601                 //iterate over the rest of the list
 602                 for(TaxonNode tn : listOfTaxonNodes){
 603                         //if TaxonNode has a parent and this is not the classification then skip it
 604                         //and add to new classification via the parentNode as children of it
 605                         //this should assures to keep the already existing hierarchy
 606                         //FIXME: Assert is not rootnode --> entrypoint is not classification in future but rather rootNode
 607
 608                         if(!tn.isTopmostNode()){
 609                                 continue; //skip to next taxonNode
 610                         }
 611
 612                         TaxonNode clone = (TaxonNode) tn.clone();
 613                         //FIXME: citation from node
 614                         //TODO: addchildNode without citation and references
 615 //                      TaxonNode taxonNode = parentNode.addChildNode(clone, classification.getCitation(), classification.getMicroReference());
 616                         TaxonNode taxonNode = parentNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
 617                         result.addUnChangedObject(clone);
 618                         if(tn.hasChildNodes()){
 619                                 //save hierarchy in new classification
 620                                 List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tn, taxonNode, result);
 621                                 if(copyAllChildrenToTaxonNode != null){
 622                                         listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
 623                                 }
 624                         }
 625                 }
 626         }
 627         dao.saveOrUpdate(newClassification);
 628         result.setCdmEntity(newClassification);
 629         return result;
 630     }
 631
 632     /**
 633      *
 634      * recursive method to get all childnodes of taxonNode in classification.
 635      *
 636      * @param classification just for References and Citation, can be null
 637      * @param copyFromNode TaxonNode with Children
 638      * @param copyToNode TaxonNode which will receive the children
 639      * @return List of ChildNode which has been added. If node has no children returns null
 640      */
 641    private List<TaxonNode> copyAllChildrenToTaxonNode(TaxonNode copyFromNode, TaxonNode copyToNode, UpdateResult result) {
 642                 List<TaxonNode> childNodes;
 643                 if(!copyFromNode.hasChildNodes()){
 644                         return null;
 645                 }else{
 646                         childNodes = copyFromNode.getChildNodes();
 647                 }
 648                 for(TaxonNode childNode:childNodes){
 649                         TaxonNode clone = (TaxonNode) childNode.clone();
 650                         result.addUnChangedObject(clone);
 651                         if(childNode.hasChildNodes()){
 652                                 copyAllChildrenToTaxonNode(childNode, clone, result);
 653                         }
 654                         //FIXME: citation from node instead of classification
 655 //                      copyToNode.addChildNode(clone,classification.getCitation(), classification.getMicroReference());
 656                         copyToNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
 657                 }
 658                 return childNodes;
 659         }
 660
 661     /**
 662      * {@inheritDoc}
 663      */
 664     @Override
 665     public ClassificationLookupDTO classificationLookup(Classification classification) {
 666         return dao.classificationLookup(classification);
 667     }
 668
 669
 670     @Override
 671     @Transactional
 672     public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config){
 673         DeleteResult result = new DeleteResult();
 674         Classification classification = dao.findByUuid(classificationUuid);
 675         if (classification == null){
 676             result.addException(new IllegalArgumentException("The classification does not exist in database."));
 677             result.setAbort();
 678             return result;
 679         }
 680         if (!classification.hasChildNodes()){
 681             dao.delete(classification);
 682             result.addDeletedObject(classification);
 683             return result;
 684         }
 685         if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)){
 686 //            TaxonNode root = classification.getRootNode();
 687 //            result.includeResult(taxonNodeService.deleteTaxonNode(HibernateProxyHelper.deproxy(root), config));
 688 //            result.addDeletedObject(classification);
 689             dao.delete(classification);
 690             result.addDeletedObject(classification);
 691             return result;
 692         }
 693
 694
 695         return result;
 696     }
 697
 698     @Override
 699     public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> originalTaxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank){
 700         List<GroupedTaxonDTO> result = new ArrayList<>();
 701
 702         //get treeindex for each taxonUUID
 703         Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
 704
 705         //build treeindex list (or tree)
 706         //TODO make it work with TreeIndex or move there
 707         List<String> treeIndexClosureStr = new ArrayList<>();
 708         for (TreeIndex treeIndex : taxonIdTreeIndexMap.values()){
 709             String[] splits = treeIndex.toString().substring(1).split(ITreeNode.separator);
 710             String currentIndex = ITreeNode.separator;
 711             for (String split : splits){
 712                 if (split.equals("")){
 713                     continue;
 714                 }
 715                 currentIndex += split + ITreeNode.separator;
 716                 if (!treeIndexClosureStr.contains(currentIndex) && !split.startsWith(ITreeNode.treePrefix)){
 717                     treeIndexClosureStr.add(currentIndex);
 718                 }
 719             }
 720         }
 721
 722         //get rank sortindex for all parent taxa with sortindex <= minRank and sortIndex >= maxRank (if available)
 723         Integer minRankOrderIndex = minRank == null ? null : minRank.getOrderIndex();
 724         Integer maxRankOrderIndex = maxRank == null ? null : maxRank.getOrderIndex();
 725         List<TreeIndex> treeIndexClosure = TreeIndex.NewListInstance(treeIndexClosureStr);
 726
 727         Map<TreeIndex, Integer> treeIndexSortIndexMapTmp = taxonNodeDao.rankOrderIndexForTreeIndex(treeIndexClosure, minRankOrderIndex, maxRankOrderIndex);
 728
 729         //remove all treeindex with "exists child in above map(and child.sortindex > xxx)
 730         List<TreeIndex> treeIndexList = TreeIndex.sort(treeIndexSortIndexMapTmp.keySet());
 731
 732         Map<TreeIndex, Integer> treeIndexSortIndexMap = new HashMap<>();
 733         TreeIndex lastTreeIndex = null;
 734         for (TreeIndex treeIndex : treeIndexList){
 735             if (lastTreeIndex != null && lastTreeIndex.hasChild(treeIndex)){
 736                 treeIndexSortIndexMap.remove(lastTreeIndex);
 737             }
 738             treeIndexSortIndexMap.put(treeIndex, treeIndexSortIndexMapTmp.get(treeIndex));
 739             lastTreeIndex = treeIndex;
 740         }
 741
 742         //get taxonID for treeIndexes
 743         Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(treeIndexSortIndexMap.keySet());
 744
 745         //fill result list
 746         for (UUID originalTaxonUuid : originalTaxonUuids){
 747             GroupedTaxonDTO item = new GroupedTaxonDTO();
 748             result.add(item);
 749             item.setTaxonUuid(originalTaxonUuid);
 750             TreeIndex groupTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
 751             String groupIndexX = TreeIndex.toString(groupTreeIndex);
 752             while (groupTreeIndex != null){
 753                 if (treeIndexTaxonIdMap.get(groupTreeIndex) != null){
 754                     UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
 755                     item.setGroupTaxonUuid(uuidAndLabel.getUuid());
 756                     item.setGroupTaxonName(uuidAndLabel.getTitleCache());
 757                     break;
 758                 }else{
 759                     groupTreeIndex = groupTreeIndex.parent();
 760 //                    int index = groupIndex.substring(0, groupIndex.length()-1).lastIndexOf(ITreeNode.separator);
 761 //                    groupIndex = index < 0 ? null : groupIndex.substring(0, index+1);
 762                 }
 763             }
 764         }
 765
 766         return result;
 767     }
 768
 769     /**
 770      * {@inheritDoc}
 771      */
 772     @Override
 773     public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> originalTaxonUuids, UUID classificationUuid,
 774             MarkerType markerType, Boolean flag) {
 775
 776         List<GroupedTaxonDTO> result = new ArrayList<>();
 777
 778         //get treeindex for each taxonUUID
 779         Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
 780
 781         //get all marked tree indexes
 782         Set<TreeIndex> markedTreeIndexes = dao.getMarkedTreeIndexes(markerType, flag);
 783
 784
 785         Map<TreeIndex, TreeIndex> groupedMap = TreeIndex.group(markedTreeIndexes, taxonIdTreeIndexMap.values());
 786         Set<TreeIndex> notNullGroups = new HashSet<>(groupedMap.values());
 787         notNullGroups.remove(null);
 788
 789         //get taxonInfo for treeIndexes
 790         Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(notNullGroups);
 791
 792         //fill result list
 793         for (UUID originalTaxonUuid : originalTaxonUuids){
 794             GroupedTaxonDTO item = new GroupedTaxonDTO();
 795             result.add(item);
 796             item.setTaxonUuid(originalTaxonUuid);
 797
 798             TreeIndex toBeGroupedTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
 799             TreeIndex groupTreeIndex = groupedMap.get(toBeGroupedTreeIndex);
 800             UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
 801             if (uuidAndLabel != null){
 802                 item.setGroupTaxonUuid(uuidAndLabel.getUuid());
 803                 item.setGroupTaxonName(uuidAndLabel.getTitleCache());
 804             }
 805         }
 806
 807         return result;
 808     }
 809
 810     /**
 811      * {@inheritDoc}
 812      */
 813     @Override
 814     public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid) {
 815         Map<UUID, UUID> map = dao.getTaxonNodeUuidByTaxonUuid(classificationUuid, Arrays.asList(taxonUuid));
 816         UUID taxonNodeUuid = map.get(taxonUuid);
 817         return taxonNodeUuid;
 818     }
 819
 820     /**
 821      * {@inheritDoc}
 822      */
 823     @Override
 824     public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonBaseUuid,
 825             Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
 826             NodeSortMode sortMode) {
 827         TaxonInContextDTO result = new TaxonInContextDTO();
 828
 829         TaxonBase<?> taxonBase = taxonDao.load(taxonBaseUuid);
 830         if (taxonBase == null){
 831             throw new EntityNotFoundException("Taxon with uuid " + taxonBaseUuid + " not found in datasource");
 832         }
 833         boolean isSynonym = false;
 834         Taxon acceptedTaxon;
 835         if (taxonBase.isInstanceOf(Synonym.class)){
 836             isSynonym = true;
 837             Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
 838             acceptedTaxon = synonym.getAcceptedTaxon();
 839             if (acceptedTaxon == null) {
 840                 throw new EntityNotFoundException("Accepted taxon not found for synonym"  );
 841             }
 842             TaxonStatus taxonStatus = TaxonStatus.Synonym;
 843             if (synonym.getName()!= null && acceptedTaxon.getName() != null
 844                     && synonym.getName().getHomotypicalGroup().equals(acceptedTaxon.getName().getHomotypicalGroup())){
 845                 taxonStatus = TaxonStatus.SynonymObjective;
 846             }
 847             result.setTaxonStatus(taxonStatus);
 848
 849         }else{
 850             acceptedTaxon = CdmBase.deproxy(taxonBase, Taxon.class);
 851             result.setTaxonStatus(TaxonStatus.Accepted);
 852         }
 853         UUID acceptedTaxonUuid = acceptedTaxon.getUuid();
 854
 855         UUID taxonNodeUuid = getTaxonNodeUuidByTaxonUuid(classificationUuid, acceptedTaxonUuid);
 856         if (taxonNodeUuid == null) {
 857             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 );
 858         }
 859         result.setTaxonNodeUuid(taxonNodeUuid);
 860
 861         //TODO make it a dao call
 862         Taxon parentTaxon = getParentTaxon(classificationUuid, acceptedTaxon);
 863         if (parentTaxon != null){
 864             result.setParentTaxonUuid(parentTaxon.getUuid());
 865             result.setParentTaxonLabel(parentTaxon.getTitleCache());
 866             if (parentTaxon.getName() != null){
 867                 result.setParentNameLabel(parentTaxon.getName().getTitleCache());
 868             }
 869         }
 870
 871         result.setTaxonUuid(taxonBaseUuid);
 872         result.setClassificationUuid(classificationUuid);
 873         if (taxonBase.getSec() != null){
 874             result.setSecundumUuid(taxonBase.getSec().getUuid());
 875             result.setSecundumLabel(taxonBase.getSec().getTitleCache());
 876         }
 877         result.setTaxonLabel(taxonBase.getTitleCache());
 878
 879         TaxonName name = taxonBase.getName();
 880         result.setNameUuid(name.getUuid());
 881         result.setNameLabel(name.getTitleCache());
 882         result.setNameWithoutAuthor(name.getNameCache());
 883         result.setGenusOrUninomial(name.getGenusOrUninomial());
 884         result.setInfraGenericEpithet(name.getInfraGenericEpithet());
 885         result.setSpeciesEpithet(name.getSpecificEpithet());
 886         result.setInfraSpecificEpithet(name.getInfraSpecificEpithet());
 887
 888         result.setAuthorship(name.getAuthorshipCache());
 889
 890         Rank rank = name.getRank();
 891         if (rank != null){
 892             result.setRankUuid(rank.getUuid());
 893             String rankLabel = rank.getAbbreviation();
 894             if (StringUtils.isBlank(rankLabel)){
 895                 rankLabel = rank.getLabel();
 896             }
 897             result.setRankLabel(rankLabel);
 898         }
 899
 900         boolean recursive = false;
 901         Integer pageSize = null;
 902         Integer pageIndex = null;
 903         Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, includeUnpublished, doSynonyms,
 904                 sortMode, pageSize, pageIndex);
 905
 906         //children
 907         if(! isSynonym) {
 908             for (TaxonNodeDto childDto : children.getRecords()){
 909                 if (doChildren && childDto.getStatus().equals(TaxonStatus.Accepted)){
 910                     EntityDTO<Taxon> child = new EntityDTO<Taxon>(childDto.getTaxonUuid(), childDto.getTitleCache());
 911                     result.addChild(child);
 912                 }else if (doSynonyms && childDto.getStatus().isSynonym()){
 913                     EntityDTO<Synonym> child = new EntityDTO<>(childDto.getTaxonUuid(), childDto.getTitleCache());
 914                     result.addSynonym(child);
 915                 }
 916             }
 917         }else{
 918             result.setAcceptedTaxonUuid(acceptedTaxonUuid);
 919             String nameTitel = acceptedTaxon.getName() == null ? null : acceptedTaxon.getName().getTitleCache();
 920             result.setAcceptedTaxonLabel(acceptedTaxon.getTitleCache());
 921             result.setAcceptedNameLabel(nameTitel);
 922         }
 923
 924         //marked ancestors
 925         if (ancestorMarkers != null && !ancestorMarkers.isEmpty()){
 926             @SuppressWarnings("rawtypes")
 927             List<DefinedTermBase> markerTypesTerms = termDao.list(ancestorMarkers, pageSize, null, null, null);
 928             List<MarkerType> markerTypes = new ArrayList<>();
 929             for (DefinedTermBase<?> term : markerTypesTerms){
 930                 if (term.isInstanceOf(MarkerType.class)){
 931                     markerTypes.add(CdmBase.deproxy(term, MarkerType.class));
 932                 }
 933             }
 934             if (! markerTypes.isEmpty()){
 935                 TaxonNode node = taxonNodeDao.findByUuid(taxonNodeUuid);
 936                 handleAncestorsForMarkersRecursive(result, markerTypes, node);
 937             }
 938         }
 939
 940         return result;
 941     }
 942
 943     /**
 944      * @param classificationUuid
 945      * @param acceptedTaxon
 946      * @return
 947      */
 948     private Taxon getParentTaxon(UUID classificationUuid, Taxon acceptedTaxon) {
 949         if (classificationUuid == null){
 950             return null;
 951         }
 952         TaxonNode parent = null;
 953         for (TaxonNode node : acceptedTaxon.getTaxonNodes()){
 954             if (classificationUuid.equals(node.getClassification().getUuid())){
 955                 parent = node.getParent();
 956             }
 957         }
 958         if (parent != null){
 959             return parent.getTaxon();
 960         }
 961         return null;
 962     }
 963
 964     /**
 965      * @param result
 966      * @param markerTypes
 967      * @param node
 968      */
 969     private void handleAncestorsForMarkersRecursive(TaxonInContextDTO result, List<MarkerType> markerTypes, TaxonNode node) {
 970        for (MarkerType type : markerTypes){
 971             Taxon taxon = node.getTaxon();
 972             if (taxon != null && taxon.hasMarker(type, true)){
 973                 String label =  taxon.getName() == null? taxon.getTitleCache() : taxon.getName().getTitleCache();
 974                 MarkedEntityDTO<Taxon> dto = new MarkedEntityDTO<>(type, true, taxon.getUuid(), label);
 975                 result.addMarkedAncestor(dto);
 976             }
 977         }
 978         TaxonNode parentNode = node.getParent();
 979         if (parentNode != null){
 980             handleAncestorsForMarkersRecursive(result, markerTypes, parentNode);
 981         }
 982     }
 983
 984     /**
 985      * {@inheritDoc}
 986      */
 987     @Override
 988     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 989             Classification classification) {
 990         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, false);
 991     }
 992
 993     /**
 994      * {@inheritDoc}
 995      */
 996     @Override
 997     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 998             UUID classificationUuid) {
 999         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, false);
1000     }
1001
1002     /**
1003      * {@inheritDoc}
1004      */
1005     @Override
1006     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1007             UUID classificationUuid, Integer limit, String pattern) {
1008         return  getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid,  limit, pattern, false);
1009     }
1010
1011     /**
1012      * {@inheritDoc}
1013      */
1014     @Override
1015     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
1016             Classification classification, Integer limit, String pattern) {
1017         return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, false);
1018     }
1019 }